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US20130305398A1 - Genes and uses for plant enhacement - Google Patents

Genes and uses for plant enhacement Download PDF

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US20130305398A1
US20130305398A1 US13/385,376 US201213385376A US2013305398A1 US 20130305398 A1 US20130305398 A1 US 20130305398A1 US 201213385376 A US201213385376 A US 201213385376A US 2013305398 A1 US2013305398 A1 US 2013305398A1
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protein
recombinant dna
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Marie Coffin
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Priority to US14/757,273 priority patent/US10167482B2/en
Priority to US16/350,499 priority patent/US10760091B2/en
Priority to US16/873,863 priority patent/US11371054B2/en
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    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
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    • C12N15/8271—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance
    • C12N15/8273—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for drought, cold, salt resistance
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    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
    • C12N15/8271—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance
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    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
    • C12N15/8271—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance
    • C12N15/8274—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for herbicide resistance
    • C12N15/8275—Glyphosate
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
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    • Y02A40/10—Adaptation technologies in agriculture, forestry, livestock or agroalimentary production in agriculture
    • Y02A40/146—Genetically Modified [GMO] plants, e.g. transgenic plants

Definitions

  • recombinant DNA useful for providing enhanced traits to transgenic plants, seeds, pollen, plant cells and plant nuclei of such transgenic plants, methods of making and using such recombinant DNA, plants, seeds, pollen, plant cells and plant nuclei. Also disclosed are methods of producing hybrid seed comprising such recombinant DNA.
  • This invention provides recombinant DNA constructs comprising polynucleotides characterized by SEQ ID NO:1-759 and the cognate amino acid sequences of SEQ ID NO:760-1518.
  • the recombinant DNA is useful for providing enhanced traits when stably integrated into the chromosomes and expressed in the nuclei of transgenic plants cells.
  • the recombinant DNA encodes a protein; in other aspects the recombinant DNA is transcribed to RNA that suppresses the expression of a native gene.
  • Such recombinant DNA in a plant cell nucleus of this invention is provided in as a construct comprising a promoter that is functional in plant cells and that is operably linked to DNA that encodes a protein or to DNA that results in gene suppression.
  • DNA in the construct is sometimes defined by protein domains of an encoded protein targeted for production or suppression, e.g. a “Pfam domain module” (as defined herein below) from the group of Pfam domain modules identified in Table 17.
  • a Pfam domain module as defined herein below
  • DNA in the construct is defined a consensus amino acid sequence of an encoded protein that is targeted for production e.g.
  • the recombinant DNA is characterized by its cognate amino acid sequence that has at least 70% identity to any of SEQ ID NO:760-1518.
  • transgenic plant cell nuclei comprising the recombinant DNA of the invention, transgenic plant cells comprising such nuclei, transgenic plants comprising a plurality of such transgenic plant cells, and transgenic seeds and transgenic pollen of such plants.
  • Such transgenic plants are selected from a population of transgenic plants regenerated from plant cells transformed with recombinant DNA by screening transgenic plants for an enhanced trait as compared to control plants.
  • the enhanced trait is one or more of enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced heat tolerance, enhanced shade tolerance, enhanced high salinity tolerance, enhanced seed protein and enhanced seed oil.
  • Such recombinant DNA in a plant cell nuclus of this invention is provided in as a construct comprising a promoter that is functional in plant cells and that is operably linked to DNA that encodes a protein or to DNA that results in gene suppression.
  • DNA in the construct is sometimes defined by protein domains of an encoded protein targeted for production or suppression, e.g. a “Pfam domain module” (as defined herein below) from the group of Pfam domain modules identified in Table 17.
  • a Pfam domain module is not available
  • such DNA in the construct is defined a consensus amino acid sequence of an encoded protein that is targeted for production e.g. a protein having amino acid sequence with at least 90% identity to a consensus amino acid sequence in the group of SEQ ID NO: 67782 through SEQ ID NO: 67894.
  • the plant cell nuclei, cells, plants, seeds, and pollen further comprise DNA expressing a protein that provides tolerance from exposure to an herbicide applied at levels that are lethal to a wild type plant cell.
  • This invention also provides methods for manufacturing non-natural, transgenic seed that can be used to produce a crop of transgenic plants with an enhanced trait resulting from expression of stably-integrated, recombinant DNA in the nucleus of the plant cells. More specifically the method comprises (a) screening a population of plants for an enhanced trait and recombinant DNA, where individual plants in the population can exhibit the trait at a level less than, essentially the same as or greater than the level that the trait is exhibited in control plants which do not express the recombinant DNA; (b) selecting from the population one or more plants that exhibit the trait at a level greater than the level that said trait is exhibited in control plants and (c) collecting seed from a selected plant.
  • Such method further comprises steps (a) verifying that the recombinant DNA is stably integrated in said selected plants; and (b) analyzing tissue of a selected plant to determine the production of a protein having the function of a protein encoded by a recombinant DNA with a sequence of one of SEQ ID NO: 1-759;
  • the plants in the population further comprise DNA expressing a protein that provides tolerance to exposure to an herbicide applied at levels that are lethal to wild type plant cells and where the selecting is effected by treating the population with the herbicide, e.g. a glyphosate, dicamba, or glufosinate compound.
  • the plants are selected by identifying plants with the enhanced trait. The methods are especially useful for manufacturing corn, soybean, cotton, canola, alfalfa, wheat or rice seed selected as having one of the enhanced traits described above.
  • Another aspect of the invention provides a method of producing hybrid corn seed comprising acquiring hybrid corn seed from a herbicide tolerant corn plant which also has a nucleus of this invention with stably-integrated, recombinant DNA
  • the method further comprises producing corn plants from said hybrid corn seed, where a fraction of the plants produced from said hybrid corn seed is homozygous for said recombinant DNA, a fraction of the plants produced from said hybrid corn seed is hemizygous for said recombinant DNA, and a fraction of the plants produced from said hybrid corn seed has none of said recombinant DNA; selecting corn plants which are homozygous and hemizygous for said recombinant DNA by treating with an herbicide; collecting seed from herbicide-treated-surviving corn plants and planting said seed to produce further progeny corn plants; repeating the selecting and collecting steps at least once to produce an inbred corn line; and crossing the inbred corn line with a second corn line to produce hybrid seed.
  • this invention provides methods of growing a corn, cotton, soybean, or canola crop without irrigation water comprising planting seed having plant cells of the invention which are selected for enhanced water use efficiency.
  • methods comprise applying reduced irrigation water, e.g. providing up to 300 millimeters of ground water during the production of a corn crop.
  • This invention also provides methods of growing a corn, cotton, soybean or canola crop without added nitrogen fertilizer comprising planting seed having plant cells of the invention which are selected for enhanced nitrogen use efficiency.
  • transgenic plants comprise recombinant DNA constructs which affect the expression of two or more proteins disclosed herein.
  • FIGS. 1 , 2 and 3 illustrate plasmid maps.
  • FIG. 4 illustrates a consensus amino acid sequence of SEQ ID NO: 768 and its homologs.
  • SEQ ID NO: 1-759 are nucleotide sequences of the protein coding strand of DNA” used in the recombinant DNA for imparting an enhanced trait in plant cells;
  • SEQ ID NO: 760-1518 are amino acid sequences of the cognate protein of the nucleotide sequences of SEQ ID NO:1-759;
  • SEQ ID NO: 1519-67778 are amino acid sequences of homologous proteins
  • SEQ ID NO:67779 is a nucleotide sequence of a plasmid base vector useful for corn transformation.
  • SEQ ID NO:67780 is a DNA sequence of a plasmid base vector useful for soybean transformation.
  • SEQ ID NO:67781 is a DNA sequence of a plasmid base vector useful for cotton transformation.
  • SEQ ID NO: 67782-67894 are consensus sequences.
  • Table 1 lists the protein SEQ ID NOs and their corresponding consensus SEQ ID NOs.
  • the nuclei of this invention are identified by screening transgenic plants for one or more traits including enhanced drought stress tolerance, enhanced heat stress tolerance, enhanced cold stress tolerance, enhanced high salinity stress tolerance, enhanced low nitrogen availability stress tolerance, enhanced shade stress tolerance, enhanced plant growth and development at the stages of seed imbibition through early vegetative phase, and enhanced plant growth and development at the stages of leaf development, flower production and seed maturity.
  • a “plant cell” means a plant cell that is transformed with stably-integrated, non-natural, recombinant DNA, e.g. by Agrobacterium -mediated transformation or by bombardment using microparticles coated with recombinant DNA or other means.
  • a plant cell of this invention can be an originally-transformed plant cell that exists as a microorganism or as a progeny plant cell that is regenerated into differentiated tissue, e.g. into a transgenic plant with stably-integrated, non-natural recombinant DNA, or seed or pollen derived from a progeny transgenic plant.
  • transgenic plant means a plant whose genome has been altered by the stable integration of recombinant DNA.
  • a transgenic plant includes a plant regenerated from an originally-transformed plant cell and progeny transgenic plants from later generations or crosses of a transformed plant.
  • recombinant DNA means DNA which has been a genetically engineered and constructed outside of a cell including DNA containing naturally occurring DNA or cDNA or synthetic DNA.
  • a “homolog” means a protein in a group of proteins that perform the same biological function, e.g. proteins that belong to the same Pfam protein family and that provide a common enhanced trait in transgenic plants of this invention.
  • Homologs are expressed by homologous genes.
  • Homologous genes include naturally occurring alleles and artificially-created variants. Degeneracy of the genetic code provides the possibility to substitute at least one base of the protein encoding sequence of a gene with a different base without causing the amino acid sequence of the polypeptide produced from the gene to be changed.
  • a polynucleotide useful in the present invention may have any base sequence that has been changed from SEQ ID NO:1 through SEQ ID NO: 803 through substitution in accordance with degeneracy of the genetic code.
  • Homologs are proteins that, when optimally aligned, have at least 60% identity, more preferably about 70% or higher, more preferably at least 80% and even more preferably at least 90% identity over the full length of a protein identified as being associated with imparting an enhanced trait when expressed in plant cells.
  • Homologs include proteins with an amino acid sequence that has at least 90% identity to a consensus amino acid sequence of proteins and homologs disclosed herein.
  • Homologs are identified by comparison of amino acid sequence, e.g. manually or by use of a computer-based tool using known homology-based search algorithms such as those commonly known and referred to as BLAST, FASTA, and Smith-Waterman.
  • a local sequence alignment program e.g. BLAST
  • BLAST can be used to search a database of sequences to find similar sequences, and the summary Expectation value (E-value) used to measure the sequence base similarity.
  • E-value Expectation value
  • a reciprocal query is used in the present invention to filter hit sequences with significant E-values for ortholog identification.
  • the reciprocal query entails search of the significant hits against a database of amino acid sequences from the base organism that are similar to the sequence of the query protein.
  • a hit can be identified as an ortholog, when the reciprocal query's best hit is the query protein itself or a protein encoded by a duplicated gene after speciation.
  • a further aspect of the homologs encoded by DNA useful in the transgenic plants of the invention are those proteins that differ from a disclosed protein as the result of deletion or insertion of one or more amino acids in a native sequence.
  • percent identity means the extent to which two optimally aligned DNA or protein segments are invariant throughout a window of alignment of components, for example nucleotide sequence or amino acid sequence.
  • An “identity fraction” for aligned segments of a test sequence and a reference sequence is the number of identical components that are shared by sequences of the two aligned segments divided by the total number of sequence components in the reference segment over a window of alignment which is the smaller of the full test sequence or the full reference sequence.
  • Percent identity (“% identity”) is the identity fraction times 100. Such optimal alignment is understood to be deemed as local alignment of DNA sequences. For protein alignment, a local alignment of protein sequences should allow introduction of gaps to achieve optimal alignment. Percent identity is calculated over the aligned length not including the gaps introduced by the alignment per se.
  • promoter means regulatory DNA for initializing transcription.
  • a “plant promoter” is a promoter capable of initiating transcription in plant cells whether or not its origin is a plant cell, e.g. is it well known that Agrobacterium promoters are functional in plant cells.
  • plant promoters include promoter DNA obtained from plants, plant viruses and bacteria such as Agrobacterium and Bradyrhizobium bacteria.
  • Examples of promoters under developmental control include promoters that preferentially initiate transcription in certain tissues, such as leaves, roots, or seeds. Such promoters are referred to as “tissue preferred”. Promoters that initiate transcription only in certain tissues are referred to as “tissue specific”.
  • a “cell type” specific promoter primarily drives expression in certain cell types in one or more organs, for example, vascular cells in roots or leaves.
  • An “inducible” or “repressible” promoter is a promoter which is under environmental control. Examples of environmental conditions that may effect transcription by inducible promoters include anaerobic conditions, or certain chemicals, or the presence of light. Tissue specific, tissue preferred, cell type specific, and inducible promoters constitute the class of “non-constitutive”promoters.
  • a “constitutive” promoter is a promoter which is active under most conditions.
  • operably linked means the association of two or more DNA fragments in a DNA construct so that the function of one, e.g. protein-encoding DNA, is controlled by the other, e.g. a promoter.
  • expressed means produced, e.g. a protein is expressed in a plant cell when its cognate DNA is transcribed to mRNA that is translated to the protein.
  • “suppressed” means decreased, e.g. a protein is suppressed in a plant cell when there is a decrease in the amount and/or activity of the protein in the plant cell.
  • the presence or activity of the protein can be decreased by any amount up to and including a total loss of protein expression and/or activity.
  • control plant means a plant that does not contain the recombinant DNA that expressed a protein that imparts an enhanced trait.
  • a control plant is to identify and select a transgenic plant that has an enhance trait.
  • a suitable control plant can be a non-transgenic plant of the parental line used to generate a transgenic plant, i.e. devoid of recombinant DNA.
  • a suitable control plant may in some cases be a progeny of a hemizygous transgenic plant line that is does not contain the recombinant DNA, known as a negative segregant.
  • an “enhanced trait” means a characteristic of a transgenic plant that includes, but is not limited to, an enhance agronomic trait characterized by enhanced plant morphology, physiology, growth and development, yield, nutritional enhancement, disease or pest resistance, or environmental or chemical tolerance.
  • enhanced trait is selected from group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
  • the enhanced trait is enhanced yield including increased yield under non-stress conditions and increased yield under environmental stress conditions.
  • Stress conditions may include, for example, drought, shade, fungal disease, viral disease, bacterial disease, insect infestation, nematode infestation, cold temperature exposure, heat exposure, osmotic stress, reduced nitrogen nutrient availability, reduced phosphorus nutrient availability and high plant density.
  • Yield can be affected by many properties including without limitation, plant height, pod number, pod position on the plant, number of internodes, incidence of pod shatter, grain size, efficiency of nodulation and nitrogen fixation, efficiency of nutrient assimilation, resistance to biotic and abiotic stress, carbon assimilation, plant architecture, resistance to lodging, percent seed germination, seedling vigor, and juvenile traits. Yield can also be affected by efficiency of germination (including germination in stressed conditions), growth rate (including growth rate in stressed conditions), ear number, seed number per ear, seed size, composition of seed (starch, oil, protein) and characteristics of seed fill.
  • Increased yield of a transgenic plant of the present invention can be measured in a number of ways, including test weight, seed number per plant, seed weight, seed number per unit area (i.e. seeds, or weight of seeds, per acre), bushels per acre, tonnes per acre, tons per acre, kilo per hectare.
  • maize yield may be measured as production of shelled corn kernels per unit of production area, for example in bushels per acre or metric tons per hectare, often reported on a moisture adjusted basis, for example at 15.5 percent moisture.
  • Increased yield may result from improved utilization of key biochemical compounds, such as nitrogen, phosphorous and carbohydrate, or from improved responses to environmental stresses, such as cold, heat, drought, salt, and attack by pests or pathogens.
  • Recombinant DNA used in this invention can also be used to provide plants having improved growth and development, and ultimately increased yield, as the result of modified expression of plant growth regulators or modification of cell cycle or photosynthesis pathways. Also of interest is the generation of transgenic plants that demonstrate enhanced yield with respect to a seed component that may or may not correspond to an increase in overall plant yield. Such properties include enhancements in seed oil, seed molecules such as tocopherol, protein and starch, or oil particular oil components as may be manifest by an alterations in the ratios of seed components.
  • Arabidopsis means plants of Arabidopsis thaliana.
  • Pfam database is a large collection of multiple sequence alignments and hidden Markov models covering many common protein families, e.g. Pfam version 19.0 (December 2005) contains alignments and models for 8183 protein families and is based on the Swissprot 47.0 and SP-TrEMBL 30.0 protein sequence databases. See S. R. Eddy, “Profile Hidden Markov Models”, Bioinformatics 14:755-763, 1998. The Pfam database is currently maintained and updated by the Pfam Consortium. The alignments represent some evolutionary conserved structure that has implications for the protein's function. Profile hidden Markov models (profile HMMs) built from the protein family alignments are useful for automatically recognizing that a new protein belongs to an existing protein family even if the homology by alignment appears to be low.
  • profile HMMs Profile hidden Markov models
  • a “Pfam domain module” is a representation of Pfam domains in a protein, in order from N terminus to C terminus. In a Pfam domain module individual Pfam domains are separated by double colons “::”. The order and copy number of the Pfam domains from N to C terminus are attributes of a Pfam domain module. Although the copy number of repetitive domains is important, varying copy number often enables a similar function. Thus, a Pfam domain module with multiple copies of a domain should define an equivalent Pfam domain module with variance in the number of multiple copies.
  • a Pfam domain module is not specific for distance between adjacent domains, but contemplates natural distances and variations in distance that provide equivalent function.
  • the Pfam database contains both narrowly- and broadly-defined domains, leading to identification of overlapping domains on some proteins.
  • a Pfam domain module is characterized by non-overlapping domains. Where there is overlap, the domain having a function that is more closely associated with the function of the protein (based on the E value of the Pfam match) is selected.
  • the relevant Pfam modules for use in this invention are Saccharop_dh, Isoamylase_N::Alpha-amylase, RRM — 1, Pribosyltran, Skp1_POZ::Skp1, PTR2, PSI_PsaH, OTU, Aldedh, p450, AP2, CBS, TPT, zf-UBR, zf-C3HC4, ADH_N::ADH_zinc_N, Pre-SET::SET, OstA, Myb_DNA-binding, Cpn60_TCP1, SKI, Cyt-b5::FA_desaturase, Pkinase, KTI12, SNARE, NLE::WD40::WD40::WD40::WD40, zf-C3HC4, Complex1 — 30 kDa::Complex1 — 49 kDa, iPGM_N::Metalloenzyme, adh_short, IQ
  • the invention uses recombinant DNA for imparting one or more enhanced traits to transgenic plant when incorporated into the nucleus of the plant cells.
  • DNA constructs comprising one or more polynucleotides disclosed herein are assembled using methods well known to persons of ordinary skill in the art and typically comprise a promoter operably linked to DNA, the expression of which provides the enhanced agronomic trait.
  • Other construct components may include additional regulatory elements, such as 5′ leasders and introns for enhancing transcription, 3′ untranslated regions (such as polyadenylation signals and sites), DNA for transit or signal peptides.
  • promoters that are active in plant cells have been described in the literature. These include promoters present in plant genomes as well as promoters from other sources, including nopaline synthase (NOS) promoter and octopine synthase (OCS) promoters carried on tumor-inducing plasmids of Agrobacterium tumefaciens and the CaMV35S promoters from the cauliflower mosaic virus as disclosed in U.S. Pat. Nos. 5,164,316 and 5,322,938.
  • Useful promoters derived from plant genes are found in U.S. Pat. No. 5,641,876, which discloses a rice actin promoter, U.S. Pat. No.
  • Promoters of interest for such uses include those from genes such as Arabidopsis thaliana ribulose-1,5-bisphosphate carboxylase (Rubisco) small subunit (Fischhoff et al. (1992) Plant Mol. Biol. 20:81-93), aldolase and pyruvate orthophosphate dikinase (PPDK) (Taniguchi et al. (2000) Plant Cell Physiol. 41(1):42-48).
  • Rubisco Arabidopsis thaliana ribulose-1,5-bisphosphate carboxylase
  • PPDK pyruvate orthophosphate dikinase
  • the promoters may be altered to contain multiple “enhancer sequences” to assist in elevating gene expression.
  • enhancers are known in the art.
  • the expression of the selected protein may be enhanced.
  • These enhancers often are found 5′ to the start of transcription in a promoter that functions in eukaryotic cells, but can often be inserted upstream (5′) or downstream (3′) to the coding sequence.
  • these 5′ enhancing elements are introns.
  • Particularly useful as enhancers are the 5′ introns of the rice actin 1 (see U.S. Pat. No. 5,641,876) and rice actin 2 genes, the maize alcohol dehydrogenase gene intron, the maize heat shock protein 70 gene intron (U.S. Pat. No. 5,593,874) and the maize shrunken 1 gene.
  • promoters for use for seed composition modification include promoters from seed genes such as napin (U.S. Pat. No. 5,420,034), maize L3 oleosin (U.S. Pat. No. 6,433,252), zein Z27 (Russell et al. (1997) Transgenic Res. 6(2):157-166), globulin 1 (Belanger et al (1991) Genetics 129:863-872), glutelin 1 (Russell (1997) supra), and peroxiredoxin antioxidant (Perl) (Stacy et al., (1996) Plant Mol. Biol. 31(6)1205-1216).
  • seed genes such as napin (U.S. Pat. No. 5,420,034), maize L3 oleosin (U.S. Pat. No. 6,433,252), zein Z27 (Russell et al. (1997) Transgenic Res. 6(2):157-166), globulin 1 (Belanger et al (1991) Genetic
  • Recombinant DNA constructs prepared in accordance with the invention will also generally include a 3′ element that typically contains a polyadenylation signal and site.
  • 3′ elements include those from Agrobacterium tumefaciens genes such as nos 3′, tml 3′, tmr 3′, tms 3′, ocs 3′, tr7 3′, for example disclosed in U.S. Pat. No.
  • 3′ elements from plant genes such as wheat ( Triticum aesevitum ) heat shock protein 17 (Hsp17 3), a wheat ubiquitin gene, a wheat fructose-1,6-biphosphatase gene, a rice glutelin gene, a rice lactate dehydrogenase gene and a rice beta-tubulin gene, all of which are disclosed in U.S. published patent application 2002/0192813 A1, incorporated herein by reference; and the pea ( Pisum sativum ) ribulose biphosphate carboxylase gene (rbs 3), and 3′ elements from the genes within the host plant.
  • wheat Triticum aesevitum
  • Hsp17 3 heat shock protein 17
  • rbs 3 pea ribulose biphosphate carboxylase gene
  • Constructs and vectors may also include a transit peptide for targeting of a gene to a plant organelle, particularly to a chloroplast, leucoplast or other plastid organelle.
  • a transit peptide for targeting of a gene to a plant organelle, particularly to a chloroplast, leucoplast or other plastid organelle.
  • chloroplast transit peptides see U.S. Pat. No. 5,188,642 and U.S. Pat. No. 5,728,925, incorporated herein by reference.
  • the transit peptide region of an Arabidopsis EPSPS gene useful in the present invention, see Klee, H. J. et al ( MGG (1987) 210:437-442).
  • Gene suppression includes any of the well-known methods for suppressing transcription of a gene or the accumulation of the mRNA corresponding to that gene thereby preventing translation of the transcript into protein.
  • Posttranscriptional gene suppression is mediated by transcription of RNA that forms double-stranded RNA (dsRNA) having homology to a gene targeted for suppression.
  • dsRNA double-stranded RNA
  • Suppression can also be achieved by insertion mutations created by transposable elements may also prevent gene function.
  • transformation with the T-DNA of Agrobacterium may be readily achieved and large numbers of transformants can be rapidly obtained.
  • some species have lines with active transposable elements that can efficiently be used for the generation of large numbers of insertion mutations, while some other species lack such options.
  • Mutant plants produced by Agrobacterium or transposon mutagenesis and having altered expression of a polypeptide of interest can be identified using the polynucleotides of the present invention. For example, a large population of mutated plants may be screened with polynucleotides encoding the polypeptide of interest to detect mutated plants having an insertion in the gene encoding the polypeptide of interest.
  • Transgenic plants comprising or derived from plant cells of this invention transformed with recombinant DNA can be further enhanced with stacked traits, e.g. a crop plant having an enhanced trait resulting from expression of DNA disclosed herein in combination with herbicide and/or pest resistance traits.
  • genes of the current invention can be stacked with other traits of agronomic interest, such as a trait providing herbicide resistance, or insect resistance, such as using a gene from Bacillus thuringensis to provide resistance against lepidopteran, coliopteran, homopteran, hemiopteran, and other insects.
  • Herbicides for which transgenic plant tolerance has been demonstrated and the method of the present invention can be applied include, but are not limited to, glyphosate, dicamba, glufosinate, sulfonylurea, bromoxynil and norflurazon herbicides.
  • Polynucleotide molecules encoding proteins involved in herbicide tolerance are well-known in the art and include, but are not limited to, a polynucleotide molecule encoding 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) disclosed in U.S. Pat. Nos.
  • EPSPS 5-enolpyruvylshikimate-3-phosphate synthase
  • Patent Application publication 2003/0135879 A1 for imparting dicamba tolerance a polynucleotide molecule encoding bromoxynil nitrilase (Bxn) disclosed in U.S. Pat. No. 4,810,648 for imparting bromoxynil tolerance; a polynucleotide molecule encoding phytoene desaturase (crtI) described in Misawa et al, (1993) Plant J. 4:833-840 and in Misawa et al, (1994) Plant J.
  • Bxn bromoxynil nitrilase
  • crtI phytoene desaturase
  • Patent Application Publication 2003/010609 A1 for imparting N-amino methyl phosphonic acid tolerance polynucleotide molecules disclosed in U.S. Pat. No. 6,107,549 for impartinig pyridine herbicide resistance; molecules and methods for imparting tolerance to multiple herbicides such as glyphosate, atrazine, ALS inhibitors, isoxoflutole and glufosinate herbicides are disclosed in U.S. Pat. No. 6,376,754 and U.S. Patent Application Publication 2002/0112260, all of said U.S. Patents and Patent Application Publications are incorporated herein by reference. Molecules and methods for imparting insect/nematode/virus resistance are disclosed in U.S. Pat. Nos. 5,250,515; 5,880,275; 6,506,599; 5,986,175 and U.S. Patent Application Publication 2003/0150017 A1, all of which are incorporated herein by reference.
  • Table 2 provides a list of genes that provided recombinant DNA that was expressed in a model plant and identified from screening as imparting an enhanced trait.
  • the expression of the gene or a homolog in a crop plant provides the means to identify transgenic events that provide an enhanced trait in the crop plant.
  • the stated orientation is “antisense”
  • the suppression of the native homolog in a crop plant provides the means to identify transgenic events that provide an enhanced trait in the crop plant.
  • the expression/suppression in the model plant exhibited an enhanced trait that corresponds to an enhanced agronomic trait, e.g. cold stress tolerance, water deficit stress tolerance, low nitrogen stress tolerance and the like.
  • the expression/suppression in the model plant exhibited an enhanced trait that is a surrogate to an enhanced agronomic trait, e.g. salinity stress tolerance being a surrogate to drought tolerance or improvement in plant growth and development being a surrogate to enhanced yield.
  • an enhanced trait e.g. salinity stress tolerance being a surrogate to drought tolerance or improvement in plant growth and development being a surrogate to enhanced yield.
  • transgenic plant cell nuclei, cell, plant or seed of this invention can be identified by making a reasonable number of transgenic events and engaging in screening process identified in this specification and illustrated in the examples.
  • An understanding of Table 2 is facilitated by the following description of the headings:
  • NUC SEQ ID NO refers to a SEQ ID NO. for particular DNA sequence in the Sequence Listing.
  • PEP SEQ ID NO refers to a SEQ ID NO. in the Sequence Listing for the amino acid sequence of a protein cognate to a particular DNA
  • construct_id refers to an arbitrary number used to identify a particular recombinant DNA construct comprising the particular DNA.
  • Gene ID refers to an arbitrary name used to identify the particular DNA.
  • orientation refers to the orientation of the particular DNA in a recombinant DNA construct relative to the promoter.
  • DNA for use in the present invention to improve traits in plants have a nucleotide sequence of SEQ ID NO:1 through SEQ ID NO:759, as well as the homologs of such DNA molecules.
  • a subset of the DNA for gene suppression aspects of the invention includes fragments of the disclosed full polynucleotides consisting of oligonucleotides of 21 or more consecutive nucleotides. Oligonucleotides the larger molecules having a sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 759 are useful as probes and primers for detection of the polynucleotides used in the invention. Also useful in this invention are variants of the DNA.
  • Such variants may be naturally occurring, including DNA from homologous genes from the same or a different species, or may be non-natural variants, for example DNA synthesized using chemical synthesis methods, or generated using recombinant DNA techniques.
  • Degeneracy of the genetic code provides the possibility to substitute at least one base of the protein encoding sequence of a gene with a different base without causing the amino acid sequence of the polypeptide produced from the gene to be changed.
  • a DNA useful in the present invention may have any base sequence that has been changed from the sequences provided herein by substitution in accordance with degeneracy of the genetic code.
  • DNA is substantially identical to a reference DNA it when the sequences of the polynucleotides are optimally aligned there is about 60% nucleotide equivalence; more preferably 70%; more preferably 80% equivalence; more preferably 85% equivalence; more preferably 90%; more preferably 95%; and/or more preferably 98% or 99% equivalence over a comparison window.
  • a comparison window is preferably at least 50-100 nucleotides, and more preferably is the entire length of the polynucleotide provided herein.
  • Optimal alignment of sequences for aligning a comparison window may be conducted by algorithms; preferably by computerized implementations of these algorithms (for example, the Wisconsin Genetics Software Package Release 7.0-10.0, Genetics Computer Group, 575 Science Dr., Madison, Wis.).
  • the reference polynucleotide may be a full-length molecule or a portion of a longer molecule.
  • the window of comparison for determining polynucleotide identity of protein encoding sequences is the entire coding region.
  • Proteins useful for imparting enhanced traits are entire proteins or at least a sufficient portion of the entire protein to impart the relevant biological activity of the protein. Proteins useful for generation of transgenic plants having enhanced traits include the proteins with an amino acid sequence provided herein as SEQ ID NO: 760 through SEQ ID NO: 1518, as well as homologs of such proteins.
  • Homologs of the proteins useful in the invention are identified by comparison of the amino acid sequence of the protein to amino acid sequences of proteins from the same or different plant sources, e.g. manually or by using known homology-based search algorithms such as those commonly known and referred to as BLAST, FASTA, and Smith-Waterman.
  • a homolog is a protein from the same or a different organism that performs the same biological function as the polypeptide to which it is compared.
  • An orthologous relation between two organisms is not necessarily manifest as a one-to-one correspondence between two genes, because a gene can be duplicated or deleted after organism phylogenetic separation, such as speciation. For a given protein, there may be no ortholog or more than one ortholog.
  • a local sequence alignment program e.g., BLAST
  • E-value Expectation value
  • BLAST BLAST
  • a reciprocal BLAST search is used in the present invention to filter hit sequences with significant E-values for ortholog identification.
  • the reciprocal BLAST entails search of the significant hits against a database of amino acid sequences from the base organism that are similar to the sequence of the query protein.
  • a hit is a likely ortholog, when the reciprocal BLAST's best hit is the query protein itself or a protein encoded by a duplicated gene after speciation.
  • homolog is used herein to describe proteins that are assumed to have functional similarity by inference from sequence base similarity.
  • the relationship of homologs with amino acid sequences of SEQ ID NO: 1519 to SEQ ID NO: 67778 to the proteins with amino acid sequences of SEQ ID NO: to 760 to SEQ ID NO: 1518 are found in the listing of Table 16.
  • Other functional homolog proteins differ in one or more amino acids from those of a trait-improving protein disclosed herein as the result of one or more of the well-known conservative amino acid substitutions, e.g., valine is a conservative substitute for alanine and threonine is a conservative substitute for serine.
  • Conservative substitutions for an amino acid within the native sequence can be selected from other members of a class to which the naturally occurring amino acid belongs.
  • amino acids within these various classes include, but are not limited to: (1) acidic (negatively charged) amino acids such as aspartic acid and glutamic acid; (2) basic (positively charged) amino acids such as arginine, histidine, and lysine; (3) neutral polar amino acids such as glycine, serine, threonine, cysteine, tyrosine, asparagine, and glutamine; and (4) neutral nonpolar (hydrophobic) amino acids such as alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan, and methionine.
  • conserveed substitutes for an amino acid within a native amino acid sequence can be selected from other members of the group to which the naturally occurring amino acid belongs.
  • a group of amino acids having aliphatic side chains is glycine, alanine, valine, leucine, and isoleucine
  • a group of amino acids having aliphatic-hydroxyl side chains is serine and threonine
  • a group of amino acids having amide-containing side chains is asparagine and glutamine
  • a group of amino acids having aromatic side chains is phenylalanine, tyrosine, and tryptophan
  • a group of amino acids having basic side chains is lysine, arginine, and histidine
  • a group of amino acids having sulfur-containing side chains is cysteine and methionine.
  • Naturally conservative amino acids substitution groups are: valine-leucine, valine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, aspartic acid-glutamic acid, and asparagine-glutamine.
  • a further aspect of the invention comprises proteins that differ in one or more amino acids from those of a described protein sequence as the result of deletion or insertion of one or more amino acids in a native sequence.
  • Homologs of the trait-improving proteins provided herein will generally demonstrate significant sequence identity.
  • useful proteins also include those with higher identity, e.g., 90% to 99% identity.
  • Identity of protein homologs is determined by optimally aligning the amino acid sequence of a putative protein homolog with a defined amino acid sequence and by calculating the percentage of identical and conservatively substituted amino acids over the window of comparison.
  • the window of comparison for determining identity can be the entire amino acid sequence disclosed herein, e.g., the full sequence of any of SEQ ID NO: 760 through SEQ ID NO: 1518.
  • Protein homologs include proteins with an amino acid sequence that has at least 90% identity to such a consensus amino acid sequence sequences.
  • the present invention also contemplates that the trait-improving recombinant DNA provided herein can be used in combination with other recombinant DNA to create plants with multiple desired traits or a further enhanced trait.
  • the combinations generated can include multiple copies of any one or more of the recombinant DNA constructs. These stacked combinations can be created by any method, including but not limited to cross breeding of transgenic plants, or multiple genetic transformation.
  • Transformation of plant material is practiced in tissue culture on a nutrient media, i.e. a mixture of nutrients that will allow cells to grow in vitro.
  • Recipient cell targets include, but are not limited to, meristem cells, hypocotyls, calli, immature embryos and gametic cells such as microspores, pollen, sperm and egg cells.
  • Callus may be initiated from tissue sources including, but not limited to, immature embryos, hypocotyls, seedling apical meristems, microspores and the like. Cells containing a transgenic nucleus are grown into transgenic plants.
  • a transgenic plant cell nucleus can be prepared by crossing a first plant having cells with a transgenic nucleus with recombinant DNA with a second plant lacking the trangenci nucleus.
  • recombinant DNA can be introduced into a nucleus from a first plant line that is amenable to transformation to transgenic nucleus in cells that are grown into a transgenic plant which can be crossed with a second plant line to introgress the recombinant DNA into the second plant line.
  • a transgenic plant with recombinant DNA providing an enhanced trait, e.g.
  • transgenic plant line having other recombinant DNA that confers another trait for example herbicide resistance or pest resistance
  • progeny plants having recombinant DNA that confers both traits Typically, in such breeding for combining traits the transgenic plant donating the additional trait is a male line and the transgenic plant carrying the base traits is the female line.
  • the progeny of this cross will segregate such that some of the plants will carry the DNA for both parental traits and some will carry DNA for one parental trait; such plants can be identified by markers associated with parental recombinant DNA, e.g.
  • Progeny plants carrying DNA for both parental traits can be crossed back into the female parent line multiple times, for example usually 6 to 8 generations, to produce a progeny plant with substantially the same genotype as one original transgenic parental line but for the recombinant DNA of the other transgenic parental line
  • Marker genes are used to provide an efficient system for identification of those cells that are stably transformed by, receiving and integrating a recombinant DNA molecule into their genomes.
  • Preferred marker genes provide selective markers which confer resistance to a selective agent, such as an antibiotic or a herbicide. Any of the herbicides to which plants of this invention may be resistant are useful agents for selective markers.
  • Potentially transformed cells are exposed to the selective agent. In the population of surviving cells will be those cells where, generally, the resistance-conferring gene is integrated and expressed at sufficient levels to permit cell survival. Cells may be tested further to confirm stable integration of the exogenous DNA.
  • Select marker genes include those conferring resistance to antibiotics such as kanamycin and paromomycin (nptlI), hygromycin B (aph IV), spectinomycin (aadA) and gentamycin (aac3 and aacC4) or resistance to herbicides such as glufosinate (bar or pat), dicamba (DMO) and glyphosate (aroA or EPSPS). Examples of such selectable markers are illustrated in U.S. Pat. Nos. 5,550,318; 5,633,435; 5,780,708 and 6,118,047, all of which are incorporated herein by reference.
  • Selectable markers which provide an ability to visually identify transformants can also be employed, for example, a gene expressing a colored or fluorescent protein such as a luciferase or green fluorescent protein (GFP) or a gene expressing a beta-glucuronidase or uidA gene (GUS) for which various chromogenic substrates are known.
  • a gene expressing a colored or fluorescent protein such as a luciferase or green fluorescent protein (GFP) or a gene expressing a beta-glucuronidase or uidA gene (GUS) for which various chromogenic substrates are known.
  • Plant cells that survive exposure to the selective agent, or plant cells that have been scored positive in a screening assay may be cultured in regeneration media and allowed to mature into plants.
  • Developing plantlets regenerated from transformed plant cells can be transferred to plant growth mix, and hardened off, for example, in an environmentally controlled chamber at about 85% relative humidity, 600 ppm CO 2 , and 25-250 microeinsteins m ⁇ 2 s ⁇ 1 of light, prior to transfer to a greenhouse or growth chamber for maturation.
  • Plants are regenerated from about 6 weeks to 10 months after a transformant is identified, depending on the initial tissue, and plant species. Plants may be pollinated using conventional plant breeding methods known to those of skill in the art and seed produced, for example self-pollination is commonly used with transgenic corn.
  • the regenerated transformed plant or its progeny seed or plants can be tested for expression of the recombinant DNA and selected for the presence of enhanced agronomic trait.
  • Transgenic plants derived from transgenic plant cells having a transgenic nucleus of this invention are grown to generate transgenic plants having an enhanced trait as compared to a control plant and produce transgenic seed and haploid pollen of this invention.
  • Such plants with enhanced traits are identified by selection of transformed plants or progeny seed for the enhanced trait.
  • a selection method is designed to evaluate multiple transgenic plants (events) comprising the recombinant DNA, for example multiple plants from 2 to 20 or more transgenic events.
  • Transgenic plants grown from transgenic seed provided herein demonstrate improved agronomic traits that contribute to increased yield or other trait that provides increased plant value, including, for example, improved seed quality.
  • plants having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil are plants having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
  • Arabidopsis thaliana was transformed with a candidate recombinant DNA construct and screened for an enhanced trait.
  • Arabidopsis thaliana is used a model for genetics and metabolism in plants. Arabidopsis has a small genome, and well-documented studies are available. It is easy to grow in large numbers and mutants defining important genetically controlled mechanisms are either available, or can readily be obtained. Various methods to introduce and express isolated homologous genes are available (see Koncz, e.g., Methods in Arabidopsis Research e.g., (1992), World Scientific, New Jersey, New Jersey, in “Preface”).
  • a two-step screening process was employed which comprised two passes of trait characterization to ensure that the trait modification was dependent on expression of the recombinant DNA, but not due to the chromosomal location of the integration of the transgene. Twelve independent transgenic lines for each recombinant DNA construct were established and assayed for the transgene expression levels. Five transgenic lines with high transgene expression levels were used in the first pass screen to evaluate the transgene's function in T2 transgenic plants. Subsequently, three transgenic events, which had been shown to have one or more enhanced traits, were further evaluated in the second pass screen to confirm the transgene's ability to impart an enhanced trait.
  • Table 3 summarizes the enhanced traits that have been confirmed as provided by a recombinant DNA construct.
  • PEP SEQ ID which is the amino acid sequence of the protein cognate to the DNA in the recombinant DNA construct corresponding to a protein sequence of a SEQ ID NO. in the Sequence Listing.
  • construct_id is an arbitrary name for the recombinant DNA describe more particularly in Table 1.
  • “annotation” refers to a description of the top hit protein obtained from an amino acid sequence query of each PEP SEQ ID NO to GenBank database of the National Center for Biotechnology Information (ncbi). More particularly, “gi” is the GenBank ID number for the top BLAST hit.
  • “description” refers to the description of the top BLAST hit.
  • e-value provides the expectation value for the BLAST hit.
  • % id refers to the percentage of identically matched amino acid residues along the length of the portion of the sequences which is aligned by BLAST between the sequence of interest provided herein and the hit sequence in GenBank.
  • “traits” identify by two letter codes the confirmed enhancement in a transgenic plant provided by the recombinant DNA.
  • the codes for enhanced traits are:
  • PEG which indicates osmotic stress tolerance enhancement identified by a PEG induced osmotic stress tolerance screen
  • PP which indicates enhanced growth and development at early stages identified by an early plant growth and development screen
  • SP which indicates enhanced growth and development at late stages identified by a late plant growth and development screen provided herein.
  • subtilis str. 168 1178 73437 0 99 ref
  • subtilis str. 168 1189 73436 0 91 ref
  • subtilis str. 168 1203 74175 0 96 ref
  • PCC 6803 1208 74110 0 92 ref
  • CS PP SS PCC 6803 1215 74582 1.00E ⁇ 164 99 ref
  • PDH pyruvate dehydrogenase CS
  • Atroseptica SCRI1043 1227 74514 0 100 ref
  • PCC PP 7120 1385 75903 0 95 ref
  • PCC CS 7120 1390 75954 0 100 ref
  • PCC 6803 1392 75967 0 96 ref
  • PCC 7120 1493 77167 1.00E ⁇ 141 92 gb
  • Drought or water deficit conditions impose mainly osmotic stress on plants. Plants are particularly vulnerable to drought during the flowering stage.
  • the drought condition in the screening process disclosed in Example 1B started from the flowering time and was sustained to the end of harvesting.
  • the present invention provides recombinant DNA that can improve the plant survival rate under such sustained drought condition. Exemplary recombinant DNA for conferring such drought tolerance are identified as such in Table 3. Such recombinant DNA may find particular use in generating transgenic plants that are tolerant to the drought condition imposed during flowering time and in other stages of the plant life cycle.
  • transgenic plants with trait-improving recombinant DNA grown under such sustained drought condition can also have increased total seed weight per plant in addition to the increased survival rate within a transgenic population, providing a higher yield potential as compared to control plants.
  • Various drought levels can be artificially induced by using various concentrations of polyethylene glycol (PEG) to produce different osmotic potentials (Pilon-Smits e.g., (1995) Plant Physiol. 107:125-130).
  • PEG polyethylene glycol
  • Several physiological characteristics have been reported as being reliable indications for selection of plants possessing drought tolerance. These characteristics include the rate of seed germination and seedling growth. The traits can be assayed relatively easily by measuring the growth rate of seedling in PEG solution.
  • a PEG-induced osmotic stress tolerance screen is a useful surrogate for drought tolerance screen.
  • embodiments of transgenic plants with trait-improving recombinant DNA identified in the PEG-induced osmotic stress tolerance screen can survive better drought conditions providing a higher yield potential as compared to control plants.
  • the present invention provides genes that help plants maintain biomass, root growth, and/or plant development in high salinity conditions, which are identified as such in Table 3. Since osmotic effect is one of the major components of salt stress, which is common to the drought stress, trait-improving recombinant DNA identified in a high salinity stress tolerance screen can also provide transgenic crops with enhanced drought tolerance. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a high salinity stress tolerance screen can survive better drought conditions and/or high salinity conditions providing a higher yield potential as compared to to control plants.
  • genes identified by the present invention as heat stress tolerance conferring genes may also impart enhanced drought tolerance to plants.
  • embodiments of transgenic plants with trait-improving recombinant DNA identified in a heat stress tolerance screen can survive better heat stress conditions and/or drought conditions providing a higher yield potential as compared to control plants.
  • cold shock tolerance screen CK
  • cold germination tolerance screen the transgenic Arabidopsis plants were exposed to a constant temperature of 8° C. from planting until day 28 post plating.
  • the trait-improving recombinant DNA identified by such screen are particular useful for the production of transgenic plant that can germinate more robustly in a cold temperature as compared to the wild type plants.
  • cold shock tolerance screen the transgenic plants were first grown under the normal growth temperature of 22° C.
  • transgenic plants with trait-improving recombinant DNA identified in a cold shock stress tolerance screen and/or a cold germination stress tolerance screen can survive better cold conditions providing a higher yield potential as compared to control plants.
  • PEP SEQ ID NO: 892 can be used to enhance both salt stress tolerance and cold stress tolerance in plants.
  • plants transformed with PEP SEQ ID NO: 835 can resist heat stress, salt stress and cold stress. Plants transformed with PEP SEQ ID NO: 835 can also improve growth in early stage and under osmotic stress.
  • the stress tolerance conferring genes provided by the present invention may be used in combinations to generate transgenic plants that can resist multiple stress conditions.
  • the present invention provides genes that are useful to produce transgenic plants that have advantages in one or more processes including, but not limited to, germination, seedling vigor, root growth and root morphology under non-stressed conditions.
  • the transgenic plants starting from a more robust seedling are less susceptible to the fungal and bacterial pathogens that attach germinating seeds and seedling.
  • seedlings with advantage in root growth are more resistant to drought stress due to extensive and deeper root architecture. Therefore, it can be recognized by those skilled in the art that genes conferring the growth advantage in early stages to plants may also be used to generate transgenic plants that are more resistant to various stress conditions due to enhanced early plant development.
  • the present invention provides such exemplary, recombinant DNA that confer both the stress tolerance and growth advantages to plants, identified as such in Table 3, e.g. PEP SEQ ID NO: 799 which can improve the plant early growth and development, and impart heat and cold tolerance to plants.
  • PEP SEQ ID NO: 799 which can improve the plant early growth and development, and impart heat and cold tolerance to plants.
  • embodiments of transgenic plants with trait-improving recombinant DNA identified in the early plant development screen can grow better under non-stress conditions and/or stress conditions providing a higher yield potential as compared to control plants.
  • “Late growth and development” used herein encompasses the stages of leaf development, flower production, and seed maturity.
  • transgenic plants produced using genes that confer growth advantages to plants provided by the present invention, identified as such in Table 3 exhibit at least one phenotypic characteristics including, but not limited to, increased rosette radius, increased rosette dry weight, seed dry weight, silique dry weight, and silique length.
  • the rosette radius and rosette dry weight are used as the indexes of photosynthesis capacity, and thereby plant source strength and yield potential of a plant.
  • the seed dry weight, silique dry weight and silique length are used as the indexes for plant sink strength, which are considered as the direct determinants of yield.
  • embodiments of transgenic plants with trait-improving recombinant DNA identified in the late development screen can grow better and/or have enhanced development during leaf development and seed maturation providing a higher yield potential as compared to control plants.
  • a plant seeding develops according to a characteristic photomorphogenic pattern, in which plants have open and expanded cotyledons and short hypocotyls. Then the plant's energy is devoted to cotyledon and leaf development while longitudinal extension growth is minimized.
  • a seedling displays a shade-avoidance pattern, in which the seedling displays a reduced cotyledon expansion, and hypocotyls extension is greatly increased.
  • the present invention provides recombinant DNA that enable plants to have an attenuated shade avoidance response so that the source of plant can be contributed to reproductive growth efficiently, resulting higher yield as compared to the wild type plants.
  • embodiments of transgenic plants with trait-improving recombinant DNA identified in a shade stress tolerance screen can have attenuated shade response under shade conditions providing a higher yield potential as compared to control plants.
  • the transgenic plants generated by the present invention may be suitable for a higher density planting, thereby resulting increased yield per unit area.
  • the metabolism, growth and development of plants are profoundly affected by their nitrogen supply. Restricted nitrogen supply alters shoot to root ratio, root development, activity of enzymes of primary metabolism and the rate of senescence (death) of older leaves.
  • All field crops have a fundamental dependence on inorganic nitrogenous fertilizer. Since fertilizer is rapidly depleted from most soil types, it must be supplied to growing crops two or three times during the growing season. Enhanced nitrogen use efficiency by plants should enable crops cultivated under low nitrogen availability stress condition resulted from low fertilizer input or poor soil quality.
  • the transgenic plants provided by the present invention with enhanced nitrogen use efficiency may also have altered amino acid or protein compositions, increased yield and/or better seed quality.
  • the transgenic plants of the present invention may be productively cultivated under low nitrogen growth conditions, i.e., nitrogen-poor soils and low nitrogen fertilizer inputs, which would cause the growth of wild type plants to cease or to be so diminished as to make the wild type plants practically useless.
  • the transgenic plants also may be advantageously used to achieve earlier maturing, faster growing, and/or higher yielding crops and/or produce more nutritious foods and animal feedstocks when cultivated using nitrogen non-limiting growth conditions.
  • the present invention also encompasses transgenic plants with stacked engineered traits, e.g., a crop having an enhanced phenotype resulting from expression of a trait-improving recombinant DNA, in combination with herbicide and/or pest resistance traits.
  • genes of the current invention can be stacked with other traits of agronomic interest, such as a trait providing herbicide resistance, for example a RoundUp Ready® trait, or insect resistance, such as using a gene from Bacillus thuringensis to provide resistance against lepidopteran, coliopteran, homopteran, hemiopteran, and other insects.
  • Herbicides for which resistance is useful in a plant include glyphosate herbicides, phosphinothricin herbicides, oxynil herbicides, imidazolinone herbicides, dinitroaniline herbicides, pyridine herbicides, sulfonylurea herbicides, bialaphos herbicides, sulfonamide herbicides and gluphosinate herbicides.
  • glyphosate herbicides glyphosate herbicides, phosphinothricin herbicides, oxynil herbicides, imidazolinone herbicides, dinitroaniline herbicides, pyridine herbicides, sulfonylurea herbicides, bialaphos herbicides, sulfonamide herbicides and gluphosinate herbicides.
  • the invention provides methods for identifying a homologous gene with a DNA sequence homologous to any of SEQ ID NO: 1 through SEQ ID NO: 759, or a homologous protein with an amino acid sequence homologous to any of SEQ ID NO: 760 through SEQ ID NO: 1518.
  • the present invention provides the protein sequences of identified homologs for a sequence listed; as SEQ ID NO: 1519 through SEQ ID NO: 67778.
  • the present invention also includes linking or associating one or more desired traits, or gene function with a homolog sequence provided herein.
  • the trait-improving recombinant DNA and methods of using such trait-improving recombinant DNA for generating transgenic plants with enhanced traits provided by the present invention are not limited to any particular plant species.
  • the plants according to the present invention may be of any plant species, i.e., may be monocotyledonous or dicotyledonous.
  • they will be agricultural useful plants, i.e., plants cultivated by man for purposes of food production or technical, particularly industrial applications.
  • Of particular interest in the present invention are corn and soybean plants.
  • the recombinant DNA constructs optimized for soybean transformation and recombinant DNA constructs optimized for corn transformation are provided by the present invention.
  • Other plants of interest in the present invention for production of transgenic plants having enhanced traits include, without limitation, cotton, canola, wheat, sunflower, sorghum, alfalfa, barley, millet, rice, tobacco, fruit and vegetable crops, and turfgrass.
  • the present invention contemplates to use an orthologous gene in generating the transgenic plants with similarly enhanced traits as the transgenic Arabidopsis counterpart.
  • Enhanced physiological properties in transgenic plants of the present invention may be confirmed in responses to stress conditions, for example in assays using imposed stress conditions to detect enhanced responses to drought stress, nitrogen deficiency, cold growing conditions, or alternatively, under naturally present stress conditions, for example under field conditions.
  • Biomass measures may be made on greenhouse or field grown plants and may include such measurements as plant height, stem diameter, root and shoot dry weights, and, for corn plants, ear length and diameter.
  • Trait data on morphological changes may be collected by visual observation during the process of plant regeneration as well as in regenerated plants transferred to soil.
  • Such trait data includes characteristics such as normal plants, bushy plants, taller plants, thicker stalks, narrow leaves, striped leaves, knotted phenotype, chlorosis, albino, anthocyanin production, or altered tassels, ears or roots.
  • Other enhanced traits may be identified by measurements taken under field conditions, such as days to pollen shed, days to silking, leaf extension rate, chlorophyll content, leaf temperature, stand, seedling vigor, internode length, plant height, leaf number, leaf area, tillering, brace roots, stay green, stalk lodging, root lodging, plant health, barreness/prolificacy, green snap, and pest resistance.
  • trait characteristics of harvested grain may be confirmed, including number of kernels per row on the ear, number of rows of kernels on the ear, kernel abortion, kernel weight, kernel size, kernel density and physical grain quality.
  • hybrid yield in transgenic corn plants expressing genes of the present invention it may be desirable to test hybrids over multiple years at multiple locations in a geographical location where maize is conventionally grown, e.g., in Iowa, Illinois or other locations in the midwestern United States, under “normal” field conditions as well as under stress conditions, e.g., under drought or population density stress.
  • Transgenic plants can be used to provide plant parts according to the invention for regeneration or tissue culture of cells or tissues containing the constructs described herein.
  • Plant parts for these purposes can include leaves, stems, roots, flowers, tissues, epicotyl, meristems, hypocotyls, cotyledons, pollen, ovaries, cells and protoplasts, or any other portion of the plant which can be used to regenerate additional transgenic plants, cells, protoplasts or tissue culture.
  • Seeds of transgenic plants are provided by this invention can be used to propagate more plants containing the trait-improving recombinant DNA constructs of this invention. These descendants are intended to be included in the scope of this invention if they contain a trait-improving recombinant DNA construct of this invention, whether or not these plants are selfed or crossed with different varieties of plants.
  • Transformation vectors were prepared to constitutively transcribe DNA in either sense orientation (for enhanced protein expression) or anti-sense orientation (for endogenous gene suppression) under the control of an enhanced Cauliflower Mosaic Virus 35S promoter (U.S. Pat. No. 5,359,142) directly or indirectly (Moore, e.g., PNAS 95:376-381, 1998; Guyer, e.g., Genetics 149: 633-639, 1998; International patent application NO. PCT/EP98/07577).
  • the transformation vectors also contain a bar gene as a selectable marker for resistance to glufosinate herbicide.
  • This example describes a soil drought tolerance screen to identify Arabidopsis plants transformed with recombinant DNA that wilt less rapidly and/or produce higher seed yield when grown in soil under drought conditions
  • T2 seeds were sown in flats filled with Metro/Mix® 200 (The Scotts® Company, USA).
  • Humidity domes were added to each flat and flats were assigned locations and placed in climate-controlled growth chambers. Plants were grown under a temperature regime of 22° C. at day and 20° C. at night, with a photoperiod of 16 hours and average light intensity of 170 ⁇ mol/m 2 /s. After the first true leaves appeared, humidity domes were removed. The plants were sprayed with glufosinate herbicide and put back in the growth chamber for 3 additional days. Flats were watered for 1 hour the week following the herbicide treatment. Watering was continued every seven days until the flower bud primordia became apparent, at which time plants were watered for the last time.
  • plants were evaluated for wilting response and seed yield. Beginning ten days after the last watering, plants were examined daily until 4 plants/line had wilted. In the next six days, plants were monitored for wilting response. Five drought scores were assigned according to the visual inspection of the phenotypes: 1 for healthy, 2 for dark green, 3 for wilting, 4 severe wilting, and 5 for dead. A score of 3 or higher was considered as wilted.
  • seed yield measured as seed weight per plant under the drought condition was characterized for the transgenic plants and their controls and analyzed as a quantitative response according to example 1M.
  • This example sets forth the heat stress tolerance screen to identify Arabidopsis plants transformed with the gene of interest that are more resistant to heat stress based on primarily their seedling weight and root growth under high temperature.
  • T2 seeds were plated on 1/2 ⁇ MS salts, 1/% phytagel, with 10 ⁇ g/ml BASTA (7 per plate with 2 control seeds; 9 seeds total per plate). Plates were placed at 4° C. for 3 days to stratify seeds. Plates were then incubated at room temperature for 3 hours and then held vertically for 11 additional days at temperature of 34° C. at day and 20° C. at night. Photoperiod was 16 h. Average light intensity was ⁇ 140 ⁇ mol/m 2 /s. After 14 days of growth, plants were scored for glufosinate resistance, root length, final growth stage, visual color, and seedling fresh weight. A photograph of the whole plate was taken on day 14.
  • the seedling weight and root length were analyzed as quantitative responses according to example 1M.
  • the final grow stage at day 14 was scored as success if 50% of the plants had reached 3 rosette leaves and size of leaves are greater than 1 mm (Boyes, e.g. (2001) The Plant Cell 13, 1499-1510).
  • the growth stage data was analyzed as a qualitative response according to example 1L.
  • This example sets forth the high salinity stress screen to identify Arabidopsis plants transformed with the gene of interest that are tolerant to high levels of salt based on their rate of development, root growth and chlorophyll accumulation under high salt conditions.
  • T2 seeds were plated on glufosinate selection plates containing 90 mM NaCl and grown under standard light and temperature conditions. All seedlings used in the experiment were grown at a temperature of 22° C. at day and 20° C. at night, a 16-hour photoperiod, an average light intensity of approximately 120 umol/m 2 . On day 11, plants were measured for primary root length. After 3 more days of growth (day 14), plants were scored for transgenic status, primary root length, growth stage, visual color, and the seedlings were pooled for fresh weight measurement. A photograph of the whole plate was also taken on day 14.
  • the seedling weight and root length were analyzed as quantitative responses according to example 1M.
  • the final growth stage at day 14 was scored as success if 50% of the plants reached 3 rosette leaves and size of leaves are greater than 1 mm (Boyes, D. C., et al., (2001), The Plant Cell 13, 1499/1510).
  • the growth stage data was analyzed as a qualitative response according to example 1L.
  • T2 seeds were plated on BASTA selection plates containing 3% PEG and grown under standard light and temperature conditions. Seeds were plated on each plate containing 3% PEG, 1/2 ⁇ MS salts, 1% phytagel, and 10 ⁇ g/ml glufosinate. Plates were placed at 4° C. for 3 days to stratify seeds. On day 11, plants were measured for primary root length. After 3 more days of growth, i.e., at day 14, plants were scored for transgenic status, primary root length, growth stage, visual color, and the seedlings were pooled for fresh weight measurement. A photograph of the whole plate was taken on day 14.
  • Seedling weight and root length were analyzed as quantitative responses according to example 1M.
  • the final growth stage at day 14 was scored as success or failure based on whether the plants reached 3 rosette leaves and size of leaves are greater than 1 mm.
  • the growth stage data was analyzed as a qualitative response according to example 1L.
  • Table 7 A list of recombinant DNA constructs that improve osmotic stress tolerance in transgenic plants illustrated in Table 7.
  • This example set forth a screen to identify Arabidopsis plants transformed with the genes of interest that are more tolerant to cold stress subjected during day 8 to day 28 after seed planting. During these crucial early stages, seedling growth and leaf area increase were measured to assess tolerance when Arabidopsis seedlings were exposed to low temperatures. Using this screen, genetic alterations can be found that enable plants to germinate and grow better than wild type plants under sudden exposure to low temperatures.
  • This example sets forth a screen to identify Arabidopsis plants transformed with the genes of interests are resistant to cold stress based on their rate of development, root growth and chlorophyll accumulation under low temperature conditions.
  • T2 seeds were plated and all seedlings used in the experiment were grown at 8° C. Seeds were first surface disinfested using chlorine gas and then seeded on assay plates containing an aqueous solution of 1/2 ⁇ Gamborg's B/5 Basal Salt Mixture (Sigma/Aldrich Corp., St. Louis, Mo., USA G/5788), 1% PhytagelTM (Sigma-Aldrich, P-8169), and 10 ug/ml glufosinate with the final pH adjusted to 5.8 using KOH. Test plates were held vertically for 28 days at a constant temperature of 8° C., a photoperiod of 16 hr, and average light intensity of approximately 100 umol/m 2 /s. At 28 days post plating, root length was measured, growth stage was observed, the visual color was assessed, and a whole plate photograph was taken.
  • the root length at day 28 was analyzed as a quantitative response according to example 1M.
  • the growth stage at day 7 was analyzed as a qualitative response according to example 1L.
  • This protocol describes a screen to look for Arabidopsis plants that show an attenuated shade avoidance response and/or grow better than control plants under low light intensity. Of particular interest, we were looking for plants that didn't extend their petiole length, had an increase in seedling weight relative to the reference and had leaves that were more close to parallel with the plate surface.
  • T2 seeds were plated on glufosinate selection plates with 1 ⁇ 2 MS medium. Seeds were sown on 1/2 ⁇ MS salts, 1% Phytagel, 10 ug/ml BASTA. Plants were grown on vertical plates at a temperature of 22° C. at day, 20° C. at night and under low light (approximately 30 uE/m 2 /s, far/red ratio (655/665/725/735) ⁇ 0.35 using PLAQ lights with GAM color filter #680). Twenty-three days after seedlings were sown, measurements were recorded including seedling status, number of rosette leaves, status of flower bud, petiole leaf angle, petiole length, and pooled fresh weights. A digital image of the whole plate was taken on the measurement day. Seedling weight and petiole length were analyzed as quantitative responses according to example 1M. The number of rosette leaves, flowering bud formation and leaf angel were analyzed as qualitative responses according to example 1L.
  • the transgenic plants showed a trend of trait enhancement as compared to the reference with p ⁇ 0.2.
  • the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p ⁇ 0.2 and delta ⁇ 0, the transgenic plants showed a trend of trait enhancement as compared to the reference.
  • This example sets forth a plate based phenotypic analysis platform for the rapid detection of phenotypes that are evident during the first two weeks of growth.
  • the transgenic plants with advantages in seedling growth and development were determined by the seedling weight and root length at day 14 after seed planting.
  • T2 seeds were plated on glufosinate selection plates and grown under standard conditions ( ⁇ 100 uE/m 2 /s, 16 h photoperiod, 22° C. at day, 20° C. at night). Seeds were stratified for 3 days at 4° C. Seedlings were grown vertically (at a temperature of 22° C. at day 20° C. at night). Observations were taken on day 10 and day 14. Both seedling weight and root length at day 14 were analyzed as quantitative responses according to example 1M.
  • This example sets forth a soil based phenotypic platform to identify genes that confer advantages in the processes of leaf development, flowering production and seed maturity to plants.
  • Arabidopsis plants were grown on a commercial potting mixture (Metro Mix 360, Scotts Co., Marysville, Ohio) consisting of 30-40% medium grade horticultural vermiculite, 35-55% sphagnum peat moss, 10-20% processed bark ash, 1-15% pine bark and a starter nutrient charge. Soil was supplemented with Osmocote time-release fertilizer at a rate of 30 mg/ft 3 . T2 seeds were imbibed in 1% agarose solution for 3 days at 4° C. and then sown at a density of ⁇ 5 per 21 ⁇ 2′′ pot. Thirty-two pots were ordered in a 4 by 8 grid in standard greenhouse flat.
  • Plants were grown in environmentally controlled rooms under a 16 h day length with an average light intensity of ⁇ 200 mmoles/m 2 /s. Day and night temperature set points were 22° C. and 20° C., respectively. Humidity was maintained at 65%. Plants were watered by sub-irrigation every two days on average until mid-flowering, at which point the plants were watered daily until flowering was complete.
  • glufosinate was performed to select T2 individuals containing the target transgene. A single application of glufosinate was applied when the first true leaves were visible. Each pot was thinned to leave a single glufosinate-resistant seedling ⁇ 3 days after the selection was applied.
  • the rosette radius was measured at day 25.
  • the silique length was measured at day 40.
  • the plant parts were harvested at day 49 for dry weight measurements if flowering production was stopped. Otherwise, the dry weights of rosette and silique were carried out at day 53.
  • the seeds were harvested at day 58. All measurements were analyzed as quantitative responses according to example 1M.
  • Arabidopsis seedlings become chlorotic and have less biomass.
  • This example sets forth the limited nitrogen tolerance screen to identify Arabidopsis plants transformed with the gene of interest that are altered in their ability to accumulate biomass and/or retain chlorophyll under low nitrogen condition.
  • T2 seeds were plated on glufosinate selection plates containing 0.5 ⁇ N-Free Hoagland's T 0.1 mM NH 4 NO 3 T 0.1% sucrose T 1% phytagel media and grown under standard light and temperature conditions. At 12 days of growth, plants were scored for seedling status (i.e., viable or non-viable) and root length. After 21 days of growth, plants were scored for BASTA resistance, visual color, seedling weight, number of green leaves, number of rosette leaves, root length and formation of flowering buds. A photograph of each plant was also taken at this time point.
  • the seedling weight and root length were analyzed as quantitative responses according to example 1M.
  • the number green leaves, the number of rosette leaves and the flowerbud formation were analyzed as qualitative responses according to example 1L.
  • the leaf color raw data were collected on each plant as the percentages of five color elements (Green, DarkGreen, LightGreen, RedPurple, YellowChlorotic) using a computer imaging system.
  • a statistical logistic regression model was developed to predict an overall value based on five colors for each plant.
  • the transgenic plants showed a trend of trait enhancement as compared to the reference with p ⁇ 0.2.
  • the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p ⁇ 0.2, the transgenic plants showed a trend of trait enhancement as compared to the reference.
  • the measurements (M) of each plant were transformed by log 2 calculation.
  • the Delta was calculated as log 2 M(transgenic) ⁇ log 2 M(reference).
  • the mean delta from multiple events of the transgene of interest was evaluated for statistical significance by t-test using SAS statistical software (SAS 9, SAS/STAT User's Guide, SAS Institute Inc, Cary, N.C., USA).
  • SAS 9 SAS/STAT User's Guide, SAS Institute Inc, Cary, N.C., USA.
  • the Delta with a value greater than 0 indicates that the transgenic plants perform better than the reference.
  • the Delta with a value less than 0 indicates that the transgenic plants perform worse than the reference.
  • the Delta with a value equal to 0 indicates that the performance of the transgenic plants and the reference don't show any difference.
  • a BLAST searchable “All Protein Database” is constructed of known protein sequences using a proprietary sequence database and the National Center for Biotechnology Information (NCBI) non-redundant amino acid database (nr.aa). For each organism from which a DNA sequence provided herein was obtained, an “Organism Protein Database” is constructed of known protein sequences of the organism; the Organism Protein Database is a subset of the All Protein Database based on the NCBI taxonomy ID for the organism.
  • NCBI National Center for Biotechnology Information
  • the All Protein Database is queried using amino acid sequence of cognate protein for gene DNA used in trait-improving recombinant DNA, i.e., sequences of SEQ ID NO: 760 through SEQ ID NO: 1518 using “blastp” with E-value cutoff of 1e-8.
  • Up to 1000 top hits were kept, and separated by organism names.
  • a list is kept for hits from the query organism itself with a more significant E-value than the best hit of the organism.
  • the list contains likely duplicated genes, and is referred to as the Core List.
  • Another list was kept for all the hits from each organism, sorted by E-value, and referred to as the Hit List.
  • the Organism Protein Database is queried using amino acid sequences of SEQ ID NO: 760 through SEQ ID NO: 1518 using “blastp” with E-value cutoff of 1e-4. Up to 1000 top hits are kept. A BLAST searchable database is constructed based on these hits, and is referred to as “SubDB”. SubDB was queried with each sequence in the Hit List using “blastp” with E-value cutoff of 1e-8. The hit with the best E-value is compared with the Core List from the corresponding organism. The hit is deemed a likely ortholog if it belongs to the Core List, otherwise it is deemed not a likely ortholog and there is no further search of sequences in the Hit List for the same organism.
  • ClustalW program is selected for multiple sequence alignments of an amino acid sequence of SEQ ID NO: 760 and its homologs, through SEQ ID NO: 1518 and its homologs.
  • Three major factors affecting the sequence alignments dramatically are (1) protein weight matrices; (2) gap open penalty; (3) gap extension penalty.
  • Protein weight matrices available for ClustalW program include Blosum, Pam and Gonnet series. Those parameters with gap open penalty and gap extension penalty were extensively tested. On the basis of the test results, Blosum weight matrix, gap open penalty of 10 and gap extension penalty of 1 were chosen for multiple sequence alignment.
  • the consensus sequence of SEQ ID NO: 768 and its 17 homologs were derived according to the procedure described above and is displayed in FIG. 4 .
  • This example illustrates the identification of domain and domain module by Pfam analysis.
  • the amino acid sequence of the expressed proteins that were shown to be associated with an enhanced trait were analyzed for Pfam protein family against the current Pfam collection of multiple sequence alignments and hidden Markov models using the HMMER software.
  • the Pfam domain modules and individual protein domain for the proteins of SEQ ID NO: 760 through 1518 are shown in Table 17 and Table 18 respectively.
  • the Hidden Markov model databases for the identified patent families allow identification of other homologous proteins and their cognate encoding DNA to enable the full breadth of the invention for a person of ordinary skill in the art.
  • Certain proteins are identified by a single Pfam domain and others by multiple Pfam domains. For instance, the protein with amino acids of SEQ ID NO: 766 is characterized by two Pfam domains, i.e.
  • FHA and “PP2C”. See also the protein with amino acids of SEQ ID NO: 1515 which is characterized by seven copies of the Pfam domain “WD40”.
  • SEQ ID NO: 1515 which is characterized by seven copies of the Pfam domain “WD40”.
  • Score is the gathering score for the Hidden Markov Model of the domain which exceeds the gathering cutoff reported in Table 19.
  • This example illustrates the construction of plasmids for transferring recombinant DNA into the nucleus of a plant cell which can be regenerated into a transgenic crop plant of this invention.
  • Primers for PCR amplification of protein coding nucleotides of recombinant DNA are designed at or near the start and stop codons of the coding sequence, in order to eliminate most of the 5′ and 3′ untranslated regions.
  • DNA of interest i.e. each DNA identified in Table 2 and the DNA for the identified homologous genes, are cloned and amplified by PCR prior to insertion into the insertion site the base vector.
  • OR-Ec.oriV-RK2 The vegetative origin 6696-7092 in E. coli of replication from plasmid RK2.
  • OR-Ec.ori-ColE1 The minimal origin of 9220-9808 replication from the E. coli plasmid ColE1.
  • Plasmids for use in transformation of soybean are also prepared. Elements of an exemplary common expression vector plasmid pMON82053 are shown in Table 21 below.
  • This exemplary soybean transformation base vector illustrated in FIG. 2 is assembled using the technology known in the art. DNA of interest, i.e. each DNA identified in Table 2 and the DNA for the identified homologous genes, is cloned and amplified by PCR prior to insertion into the insertion site the base vector at the insertion site between the enhanced 35S CaMV promoter and the termination sequence of cotton E6 gene.
  • T-AGRtu.nos A 3′ non-translated region of the 9466-9718 nopaline synthase gene of Agrobacterium tumefaciens Ti plasmid which functions to direct polyadenylation of the mRNA.
  • Gene of P-CaMV.35S-enh Promoter for 35S RNA from CaMV 1-613 interest containing a duplication of the ⁇ 90 expression to ⁇ 350 region.
  • cassette T-Gb.E6-3b 3′ untranslated region from the fiber 688-1002 protein E6 gene of sea-island cotton; Agrobaterium B-AGRtu.right Agro right border sequence, essential 1033-1389 T-DNA border for transfer of T-DNA.
  • OR-Ec.oriV-RK2 The vegetative origin of replication 5661-6057 in E. coli from plasmid RK2.
  • OR-Ec.ori-ColE1 The minimal origin of replication 2945-3533 from the E. coli plasmid ColE1.
  • Plasmids for use in transformation of cotton are also prepared. Elements of an exemplary common expression vector plasmid pMON99053 are shown in Table 22 below and FIG. 3 . Primers for PCR amplification of protein coding nucleotides of recombinant DNA are designed at or near the start and stop codons of the coding sequence, in order to eliminate most of the 5′ and 3′ untranslated regions. Each recombinant DNA coding for a protein identified in Table 2 is amplified by PCR prior to insertion into the insertion site within the gene of interest expression cassette of one of the base.
  • OR-Ec.oriV-RK2 The vegetative origin of 2739-3135 in E. coli replication from plasmid RK2.
  • OR-Ec.ori-ColE1 The minimal origin of 5263-5851 replication from the E. coli plasmid ColE1.
  • transgenic corn cells are prepared with recombinant DNA expressing each of the protein encoding DNAs listed in Table 2 by Agrobacterium -mediated transformation using the corn transformation constructs as disclosed in Example 5.
  • Corn transformation is effected using methods disclosed in U.S. Patent Application Publication 2004/0344075 A 1 where corn embryos are inoculated and co-cultured with the Agrobacterium tumefaciens strain ABI and the corn transformation vector.
  • To regenerate transgenic corn plants the transgenic callus resulting from transformation is placed on media to initiate shoot development in plantlets which are transferred to potting soil for initial growth in a growth chamber followed by a mist bench before transplanting to pots where plants are grown to maturity.
  • the plants are self fertilized and seed is harvested for screening as seed, seedlings or progeny R2 plants or hybrids, e.g., for yield trials in the screens indicated above.
  • transgenic plants and seeds having the transgenic cells of this invention which have recombinant DNA imparting the enhanced agronomic traits are identified by screening for nitrogen use efficiency, yield, water use efficiency, cold tolerance and enhanced seed composition.
  • transgenic soybean cells are prepared with recombinant DNA expressing each of the protein encoding DNAs listed in Table 1 by Agrobacterium -mediated transformation using the soybean transformation constructs disclosed in Example 5. Soybean transformation is effected using methods disclosed in U.S. Pat. No. 6,384,301 where soybean meristem explants are wounded then inoculated and co-cultured with the soybean transformation vector, then transferred to selection media for 6-8 weeks to allow selection and growth of transgenic shoots.
  • Transgenic shoots producing roots are transferred to the greenhouse and potted in soil. Many transgenic events which survive to fertile transgenic plants that produce seeds and progeny plants do not exhibit an enhanced agronomic trait.
  • the transgenic plants and seeds having the transgenic cells of this invention which have recombinant DNA imparting the enhanced agronomic traits are identified by screening for nitrogen use efficiency, yield, water use efficiency, cold tolerance and enhanced seed composition.
  • Transgenic seed and plants in corn, soybean, cotton or canola with recombinant DNA identified in Table 2 are prepared by plant cells transformed with DNA that is stably integrated into the genome of the corn cell.
  • Transgenic corn plant cells are transformed with recombinant DNA from each of the genes identified in Table 2.
  • Progeny transgenic plants and seed of the transformed plant cells are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil as compared to control plants
  • Transgenic corn seeds provided by the present invention are planted in fields with three levels of nitrogen (N) fertilizer being applied, i.e. low level (0 N), medium level (80 lb/ac) and high level (180 lb/ac). A variety of physiological traits are monitored. Plants with enhanced NUE provide higher yield as compared to control plants.
  • N nitrogen
  • Effective selection of enhanced yielding transgenic plants uses hybrid progeny of the transgenic plants for corn, cotton, and canola, or inbred progeny of transgenic plants for soybeanplants plant such as corn, cotton, canola, or inbred plant such as soy, canola and cottoncotton over multiple locations with plants grown under optimal production management practices, and maximum pest control.
  • a useful target for improved yield is a 5% to 10% increase in yield as compared to yield produced by plants grown from seed for a control plant. Selection methods may be applied in multiple and diverse geographic locations, for example up to 16 or more locations, over one or more planting seasons, for example at least two planting seasons, to statistically distinguish yield improvement from natural environmental effects
  • the selection process imposes a water withholding period to induce stressdrought followed by watering.
  • a useful selection process imposes 3 drought/re-water cycles on plants over a total period of 15 days after an initial stress free growth period of 11 days. Each cycle consists of 5 days, with no water being applied for the first four days and a water quenching on the 5th day of the cycle.
  • the primary phenotypes analyzed by the selection method are the changes in plant growth rate as determined by height and biomass during a vegetative drought treatment.
  • Cold field efficacy trial A cold field efficacy trial is used to identify gene constructs that confer enhanced cold vigor at germination and early seedling growth under early spring planting field conditions in conventional-till and simulated no-till environments. Seeds are planted into the ground around two weeks before local farmers begin to plant corn so that a significant cold stress is exerted onto the crop, named as cold treatment. Seeds also are planted under local optimal planting conditions such that the crop has little or no exposure to cold condition, named as normal treatment. At each location, seeds are planted under both cold and normal conditions with 3 repetitions per treatment. Two temperature monitors are set up at each location to monitor both air and soil temperature daily.
  • This example sets forth a high-throughput selection for identifying plant seeds with improvement in seed composition using the Infratec 1200 series Grain Analyzer, which is a near-infrared transmittance spectrometer used to determine the composition of a bulk seed sample (Table 23).
  • Near infrared analysis is a non-destructive, high-throughput method that can analyze multiple traits in a single sample scan.
  • An NIR calibration for the analytes of interest is used to predict the values of an unknown sample.
  • the NIR spectrum is obtained for the sample and compared to the calibration using a complex chemometric software package that provides predicted values as well as information on how well the sample fits in the calibration.
  • Infratec Model 1221, 1225, or 1227 with transport module by Foss North America is used with cuvette, item #1000-4033, Foss North America or for small samples with small cell cuvette, Foss standard cuvette modified by Leon Girard Co. Corn and soy check samples of varying composition maintained in check cell cuvettes are supplied by Leon Girard Co. NIT collection software is provided by Maximum Consulting Inc. Software. Calculations are performed automatically by the software. Seed samples are received in packets or containers with barcode labels from the customer. The seed is poured into the cuvettes and analyzed as received.
  • Typical sample(s) Whole grain corn and soybean seeds
  • Analytical time to run method Less than 0.75 min per sample
  • Total elapsed time per run 1.5 minute per sample
  • Typical and minimum sample Corn typical: 50 cc; minimum 30 cc size: Soybean typical: 50 cc; minimum 5 cc
  • Typical analytical range Determined in part by the specific calibration. Corn - moisture 5-15%, oil 5-20%, protein 5-30%, starch 50-75%, and density 1.0-1.3%. Soybean - moisture 5-15%, oil 15-25%, and protein 35-50%.
  • Cotton transformation is performed as generally described in WO0036911 and in U.S. Pat. No. 5,846,797.
  • Transgenic cotton plants containing each of the recombinant DNA having a sequence of SEQ ID NO: 1 through SEQ ID NO: 759 are obtained by transforming with recombinant DNA from each of the genes identified in Table 1.
  • Progeny transgenic plants are selected from a population of transgenic cotton events under specified growing conditions and are compared with control cotton plants.
  • Control cotton plants are substantially the same cotton genotype but without the recombinant DNA, for example, either a parental cotton plant of the same genotype that was not transformed with the identical recombinant DNA or a negative isoline of the transformed plant.
  • a commercial cotton cultivar adapted to the geographical region and cultivation conditions i.e. cotton variety ST474, cotton variety FM 958, and cotton variety Siokra L-23, are used to compare the relative performance of the transgenic cotton plants containing the recombinant DNA.
  • the specified culture conditions are growing a first set of transgenic and control plants under “wet” conditions, i.e. irrigated in the range of 85 to 100 percent of evapotranspiration to provide leaf water potential of ⁇ 14 to ⁇ 18 bars, and growing a second set of transgenic and control plants under “dry” conditions, i.e. irrigated in the range of 40 to 60 percent of evapotranspiration to provide a leaf water potential of ⁇ 21 to ⁇ 25 bars.
  • Pest control such as weed and insect control is applied equally to both wet and dry treatments as needed.
  • Data gathered during the trial includes weather records throughout the growing season including detailed records of rainfall; soil characterization information; any herbicide or insecticide applications; any gross agronomic differences observed such as leaf morphology, branching habit, leaf color, time to flowering, and fruiting pattern; plant height at various points during the trial; stand density; node and fruit number including node above white flower and node above crack boll measurements; and visual wilt scoring.
  • Cotton boll samples are taken and analyzed for lint fraction and fiber quality. The cotton is harvested at the normal harvest timeframe for the trial area. Enhanced water use efficiency is indicated by increased yield, improved relative water content, enhanced leaf water potential, increased biomass, enhanced leaf extension rates, and improved fiber parameters.
  • transgenic cotton plants of this invention are identified from among the transgenic cotton plants by agronomic trait screening as having increased yield and enhanced water use efficiency.
  • This example illustrates plant transformation useful in producing the transgenic canola plants of this invention and the production and identification of transgenic seed for transgenic canola having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
  • Tissues from in vitro grown canola seedlings are prepared and inoculated with a suspension of overnight grown Agrobacterium containing plasmid DNA with the gene of interest cassette and a plant selectable marker cassette. Following co-cultivation with Agrobacterium , the infected tissues are allowed to grow on selection to promote growth of transgenic shoots, followed by growth of roots from the transgenic shoots. The selected plantlets are then transferred to the greenhouse and potted in soil. Molecular characterization are performed to confirm the presence of the gene of interest, and its expression in transgenic plants and progenies. Progeny transgenic plants are selected from a population of transgenic canola events under specified growing conditions and are compared with control canola plants.
  • Control canola plants are substantially the same canola genotype but without the recombinant DNA, for example, either a parental canola plant of the same genotype that is not transformed with the identical recombinant DNA or a negative isoline of the transformed plant
  • Transgenic canola plant cells are transformed with recombinant DNA from each of the genes identified in Table 2.
  • Transgenic progeny plants and seed of the transformed plant cells are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
  • This example illustrates the preparation and identification by selection of transgenic seeds and plants derived from transgenic plant cells of this invention where the plants and seed are identified by screening for a transgenic plant having an enhanced agronomic trait imparted by expression or suppression of a protein selected from the group including the homologous proteins identified in Example 2.
  • Transgenic plant cells of corn, soybean, cotton, canola, alfalfa, wheat and rice are transformed with recombinant DNA for expressing or suppressing each of the homologs identified in Example 2.
  • Plants are regenerated from the transformed plant cells and used to produce progeny plants and seed that are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. Plants are identified exhibiting enhanced traits imparted by expression or suppression of the homologous proteins.
  • This example illustrates monocot and dicot plant transformation to produce nuclei of this invention in cells of a transgenic plant by transformation where the recombinant DNA suppresses the expression of an endogenous protein identified in Table 24.
  • Corn, soybean, cotton, or canola tissue are transformed as described in Examples 2-5 using recombinant DNA in the nucleus with DNA that is transcribed into RNA that forms double-stranded RNA targeted to an endogenous gene with DNA encoding the protein.
  • the genes for which the double-stranded RNAs are targeted are the native gene in corn, soybean, cotton or canola that are homologs of the genes encoding the protein that has the function of the protein in Arabidopsis as identified in table 24.

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Abstract

Transgenic seed for crops with enhanced agronomic traits are provided by trait-improving recombinant DNA in the nucleus of cells of the seed where plants grown from such transgenic seed exhibit one or more enhanced traits as compared to a control plant. Of particular interest are transgenic plants that have increased yield. The present invention also provides recombinant DNA molecules for expression of a protein, and recombinant DNA molecules for suppression of a protein.

Description

    RELATED APPLICATIONS
  • This application claims benefits under 35 U.S.C. 119(e) of U.S. Provisional Application Ser. No. 60/933,428, filed Jun. 6, 2007, which is incorporated herein by reference in its entirety.
    • INCORPORATION OF SEQUENCE LISTING
  • Two copies of the sequence listing (Copy 1 and Copy 2) and a computer readable form (CRF) of the sequence listing, all on CD-Rs, each containing the file named “38-21(54866)A_seqListing.txt”, which is 239,913,045 bytes (measured in MS-WINDOWS) and was created on Jun. 5, 2008, are incorporated herein by reference in their entirety.
    • INCORPORATION OF TABLES
  • Two copies of Table 16 on CD-ROMs, each containing the file named “38-21(54866)A_table16.txt”, which is 646,705 bytes when measured in MS-WINDOWS operating system, was created on Jun. 5, 2008, and comprises 150 pages when viewed in MS Word® program, are incorporated herein by reference in their entirety.
  • LENGTHY TABLES
    The patent application contains a lengthy table section. A copy of the table is available in electronic form from the USPTO web site (http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20130305398A1). An electronic copy of the table will also be available from the USPTO upon request and payment of the fee set forth in 37 CFR 1.19(b)(3).
    • FIELD OF THE INVENTION
  • Disclosed herein are recombinant DNA useful for providing enhanced traits to transgenic plants, seeds, pollen, plant cells and plant nuclei of such transgenic plants, methods of making and using such recombinant DNA, plants, seeds, pollen, plant cells and plant nuclei. Also disclosed are methods of producing hybrid seed comprising such recombinant DNA.
    • SUMMARY OF THE INVENTION
  • This invention provides recombinant DNA constructs comprising polynucleotides characterized by SEQ ID NO:1-759 and the cognate amino acid sequences of SEQ ID NO:760-1518. The recombinant DNA is useful for providing enhanced traits when stably integrated into the chromosomes and expressed in the nuclei of transgenic plants cells. In some aspects the recombinant DNA encodes a protein; in other aspects the recombinant DNA is transcribed to RNA that suppresses the expression of a native gene.
  • Such recombinant DNA in a plant cell nucleus of this invention is provided in as a construct comprising a promoter that is functional in plant cells and that is operably linked to DNA that encodes a protein or to DNA that results in gene suppression. Such DNA in the construct is sometimes defined by protein domains of an encoded protein targeted for production or suppression, e.g. a “Pfam domain module” (as defined herein below) from the group of Pfam domain modules identified in Table 17. Alternatively, e.g. where a Pfam domain module is not available, such DNA in the construct is defined a consensus amino acid sequence of an encoded protein that is targeted for production e.g. a protein having amino acid sequence with at least 90% identity to a consensus amino acid sequence in the group of SEQ ID NO: 67782 through SEQ ID NO: 67894. In a particular aspect of the invention the recombinant DNA is characterized by its cognate amino acid sequence that has at least 70% identity to any of SEQ ID NO:760-1518.
  • This invention also provides transgenic plant cell nuclei comprising the recombinant DNA of the invention, transgenic plant cells comprising such nuclei, transgenic plants comprising a plurality of such transgenic plant cells, and transgenic seeds and transgenic pollen of such plants. Such transgenic plants are selected from a population of transgenic plants regenerated from plant cells transformed with recombinant DNA by screening transgenic plants for an enhanced trait as compared to control plants. The enhanced trait is one or more of enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced heat tolerance, enhanced shade tolerance, enhanced high salinity tolerance, enhanced seed protein and enhanced seed oil. Such recombinant DNA in a plant cell nuclus of this invention is provided in as a construct comprising a promoter that is functional in plant cells and that is operably linked to DNA that encodes a protein or to DNA that results in gene suppression. Such DNA in the construct is sometimes defined by protein domains of an encoded protein targeted for production or suppression, e.g. a “Pfam domain module” (as defined herein below) from the group of Pfam domain modules identified in Table 17. Alternatively, e.g. where a Pfam domain module is not available, such DNA in the construct is defined a consensus amino acid sequence of an encoded protein that is targeted for production e.g. a protein having amino acid sequence with at least 90% identity to a consensus amino acid sequence in the group of SEQ ID NO: 67782 through SEQ ID NO: 67894.
  • In another aspect of the invention the plant cell nuclei, cells, plants, seeds, and pollen further comprise DNA expressing a protein that provides tolerance from exposure to an herbicide applied at levels that are lethal to a wild type plant cell.
  • This invention also provides methods for manufacturing non-natural, transgenic seed that can be used to produce a crop of transgenic plants with an enhanced trait resulting from expression of stably-integrated, recombinant DNA in the nucleus of the plant cells. More specifically the method comprises (a) screening a population of plants for an enhanced trait and recombinant DNA, where individual plants in the population can exhibit the trait at a level less than, essentially the same as or greater than the level that the trait is exhibited in control plants which do not express the recombinant DNA; (b) selecting from the population one or more plants that exhibit the trait at a level greater than the level that said trait is exhibited in control plants and (c) collecting seed from a selected plant. Such method further comprises steps (a) verifying that the recombinant DNA is stably integrated in said selected plants; and (b) analyzing tissue of a selected plant to determine the production of a protein having the function of a protein encoded by a recombinant DNA with a sequence of one of SEQ ID NO: 1-759; In one aspect of the invention the plants in the population further comprise DNA expressing a protein that provides tolerance to exposure to an herbicide applied at levels that are lethal to wild type plant cells and where the selecting is effected by treating the population with the herbicide, e.g. a glyphosate, dicamba, or glufosinate compound. In another aspect of the invention the plants are selected by identifying plants with the enhanced trait. The methods are especially useful for manufacturing corn, soybean, cotton, canola, alfalfa, wheat or rice seed selected as having one of the enhanced traits described above.
  • Another aspect of the invention provides a method of producing hybrid corn seed comprising acquiring hybrid corn seed from a herbicide tolerant corn plant which also has a nucleus of this invention with stably-integrated, recombinant DNA The method further comprises producing corn plants from said hybrid corn seed, where a fraction of the plants produced from said hybrid corn seed is homozygous for said recombinant DNA, a fraction of the plants produced from said hybrid corn seed is hemizygous for said recombinant DNA, and a fraction of the plants produced from said hybrid corn seed has none of said recombinant DNA; selecting corn plants which are homozygous and hemizygous for said recombinant DNA by treating with an herbicide; collecting seed from herbicide-treated-surviving corn plants and planting said seed to produce further progeny corn plants; repeating the selecting and collecting steps at least once to produce an inbred corn line; and crossing the inbred corn line with a second corn line to produce hybrid seed.
  • Still other aspects of this invention relate to transgenic plants with enhanced water use efficiency or enhanced nitrogen use efficiency. For instance, this invention provides methods of growing a corn, cotton, soybean, or canola crop without irrigation water comprising planting seed having plant cells of the invention which are selected for enhanced water use efficiency. Alternatively methods comprise applying reduced irrigation water, e.g. providing up to 300 millimeters of ground water during the production of a corn crop. This invention also provides methods of growing a corn, cotton, soybean or canola crop without added nitrogen fertilizer comprising planting seed having plant cells of the invention which are selected for enhanced nitrogen use efficiency.
  • In another aspect of the invention transgenic plants comprise recombinant DNA constructs which affect the expression of two or more proteins disclosed herein.
    • BRIEF DESCRIPTION OF THE DRAWINGS
  • FIGS. 1, 2 and 3 illustrate plasmid maps.
  • FIG. 4 illustrates a consensus amino acid sequence of SEQ ID NO: 768 and its homologs.
    •  DETAILED DESCRIPTION OF THE INVENTION
  • In the attached sequence listing:
  • SEQ ID NO: 1-759 are nucleotide sequences of the protein coding strand of DNA” used in the recombinant DNA for imparting an enhanced trait in plant cells;
  • SEQ ID NO: 760-1518 are amino acid sequences of the cognate protein of the nucleotide sequences of SEQ ID NO:1-759;
  • SEQ ID NO: 1519-67778 are amino acid sequences of homologous proteins;
  • SEQ ID NO:67779 is a nucleotide sequence of a plasmid base vector useful for corn transformation; and
  • SEQ ID NO:67780 is a DNA sequence of a plasmid base vector useful for soybean transformation.
  • SEQ ID NO:67781 is a DNA sequence of a plasmid base vector useful for cotton transformation.
  • SEQ ID NO: 67782-67894 are consensus sequences.
  • Table 1 lists the protein SEQ ID NOs and their corresponding consensus SEQ ID NOs.
  • TABLE 1
    SEQ ID Consensus
    Gene ID NO SEQ ID NO
    CGPG1083 767 67782
    CGPG1088 768 67783
    CGPG1092 769 67784
    CGPG1108 770 67785
    CGPG1140 772 67786
    CGPG1143 773 67787
    CGPG1170 775 67788
    CGPG1192 778 67789
    CGPG1311 786 67790
    CGPG1391 792 67791
    CGPG1633 809 67792
    CGPG1715 814 67793
    CGPG1895 822 67794
    CGPG2035 836 67795
    CGPG2068 840 67796
    CGPG2118 844 67797
    CGPG2191 848 67798
    CGPG2313 855 67799
    CGPG2426 864 67800
    CGPG2437 866 67801
    CGPG2452 867 67802
    CGPG2855 882 67803
    CGPG3004 887 67804
    CGPG3084 892 67805
    CGPG3269 905 67806
    CGPG3270 906 67807
    CGPG3410 913 67808
    CGPG3605 922 67809
    CGPG3612 923 67810
    CGPG3616 924 67811
    CGPG3631 925 67812
    CGPG375 933 67813
    CGPG3931 940 67814
    CGPG3975 944 67815
    CGPG4346 974 67816
    CGPG4383 977 67817
    CGPG4437 983 67818
    CGPG4660 995 67819
    CGPG4772 1007 67820
    CGPG5196 1043 67821
    CGPG5212 1046 67822
    CGPG5304 1057 67823
    CGPG5510 1072 67824
    CGPG5732 1100 67825
    CGPG5889 1116 67826
    CGPG5921 1120 67827
    CGPG5925 1121 67828
    CGPG5926 1122 67829
    CGPG6049 1135 67830
    CGPG6120 1142 67831
    CGPG6201 1151 67832
    CGPG6311 1169 67833
    CGPG6353 1176 67834
    CGPG6636 1214 67835
    CGPG691 1235 67836
    CGPG6930 1238 67837
    / / /
    CGPG6934 1239 67838
    CGPG7056 1249 67839
    CGPG7071 1250 67840
    CGPG7243 1270 67841
    CGPG7258 1271 67842
    CGPG7324 1277 67843
    CGPG7338 1279 67844
    CGPG7352 1282 67845
    CGPG7362 1285 67846
    CGPG7430 1295 67847
    CGPG7438 1296 67848
    CGPG7450 1299 67849
    CGPG7452 1300 67850
    CGPG7480 1302 67851
    CGPG7510 1308 67852
    CGPG7517 1310 67853
    CGPG7523 1311 67854
    CGPG7532 1314 67855
    CGPG7548 1316 67856
    CGPG7599 1320 67857
    CGPG7616 1324 67858
    CGPG7793 1333 67859
    CGPG7816 1338 67860
    CGPG7826 1339 67861
    CGPG7861 1340 67862
    CGPG8054 1362 67863
    CGPG8059 1363 67864
    CGPG8084 1367 67865
    CGPG8093 1368 67866
    CGPG8097 1371 67867
    CGPG8112 1372 67868
    CGPG8120 1373 67869
    CGPG8157 1376 67870
    CGPG8158 1377 67871
    CGPG8212 1382 67872
    CGPG8375 1403 67873
    CGPG8383 1405 67874
    CGPG8544 1422 67875
    CGPG8546 1423 67876
    CGPG8549 1424 67877
    CGPG8588 1429 67878
    CGPG8597 1430 67879
    CGPG8629 1433 67880
    CGPG8636 1437 67881
    CGPG8646 1440 67882
    CGPG8677 1442 67883
    CGPG8716 1446 67884
    CGPG8754 1447 67885
    CGPG9001 1471 67886
    CGPG9069 1476 67887
    CGPG9097 1480 67888
    CGPG9106 1481 67889
    CGPG9143 1487 67890
    CGPG9188 1498 67891
    CGPG9248 1505 67892
    CGPG9285 1509 67893
    CGPG9315 1513 67894
  • The nuclei of this invention are identified by screening transgenic plants for one or more traits including enhanced drought stress tolerance, enhanced heat stress tolerance, enhanced cold stress tolerance, enhanced high salinity stress tolerance, enhanced low nitrogen availability stress tolerance, enhanced shade stress tolerance, enhanced plant growth and development at the stages of seed imbibition through early vegetative phase, and enhanced plant growth and development at the stages of leaf development, flower production and seed maturity.
  • As used herein a “plant cell” means a plant cell that is transformed with stably-integrated, non-natural, recombinant DNA, e.g. by Agrobacterium-mediated transformation or by bombardment using microparticles coated with recombinant DNA or other means. A plant cell of this invention can be an originally-transformed plant cell that exists as a microorganism or as a progeny plant cell that is regenerated into differentiated tissue, e.g. into a transgenic plant with stably-integrated, non-natural recombinant DNA, or seed or pollen derived from a progeny transgenic plant.
  • As used herein a “transgenic plant” means a plant whose genome has been altered by the stable integration of recombinant DNA. A transgenic plant includes a plant regenerated from an originally-transformed plant cell and progeny transgenic plants from later generations or crosses of a transformed plant.
  • As used herein “recombinant DNA” means DNA which has been a genetically engineered and constructed outside of a cell including DNA containing naturally occurring DNA or cDNA or synthetic DNA.
  • As used herein a “homolog” means a protein in a group of proteins that perform the same biological function, e.g. proteins that belong to the same Pfam protein family and that provide a common enhanced trait in transgenic plants of this invention. Homologs are expressed by homologous genes. Homologous genes include naturally occurring alleles and artificially-created variants. Degeneracy of the genetic code provides the possibility to substitute at least one base of the protein encoding sequence of a gene with a different base without causing the amino acid sequence of the polypeptide produced from the gene to be changed. Hence, a polynucleotide useful in the present invention may have any base sequence that has been changed from SEQ ID NO:1 through SEQ ID NO: 803 through substitution in accordance with degeneracy of the genetic code. Homologs are proteins that, when optimally aligned, have at least 60% identity, more preferably about 70% or higher, more preferably at least 80% and even more preferably at least 90% identity over the full length of a protein identified as being associated with imparting an enhanced trait when expressed in plant cells. Homologs include proteins with an amino acid sequence that has at least 90% identity to a consensus amino acid sequence of proteins and homologs disclosed herein.
  • Homologs are identified by comparison of amino acid sequence, e.g. manually or by use of a computer-based tool using known homology-based search algorithms such as those commonly known and referred to as BLAST, FASTA, and Smith-Waterman. A local sequence alignment program, e.g. BLAST, can be used to search a database of sequences to find similar sequences, and the summary Expectation value (E-value) used to measure the sequence base similarity. As a protein hit with the best E-value for a particular organism may not necessarily be an ortholog or the only ortholog, a reciprocal query is used in the present invention to filter hit sequences with significant E-values for ortholog identification. The reciprocal query entails search of the significant hits against a database of amino acid sequences from the base organism that are similar to the sequence of the query protein. A hit can be identified as an ortholog, when the reciprocal query's best hit is the query protein itself or a protein encoded by a duplicated gene after speciation. A further aspect of the homologs encoded by DNA useful in the transgenic plants of the invention are those proteins that differ from a disclosed protein as the result of deletion or insertion of one or more amino acids in a native sequence.
  • As used herein, “percent identity” means the extent to which two optimally aligned DNA or protein segments are invariant throughout a window of alignment of components, for example nucleotide sequence or amino acid sequence. An “identity fraction” for aligned segments of a test sequence and a reference sequence is the number of identical components that are shared by sequences of the two aligned segments divided by the total number of sequence components in the reference segment over a window of alignment which is the smaller of the full test sequence or the full reference sequence. “Percent identity” (“% identity”) is the identity fraction times 100. Such optimal alignment is understood to be deemed as local alignment of DNA sequences. For protein alignment, a local alignment of protein sequences should allow introduction of gaps to achieve optimal alignment. Percent identity is calculated over the aligned length not including the gaps introduced by the alignment per se.
  • As used herein “promoter” means regulatory DNA for initializing transcription. A “plant promoter” is a promoter capable of initiating transcription in plant cells whether or not its origin is a plant cell, e.g. is it well known that Agrobacterium promoters are functional in plant cells. Thus, plant promoters include promoter DNA obtained from plants, plant viruses and bacteria such as Agrobacterium and Bradyrhizobium bacteria. Examples of promoters under developmental control include promoters that preferentially initiate transcription in certain tissues, such as leaves, roots, or seeds. Such promoters are referred to as “tissue preferred”. Promoters that initiate transcription only in certain tissues are referred to as “tissue specific”. A “cell type” specific promoter primarily drives expression in certain cell types in one or more organs, for example, vascular cells in roots or leaves. An “inducible” or “repressible” promoter is a promoter which is under environmental control. Examples of environmental conditions that may effect transcription by inducible promoters include anaerobic conditions, or certain chemicals, or the presence of light. Tissue specific, tissue preferred, cell type specific, and inducible promoters constitute the class of “non-constitutive”promoters. A “constitutive” promoter is a promoter which is active under most conditions.
  • As used herein “operably linked” means the association of two or more DNA fragments in a DNA construct so that the function of one, e.g. protein-encoding DNA, is controlled by the other, e.g. a promoter.
  • As used herein “expressed” means produced, e.g. a protein is expressed in a plant cell when its cognate DNA is transcribed to mRNA that is translated to the protein.
  • As used herein “suppressed” means decreased, e.g. a protein is suppressed in a plant cell when there is a decrease in the amount and/or activity of the protein in the plant cell. The presence or activity of the protein can be decreased by any amount up to and including a total loss of protein expression and/or activity.
  • As used herein a “control plant” means a plant that does not contain the recombinant DNA that expressed a protein that imparts an enhanced trait. A control plant is to identify and select a transgenic plant that has an enhance trait. A suitable control plant can be a non-transgenic plant of the parental line used to generate a transgenic plant, i.e. devoid of recombinant DNA. A suitable control plant may in some cases be a progeny of a hemizygous transgenic plant line that is does not contain the recombinant DNA, known as a negative segregant.
  • As used herein an “enhanced trait” means a characteristic of a transgenic plant that includes, but is not limited to, an enhance agronomic trait characterized by enhanced plant morphology, physiology, growth and development, yield, nutritional enhancement, disease or pest resistance, or environmental or chemical tolerance. In more specific aspects of this invention enhanced trait is selected from group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. In an important aspect of the invention the enhanced trait is enhanced yield including increased yield under non-stress conditions and increased yield under environmental stress conditions. Stress conditions may include, for example, drought, shade, fungal disease, viral disease, bacterial disease, insect infestation, nematode infestation, cold temperature exposure, heat exposure, osmotic stress, reduced nitrogen nutrient availability, reduced phosphorus nutrient availability and high plant density. “Yield” can be affected by many properties including without limitation, plant height, pod number, pod position on the plant, number of internodes, incidence of pod shatter, grain size, efficiency of nodulation and nitrogen fixation, efficiency of nutrient assimilation, resistance to biotic and abiotic stress, carbon assimilation, plant architecture, resistance to lodging, percent seed germination, seedling vigor, and juvenile traits. Yield can also be affected by efficiency of germination (including germination in stressed conditions), growth rate (including growth rate in stressed conditions), ear number, seed number per ear, seed size, composition of seed (starch, oil, protein) and characteristics of seed fill.
  • Increased yield of a transgenic plant of the present invention can be measured in a number of ways, including test weight, seed number per plant, seed weight, seed number per unit area (i.e. seeds, or weight of seeds, per acre), bushels per acre, tonnes per acre, tons per acre, kilo per hectare. For example, maize yield may be measured as production of shelled corn kernels per unit of production area, for example in bushels per acre or metric tons per hectare, often reported on a moisture adjusted basis, for example at 15.5 percent moisture. Increased yield may result from improved utilization of key biochemical compounds, such as nitrogen, phosphorous and carbohydrate, or from improved responses to environmental stresses, such as cold, heat, drought, salt, and attack by pests or pathogens. Recombinant DNA used in this invention can also be used to provide plants having improved growth and development, and ultimately increased yield, as the result of modified expression of plant growth regulators or modification of cell cycle or photosynthesis pathways. Also of interest is the generation of transgenic plants that demonstrate enhanced yield with respect to a seed component that may or may not correspond to an increase in overall plant yield. Such properties include enhancements in seed oil, seed molecules such as tocopherol, protein and starch, or oil particular oil components as may be manifest by an alterations in the ratios of seed components.
  • “Arabidopsis” means plants of Arabidopsis thaliana.
  • “Pfam” database is a large collection of multiple sequence alignments and hidden Markov models covering many common protein families, e.g. Pfam version 19.0 (December 2005) contains alignments and models for 8183 protein families and is based on the Swissprot 47.0 and SP-TrEMBL 30.0 protein sequence databases. See S. R. Eddy, “Profile Hidden Markov Models”, Bioinformatics 14:755-763, 1998. The Pfam database is currently maintained and updated by the Pfam Consortium. The alignments represent some evolutionary conserved structure that has implications for the protein's function. Profile hidden Markov models (profile HMMs) built from the protein family alignments are useful for automatically recognizing that a new protein belongs to an existing protein family even if the homology by alignment appears to be low.
  • A “Pfam domain module” is a representation of Pfam domains in a protein, in order from N terminus to C terminus. In a Pfam domain module individual Pfam domains are separated by double colons “::”. The order and copy number of the Pfam domains from N to C terminus are attributes of a Pfam domain module. Although the copy number of repetitive domains is important, varying copy number often enables a similar function. Thus, a Pfam domain module with multiple copies of a domain should define an equivalent Pfam domain module with variance in the number of multiple copies. A Pfam domain module is not specific for distance between adjacent domains, but contemplates natural distances and variations in distance that provide equivalent function. The Pfam database contains both narrowly- and broadly-defined domains, leading to identification of overlapping domains on some proteins. A Pfam domain module is characterized by non-overlapping domains. Where there is overlap, the domain having a function that is more closely associated with the function of the protein (based on the E value of the Pfam match) is selected.
  • Once one DNA is identified as encoding a protein which imparts an enhanced trait when expressed in transgenic plants, other DNA encoding proteins with the same Pfam domain module are identified by querying the amino acid sequence of protein encoded by candidate DNA against the Hidden Markov Models which characterizes the Pfam domains using HMMER software which is publicly available from the Pfam Consortium. Candidate proteins meeting the same Pfam domain module are in the protein family and have cognate DNA that is useful in constructing recombinant DNA for the use in the plant cells of this invention. Hidden Markov Model databases for use with HMMER software in identifying DNA expressing protein with a common Pfam domain module for recombinant DNA in the plant cells of this invention are also publicly available from the Pfam Consortium.
  • Version 19.0 of the HMMER software and Pfam databases were used to identify known domains in the proteins corresponding to amino acid sequence of SEQ ID NO: 760 through SEQ ID NO:1518. All DNA encoding proteins that have scores higher than the gathering cutoff disclosed in Table 19 by Pfam analysis disclosed herein can be used in recombinant DNA of the plant cells of this invention, e.g. for selecting transgenic plants having enhanced agronomic traits. The relevant Pfam modules for use in this invention, as more specifically disclosed below, are Saccharop_dh, Isoamylase_N::Alpha-amylase, RRM—1, Pribosyltran, Skp1_POZ::Skp1, PTR2, PSI_PsaH, OTU, Aldedh, p450, AP2, CBS, TPT, zf-UBR, zf-C3HC4, ADH_N::ADH_zinc_N, Pre-SET::SET, OstA, Myb_DNA-binding, Cpn60_TCP1, SKI, Cyt-b5::FA_desaturase, Pkinase, KTI12, SNARE, NLE::WD40::WD40::WD40::WD40, zf-C3HC4, Complex1—30 kDa::Complex1—49 kDa, iPGM_N::Metalloenzyme, adh_short, IQ::IQ, Glutaredoxin, LRRNT—2::LRR—1::LRR—1::Pkinase, Pkinase, Pribosyltran, DUF623, AWPM-19, Glucokinase, Pkinase_Tyr, Ribosomal_S8, F-box::Sel1::Sel1::zf-MYND, DUF313, WRKY, Aa_trans, Aminotran—1—2, Cystatin, PFK, PGAM, F-box, Ras, WD40::WD40::WD40::WD40, C2, Gal-bind_lectim:Galactosyl_T, Pyrredox—2::Pyr_redox_dim, Ank::Ank::Pkinase_Tyr, Aminotran—1—2, AMP-binding, Aminotran—3, PEARL1-4, RRM—1, LRRNT—2::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::Pkinase, SNARE_assoc_FKBP_C, ELFV_dehydrog_N::ELFV_dehydrog, Sugar_tr, SPT2, DUF23, Dehydrin, Prefoldin, WD40::WD40::WD40::WD40::WD40::WD40::WD40, IQ::IQ, zf-Tim10_DDP, PPR::PPR::PPR::PPR::PPR::PPR::PPR, F-box::FBA—3, SH3—1, RNA_poll_A14, GAF::HisKA, Pkinase::efhand::efband, Y_phosphatase2, 60KD_IMP, ADH_zinc_N, Glutaminase, p450, p450, Transket_pyr::Transketolase_C, B3—4::B5, Zip, DUF791::MFS—1, AA_permease, Pkinase, SAC3_GANP, DUF862, Pkinase, CS, TFIIS, Ribosomal_L19, Sugar_tr, NIF, SRF-TF::K-box, MSP, PGAM, Aha1_N::AHSA1, p450, F-box::FBA—1, Amino_oxidase, Tryp_alpha_amyl, Sugar_tr, zf-CW::MBD, Cytochrom_C, Tryp_alpha_amyl, Tcp11, Cys_Met_Meta_PP, UQ_con, zf-CCHC, Pyr_redox—2, efhand::efhand::efhand, Maf, MATH::BTB, LRRNT—2::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::L RR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::Pkinas e, Glyco_hydro—17, IQ, V-SNARE, Pkinase, Thioredoxin, AA_permease, Metallothio_PEC, HLH, p450, Pyr_redox—2::efhand, PP2C, GILT, F-box::Kelch—1::Kelch—1, AlaDh_PNT_N::AlaDh_PNT_C::Saccharop_dh_N::Saccharop_dh, WD40::WD40, Molybdop_Fe4S4::Molybdopterin::Molydop_binding, Aldedh, efhand, ETC_C1_NDUFA4, PGI, Transthyretin, GRP, SpoI1E, Dirigent, NUDIX, p450, Actin, Uricase::Uricase, Xan_ur_permease, NTP_transferase::Hexapep::Hexapep, zf-C3HC4, PPDK_N::PEP-utilizers::PEP-utilizers_C, Ribosomal_L37, Globin, Peptidase_M22, NADPH_Ox::Ferric_reduct::FAD_binding—8::NAD_binding—6, Glutaminase, XG_FTase, Enolase_N::Enolase_C, F-box::FBA—1, SOR_SNZ::ThiG, ABC_tran::ABC2_membrane::PDR_assoc::ABC_tran::ABC2_membrane, HMA::HMA, GATase::GMP_synt_C, Pkinase, CN_hydrolase::NAD_synthase, Usp::Pkinase, GRAM, Pkinase, DUF6::DUF6, Sugar_tr, Iso_dh, Tim17, Band—7, Polyketide_cyc, Cyclin_N::Cyclin_C, DUF26::DUF26::Pkinase, PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR, Amidohydro—2, 2OG-FeII_Oxy, PfkB, GILT, DUF246, Response_reg, TB2_DP1_HVA22, PP2C, ArfGap, TFIIF_alpha, ABC1, Methyltransf—12, Aldedh, TB2_DP1_HVA22, DUF6::TPT, Gp_dh_N::Gp_dh_C, efhand, SRF-TF, IQ::IQ, Lectin_legB::Pkinase, Self-incomp_S1, Hin1, Aminotran—1—2, Copine, ADH_N::ADH_zinc_N, Sugar_tr, DUF860, Pkinase, Sugar_tr, Nol1_Nop2_Fmu, zf-MYND::UCH, Aldedh, F-box::Kelch—1::Kelch—1, TOM20_plant, Sugar_tr, DHDPS, CPDase, Aldedh, Invertase_neut, Metallophos, PBP, Reticulon, Histone, DUF260, Phi—1, p450, Lectin_legB::Pkinase, Abhydrolase—1, AMP-binding, DAGK_cat, Pkinase::NAF, IQ::IQ, DnaJ::DnaJ_CXXCXGXG::DnaJ_C, RRM—1, RRM—1, Citrate_synt, Glutaminase, DUF6::DUF6, PRA-CH::PRA-PH, Aldedh, adh_short, Pkinase, Cyclin_N::Cyclin_C, CCT, AP2, Cullin, Lung—7-TM_R, DUF1677, Rib—5-P_isom_A, TPK_catalytic::TPK_B1_binding, Sugar_tr, DUF926, AstE_AspA, Cyt-b5, HEAT::Arm::HEAT::Arm, Arf, SRF-TF, Aldedh, Glyco_transf—8, F-box::LRR—2::FBD, p450, DUF833, IQ::IQ, Aldedh, PI3_PI4_kinase, p450, RNA_pol_I_A49, Abhydrolase—1, TFIIS_C, HMG-CoA_red, HEAT::HEAT::HEAT::HEAT::HEAT::HEAT::HEAT::HEAT::HEAT::HEAT::HEAT::HEA T, MMR_HSR1, Ank::Ank::Ank, CorA, DUF827, Cyclin, Glyco_transf 8, DUF623, zf-C3HC4, AA_permease, RRM—1::zf-CCHC, Ras, DEAD::Helicase_C::DSHCT, PAS—2::GAF::Phytochrome::HisKA::HATPase_c, Tetraspannin, NIR_SIR_ferr::NIR_SIR::NIR_SIR_ferr::NIR_SIR, ELFV_dehydrog_N::ELFV_dehydrog, F-box::Kelch—1::Kelch—1, Aldedh, RRM—1::RRM—1, RRM—1, PPR::PPR::PPR::PPR::PPR::PPR, DUF617, HD::RelA_SpoT, Diphthamide_syn, Gp_dh_N::Gp_dh_C, ThiC, CRAL_TRIO_N::CRAL_TRIO, FTHFS, MIP, Fibrillarin, Pkinase, Pkinase, GTP_EFTU::GTP_EFTU_D2::EFG_C, PPR::PPR::PPR::PPR::PPR::PPR, PTR2, FAD_binding—4, ScpA_ScpB, NDUF_B7, TPT, DEAD::Helicase_C, DnaJ, TPT, cobW, HIT, DHquinase—1::Shikimate_dh_N::Shikimate_DH, IQ::IQ, Aldedh, DUF231, PGI, zf-C3HC4, CorA, Transketolase_N::Transket_pyr:Transketolase_C, Dehydrin, RRM—1, Sterol_desat, cIF2A, ArfGap::C2, NTP_transferase, DAO, Sugar_tr, DUF21::CBS, Pkinase::NAF, Sulfotransfer—1, p450, PGM_PMM—1::PGM_PMM_II::PGM_PMM_III::PGM_PMM_IV, CPSase_L_chain::CPSase_L_D2::CPSase_L_D3::CPSase_L_chain::CPSase_L_D2::MGS, Pro_CA, DUF617, Voltage_CLC::CBS, F-box, Histone, 14-3-3, UBX, polyprenyl_synt, Rho_GDI, TPR—2, Aldedh, LRR—1::LRR—1::LRR—1::Pkinase, DUF239, Pkinase, Glycolytic, adh_short, DUF1001, PTR2, ATP_synt_H, p450, Mito_carr:Mito_carr:Mito_carr, Gar1, Gln-synt_N::Gln-synt_C, PseudoU_synth—1::PseudoU_synth—1, DUF1635, Pkinase, Pro_dh, DUF506, Acyltransferase, DJ-1_PfpI::DJ-1_Pfp1, PAP2, IQ, Isy1, Glutaredoxin, Molybdop_Fe4S4::Molybdopterin::Molydop_binding::Fer2_BFD, DUF778, Cyclin_N, zf-C3HC4, DUF300, DUF1639, Peptidasc_C26, P21-Arc, Mo25, Pkinase, Ras, DUF788, iPGM_N::Metalloenzyme, adh_short, Pyr_redox, Gln-synt_N::Gln-synt_C, FA_desaturase, zf-MYND::UCH, Skp1_POZ::Skp1, Cornichon, IGPD, Orn_Arg_deC_N::Orn_DAP_Arg_deC, DUF260, Gln-synt_N::Gln-synt_C, RRM—1, 2OG-Fell_Oxy, SNARE, RRM—1, DUF212, F-box, Phytochelatin::DUF1984, SRF-TF, T1M, MSF1, Ribonuc_L-PSP, p450, Transaldolase, Snf7, p450, FA_desaturase, F-box, efhand_like::PI-PLC-X::PI-PLC-Y::C2, Trehalose_PPase, Aminotran—4, Thioredoxin, Chitin_bind—1::Barwin, TLD, GATase—2::Asn_synthase, Pkinase, Pyridoxal_deC, Biotin_lipoyl::E3_binding::2-oxoacid_dh, H_PPase, DUF914, WD40::WD40::WD40, SIR2, Pkinase::efhand::efhand::efhand::efhand, LSM, PetM, DUF23, DUF862, tRNA-synt—1g, Radical_SAM, LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1LRR—1::Pkinase, DUF1644, Mov34, NOI, DUF6::TPT, Transket_pyr:Transketolase_C, F-box::LRR—2, zf-C3HC4, Phosphoesterase, SET, adh_short, Exo_endo_phos, Pkinase, Stig1, TFIIS_M::SPOC, Gln-synt_N::Gln-synt_C, B56, Aminotran—1—2, Aldose_epim, DUF1645, iPGM_N::Metalloenzyme, LRRNT—2::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::Pkinase, DUF538, Not3::NOT2—3—5, YjeF_N::Carb_kinase, DUF538, F-box, Cyclin_N::Cyclin_C, Aldedh, F-box, Pyr_redox—2, ELFV_dehydrog_N::ELEV_dehydrog, BCNT, Mago-bind, RRM—1, DUF783, Aminotran—3, ADH_N::ADH_zinc_N, Pkinase_Tyr, Ribosomal_S8, Pkinase, LRR—1, UDPGT, Peptidase_C54, mTERF, Skp1_POZ::Skp1, WD40::WD40::WD40::WD40, MtN3_slv::MtN3_slv, LRRNT—2::LRR—1::LRR—1::LRR—1::LRR—1::Pkinase, Aminotran—1—2, adh_short, PP2C, Senescence, Response_reg, DEAD::Helicase_C, Pkinase, zf-LSD1::zf-LSD1::zf-LSD1, PB1::Pkinasc_Tyr, BTB::NPH3, PBD, Exo_endo_phos, Fer4::Fer4, WD40::WD40::WD40::WD40::PWP2, LysM, NTP_transferase, Tim17, Aa_trans, Ras, IPK, F-box:LRR—2, FBPase, PP2C, Aldedh, Ank::Ank::Ank::Pkinase, Brix, PTR2, 2OG-Fell_Oxy, MCM, NTP_transferase::Hexapep::Hexapep::Hexapep::Hexapep, SapB—1::SapB—2::SapB—1::SapB—2, Aldedh, DUF581, AAA, Cyclin_N, ARM—1, IQ::IQ, Pkinase, ubiquitin::UBA::XPC-binding::UBA, Pkinase, TIM, Abhydrolase—1, CBS, Pkinase, Pyr_redox—2::Pyr_redox_dim, NicO, CCT, zf-PARP::zf-PARP::PADR1::BRCT::WGR::PARP_reg::PARP, Spermine_synth, NDK, E1_dh, LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::MATH::MATH, Cyclin_N::Cyclin_C, ADH_N::ADH_zinc_N, RRM—1, DUF393, LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1, AAA, zf-C3HC4::YDG_SRA, RWD, GHMP_kinases_N::GHMP_kinases_C, DZC, Glutaredoxin, DEAD::Helicase_C, Sterol_desat, DUF212, Pkinase, DREPP, PTR2, MGDG_synth::Glyco_tran—28_C, ACT::ACT, OTU, Pkinase, Glyco_hydro—1, Nuc_sug_transp, WD40::WD40::WD40::WD40::WD40::WD40::WD40::WD40::WD40::WD40::Utp13, Nramp, MFS—1, Metallophos, DUF1005, CTP_transf—1, RNA_pol_A_bac, DUF383::DUF384, DUF676, SAC3_GANP, ADH_N::ADH_zinc_N, PLAT::Lipoxygenase, SIS::CBS, Pkinase, Bystin, Response_reg, Phi—1, MFS—1, Pkinase, Pkinase, Gln-synt_N::Gln-synt_C, NUDIX, NIR_SIR_ferr::NIR_SIR::NIR_SIR::ferr::NIR_SIR, UFD1, DUF581, p450, WD40::WD40::WD40::WD40, p450, Gp_dh_N::Gp_dh_C, Abhydrolase—3, TP_methylase, Pkinase, LRR—1::LRR—1::LRR—1::LRR—1::LRR—1, GATase::GMP_synt_C, PfkB, RRM—1, malic::Malic_M, DUF525, FBPase, DUF59, Pro_isomerase, Arm::Arm, Pkinase_Tyr, Pkinase::NAF, BNR::BNR::BNR, DUF1350, CAF1, TMEM 14, MATH, DUF1000, PC_rep::PC_rep::PC_rep::PC_rep::PC_rep::PC_rep, Pkinase, FHA::PP2C, Pkinase, Di19, WD40::WD40, 2OG-FeII_Oxy, Pkinase, adh_short, Aldedh, DUF793, DUF1749, AAA, PGK, Aminotran—3, Str_synth, eIF-1a, Hydrolase, Sugar_tr, DUF640, PCI, Sina, PBP, AOX, OPT, Pkinase_Tyr, Rib—5-P_isom_A, DUF740, PP2C, Pkinase, and Cyclin_N::Cyclin_C.
    • Recombinant DNA Constructs
  • The invention uses recombinant DNA for imparting one or more enhanced traits to transgenic plant when incorporated into the nucleus of the plant cells. DNA constructs comprising one or more polynucleotides disclosed herein are assembled using methods well known to persons of ordinary skill in the art and typically comprise a promoter operably linked to DNA, the expression of which provides the enhanced agronomic trait. Other construct components may include additional regulatory elements, such as 5′ leasders and introns for enhancing transcription, 3′ untranslated regions (such as polyadenylation signals and sites), DNA for transit or signal peptides.
  • Numerous promoters that are active in plant cells have been described in the literature. These include promoters present in plant genomes as well as promoters from other sources, including nopaline synthase (NOS) promoter and octopine synthase (OCS) promoters carried on tumor-inducing plasmids of Agrobacterium tumefaciens and the CaMV35S promoters from the cauliflower mosaic virus as disclosed in U.S. Pat. Nos. 5,164,316 and 5,322,938. Useful promoters derived from plant genes are found in U.S. Pat. No. 5,641,876, which discloses a rice actin promoter, U.S. Pat. No. 7,151,204, which discloses a maize chloroplast aldolase promoter and a maize aldolase (FDA) promoter, and U.S. Patent Application Publication 2003/0131377 A1, which discloses a maize nicotianamine synthase promoter, all of which are incorporated herein by reference. These and numerous other promoters that function in plant cells are known to those skilled in the art and available for use in recombinant polynucleotides of the present invention to provide for expression of desired genes in transgenic plant cells.
  • In other aspects of the invention, preferential expression in plant green tissues is desired. Promoters of interest for such uses include those from genes such as Arabidopsis thaliana ribulose-1,5-bisphosphate carboxylase (Rubisco) small subunit (Fischhoff et al. (1992) Plant Mol. Biol. 20:81-93), aldolase and pyruvate orthophosphate dikinase (PPDK) (Taniguchi et al. (2000) Plant Cell Physiol. 41(1):42-48).
  • Furthermore, the promoters may be altered to contain multiple “enhancer sequences” to assist in elevating gene expression. Such enhancers are known in the art. By including an enhancer sequence with such constructs, the expression of the selected protein may be enhanced. These enhancers often are found 5′ to the start of transcription in a promoter that functions in eukaryotic cells, but can often be inserted upstream (5′) or downstream (3′) to the coding sequence. In some instances, these 5′ enhancing elements are introns. Particularly useful as enhancers are the 5′ introns of the rice actin 1 (see U.S. Pat. No. 5,641,876) and rice actin 2 genes, the maize alcohol dehydrogenase gene intron, the maize heat shock protein 70 gene intron (U.S. Pat. No. 5,593,874) and the maize shrunken 1 gene.
  • In other aspects of the invention, sufficient expression in plant seed tissues is desired to affect improvements in seed composition. Exemplary promoters for use for seed composition modification include promoters from seed genes such as napin (U.S. Pat. No. 5,420,034), maize L3 oleosin (U.S. Pat. No. 6,433,252), zein Z27 (Russell et al. (1997) Transgenic Res. 6(2):157-166), globulin 1 (Belanger et al (1991) Genetics 129:863-872), glutelin 1 (Russell (1997) supra), and peroxiredoxin antioxidant (Perl) (Stacy et al., (1996) Plant Mol. Biol. 31(6)1205-1216).
  • Recombinant DNA constructs prepared in accordance with the invention will also generally include a 3′ element that typically contains a polyadenylation signal and site. Well-known 3′ elements include those from Agrobacterium tumefaciens genes such as nos 3′, tml 3′, tmr 3′, tms 3′, ocs 3′, tr7 3′, for example disclosed in U.S. Pat. No. 6,090,627, incorporated herein by reference; 3′ elements from plant genes such as wheat (Triticum aesevitum) heat shock protein 17 (Hsp17 3), a wheat ubiquitin gene, a wheat fructose-1,6-biphosphatase gene, a rice glutelin gene, a rice lactate dehydrogenase gene and a rice beta-tubulin gene, all of which are disclosed in U.S. published patent application 2002/0192813 A1, incorporated herein by reference; and the pea (Pisum sativum) ribulose biphosphate carboxylase gene (rbs 3), and 3′ elements from the genes within the host plant.
  • Constructs and vectors may also include a transit peptide for targeting of a gene to a plant organelle, particularly to a chloroplast, leucoplast or other plastid organelle. For descriptions of the use of chloroplast transit peptides see U.S. Pat. No. 5,188,642 and U.S. Pat. No. 5,728,925, incorporated herein by reference. For description of the transit peptide region of an Arabidopsis EPSPS gene useful in the present invention, see Klee, H. J. et al (MGG (1987) 210:437-442).
  • Gene suppression includes any of the well-known methods for suppressing transcription of a gene or the accumulation of the mRNA corresponding to that gene thereby preventing translation of the transcript into protein. Posttranscriptional gene suppression is mediated by transcription of RNA that forms double-stranded RNA (dsRNA) having homology to a gene targeted for suppression. Suppression can also be achieved by insertion mutations created by transposable elements may also prevent gene function. For example, in many dicot plants, transformation with the T-DNA of Agrobacterium may be readily achieved and large numbers of transformants can be rapidly obtained. Also, some species have lines with active transposable elements that can efficiently be used for the generation of large numbers of insertion mutations, while some other species lack such options. Mutant plants produced by Agrobacterium or transposon mutagenesis and having altered expression of a polypeptide of interest can be identified using the polynucleotides of the present invention. For example, a large population of mutated plants may be screened with polynucleotides encoding the polypeptide of interest to detect mutated plants having an insertion in the gene encoding the polypeptide of interest.
  • Transgenic plants comprising or derived from plant cells of this invention transformed with recombinant DNA can be further enhanced with stacked traits, e.g. a crop plant having an enhanced trait resulting from expression of DNA disclosed herein in combination with herbicide and/or pest resistance traits. For example, genes of the current invention can be stacked with other traits of agronomic interest, such as a trait providing herbicide resistance, or insect resistance, such as using a gene from Bacillus thuringensis to provide resistance against lepidopteran, coliopteran, homopteran, hemiopteran, and other insects. Herbicides for which transgenic plant tolerance has been demonstrated and the method of the present invention can be applied include, but are not limited to, glyphosate, dicamba, glufosinate, sulfonylurea, bromoxynil and norflurazon herbicides. Polynucleotide molecules encoding proteins involved in herbicide tolerance are well-known in the art and include, but are not limited to, a polynucleotide molecule encoding 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) disclosed in U.S. Pat. Nos. 5,094,945; 5,627,061; 5,633,435 and 6,040,497 for imparting glyphosate tolerance; polynucleotide molecules encoding a glyphosate oxidoreductase (GOX) disclosed in U.S. Pat. No. 5,463,175 and a glyphosate-N-acetyl transferase (GAT) disclosed in U.S. Patent Application publication 2003/0083480 A1 also for imparting glyphosate tolerance; dicamba monooxygenase disclosed in U.S. Patent Application publication 2003/0135879 A1 for imparting dicamba tolerance; a polynucleotide molecule encoding bromoxynil nitrilase (Bxn) disclosed in U.S. Pat. No. 4,810,648 for imparting bromoxynil tolerance; a polynucleotide molecule encoding phytoene desaturase (crtI) described in Misawa et al, (1993) Plant J. 4:833-840 and in Misawa et al, (1994) Plant J. 6:481-489 for norflurazon tolerance; a polynucleotide molecule encoding acetohydroxyacid synthase (AHAS, aka ALS) described in Sathasiivan et al. (1990) Nucl. Acids Res. 18:2188-2193 for imparting tolerance to sulfonylurea herbicides; polynucleotide molecules known as bar genes disclosed in DeBlock, et al. (1987) EMBO J. 6:2513-2519 for imparting glufosinate and bialaphos tolerance; polynucleotide molecules disclosed in U.S. Patent Application Publication 2003/010609 A1 for imparting N-amino methyl phosphonic acid tolerance; polynucleotide molecules disclosed in U.S. Pat. No. 6,107,549 for impartinig pyridine herbicide resistance; molecules and methods for imparting tolerance to multiple herbicides such as glyphosate, atrazine, ALS inhibitors, isoxoflutole and glufosinate herbicides are disclosed in U.S. Pat. No. 6,376,754 and U.S. Patent Application Publication 2002/0112260, all of said U.S. Patents and Patent Application Publications are incorporated herein by reference. Molecules and methods for imparting insect/nematode/virus resistance are disclosed in U.S. Pat. Nos. 5,250,515; 5,880,275; 6,506,599; 5,986,175 and U.S. Patent Application Publication 2003/0150017 A1, all of which are incorporated herein by reference.
  • Table 2 provides a list of genes that provided recombinant DNA that was expressed in a model plant and identified from screening as imparting an enhanced trait. When the stated orientation is “sense”, the expression of the gene or a homolog in a crop plant provides the means to identify transgenic events that provide an enhanced trait in the crop plant. When the stated orientation is “antisense”, the suppression of the native homolog in a crop plant provides the means to identify transgenic events that provide an enhanced trait in the crop plant. In some cases the expression/suppression in the model plant exhibited an enhanced trait that corresponds to an enhanced agronomic trait, e.g. cold stress tolerance, water deficit stress tolerance, low nitrogen stress tolerance and the like. In other cases the expression/suppression in the model plant exhibited an enhanced trait that is a surrogate to an enhanced agronomic trait, e.g. salinity stress tolerance being a surrogate to drought tolerance or improvement in plant growth and development being a surrogate to enhanced yield. Even when expression of a transgene or suppression of a native gene imparts an enhanced trait in a model plant, not every crop plant expressing the same transgene or suppressing the same native gene will necessarily demonstrate an indicated enhanced agronomic trait. For instance, it is well known that multiple transgenic events are required to identify a transgenic plant that can exhibit an enhanced agronomic trait. However, by with routine experimentation a transgenic plant cell nuclei, cell, plant or seed of this invention can be identified by making a reasonable number of transgenic events and engaging in screening process identified in this specification and illustrated in the examples. An understanding of Table 2 is facilitated by the following description of the headings:
  • “NUC SEQ ID NO” refers to a SEQ ID NO. for particular DNA sequence in the Sequence Listing.
  • “PEP SEQ ID NO” refers to a SEQ ID NO. in the Sequence Listing for the amino acid sequence of a protein cognate to a particular DNA
  • “construct_id” refers to an arbitrary number used to identify a particular recombinant DNA construct comprising the particular DNA.
  • “Gene ID” refers to an arbitrary name used to identify the particular DNA.
  • “orientation” refers to the orientation of the particular DNA in a recombinant DNA construct relative to the promoter.
  • TABLE 2
    NUC PEP
    Seq Seq Construct
    ID ID Gene ID ID Orientation
    1 760 CGPG1022 12792 ANTI-SENSE
    2 761 CGPG1035 13673 ANTI-SENSE
    3 762 CGPG1043 12020 SENSE
    4 763 CGPG105 10174 ANTI-SENSE
    5 764 CGPG1060 11827 ANTI-SENSE
    6 765 CGPG1069 12435 SENSE
    7 766 CGPG108 12015 SENSE
    8 767 CGPG1083 11836 ANTI-SENSE
    9 768 CGPG1088 12141 ANTI-SENSE
    10 769 CGPG1092 12040 SENSE
    11 770 CGPG1108 12437 SENSE
    12 771 CGPG1136 12156 ANTI-SENSE
    13 772 CGPG1140 11853 ANTI-SENSE
    14 773 CGPG1143 12224 SENSE
    15 774 CGPG1145 11856 ANTI-SENSE
    16 775 CGPG1170 12065 SENSE
    17 776 CGPG1173 12419 ANTI-SENSE
    18 777 CGPG1176 12208 SENSE
    19 778 CGPG1192 14803 SENSE
    20 779 CGPG122 10176 ANTI-SENSE
    21 780 CGPG126 18011 SENSE
    22 781 CGPG1262 12714 ANTI-SENSE
    23 782 CGPG128 10507 ANTI-SENSE
    24 783 CGPG1280 15039 SENSE
    25 784 CGPG1291 12733 ANTI-SENSE
    26 785 CGPG1295 13237 SENSE
    27 786 CGPG1311 13504 SENSE
    28 787 CGPG1315 12932 SENSE
    29 788 CGPG1335 75935 SENSE
    30 789 CGPG1344 73333 SENSE
    31 790 CGPG1352 75993 SENSE
    32 791 CGPG1364 19401 SENSE
    33 792 CGPG1391 12766 ANTI-SENSE
    34 793 CGPG1396 76025 SENSE
    35 794 CGPG1398 13708 ANTI-SENSE
    36 795 CGPG1399 13305 ANTI-SENSE
    37 796 CGPG1429 15806 SENSE
    38 797 CGPG1430 14712 SENSE
    39 798 CGPG1445 76013 SENSE
    40 799 CGPG146 10192 ANTI-SENSE
    41 800 CGPG1492 74775 SENSE
    42 801 CGPG1528 13841 ANTI-SENSE
    43 802 CGPG1530 15805 SENSE
    44 803 CGPG1535 14253 ANTI-SENSE
    45 804 CGPG1546 13650 ANTI-SENSE
    46 805 CGPG1567 13855 ANTI-SENSE
    47 806 CGPG1568 76049 SENSE
    48 807 CGPG1575 14271 ANTI-SENSE
    49 808 CGPG1619 73927 SENSE
    50 809 CGPG1633 13657 ANTI-SENSE
    51 810 CGPG1641 13938 ANTI-SENSE
    51 810 CGPG1641 14730 SENSE
    52 811 CGPG1651 73948 SENSE
    53 812 CGPG1656 18116 ANTI-SENSE
    54 813 CGPG1668 14341 ANTI-SENSE
    55 814 CGPG1715 13960 ANTI-SENSE
    55 814 CGPG1715 74391 SENSE
    56 815 CGPG1740 75957 SENSE
    57 816 CGPG177 70240 SENSE
    58 817 CGPG1785 70748 ANTI-SENSE
    59 818 CGPG182 70807 SENSE
    60 819 CGPG1837 73986 SENSE
    61 820 CGPG1873 77005 SENSE
    62 821 CGPG1891 70410 ANTI-SENSE
    63 822 CGPG1895 14827 ANTI-SENSE
    64 823 CGPG1899 19122 SENSE
    65 824 CGPG1913 16446 SENSE
    66 825 CGPG1918 15143 SENSE
    67 826 CGPG1919 70401 SENSE
    68 827 CGPG1922 16182 SENSE
    69 828 CGPG1929 15126 SENSE
    70 829 CGPG1938 15628 ANTI-SENSE
    71 830 CGPG1956 78355 SENSE
    72 831 CGPG1964 70560 SENSE
    73 832 CGPG1973 19133 SENSE
    74 833 CGPG1977 73602 SENSE
    75 834 CGPG1996 71702 SENSE
    76 835 CGPG2005 14909 ANTI-SENSE
    77 836 CGPG2035 14927 ANTI-SENSE
    78 837 CGPG2044 75945 SENSE
    79 838 CGPG2059 16553 ANTI-SENSE
    80 839 CGPG2065 75221 SENSE
    81 840 CGPG2068 70746 ANTI-SENSE
    82 841 CGPG2072 70403 SENSE
    83 842 CGPG2074 15966 ANTI-SENSE
    84 843 CGPG2116 76076 SENSE
    85 844 CGPG2118 17014 SENSE
    86 845 CGPG2142 16007 ANTI-SENSE
    87 846 CGPG2148 16208 SENSE
    88 847 CGPG2190 17310 SENSE
    89 848 CGPG2191 15716 ANTI-SENSE
    90 849 CGPG221 15627 SENSE
    91 850 CGPG2213 15409 ANTI-SENSE
    91 850 CGPG2213 17201 SENSE
    92 851 CGPG2247 15903 ANTI-SENSE
    93 852 CGPG228 10332 ANTI-SENSE
    94 853 CGPG2301 73968 SENSE
    95 854 CGPG2304 17003 SENSE
    96 855 CGPG2313 73847 SENSE
    97 856 CGPG2348 76041 SENSE
    98 857 CGPG2349 74567 SENSE
    99 858 CGPG2354 15809 ANTI-SENSE
    100 859 CGPG2369 70110 SENSE
    101 860 CGPG2382 70123 SENSE
    102 861 CGPG2392 74702 SENSE
    103 862 CGPG2397 75936 SENSE
    104 863 CGPG240 10462 ANTI-SENSE
    105 864 CGPG2426 17402 SENSE
    106 865 CGPG2433 73707 SENSE
    107 866 CGPG2437 17129 ANTI-SENSE
    108 867 CGPG2452 72665 SENSE
    109 868 CGPG2464 18206 SENSE
    110 869 CGPG2472 17151 ANTI-SENSE
    111 870 CGPG2480 17813 SENSE
    112 871 CGPG253 70845 SENSE
    113 872 CGPG2538 16607 SENSE
    114 873 CGPG2567 72675 SENSE
    115 874 CGPG2571 72677 SENSE
    116 875 CGPG258 74534 SENSE
    117 876 CGPG268 74535 SENSE
    118 877 CGPG274 10204 ANTI-SENSE
    119 878 CGPG275 10472 SENSE
    120 879 CGPG277 10431 ANTI-SENSE
    121 880 CGPG2785 72906 SENSE
    122 881 CGPG2832 78362 SENSE
    123 882 CGPG2855 17930 SENSE
    124 883 CGPG2865 18442 SENSE
    125 884 CGPG2874 73207 SENSE
    126 885 CGPG2914 19166 SENSE
    127 886 CGPG295 10469 SENSE
    128 887 CGPG3004 18415 SENSE
    129 888 CGPG3009 18418 SENSE
    130 889 CGPG3030 19532 SENSE
    131 890 CGPG3048 18423 SENSE
    132 891 CGPG3056 77909 SENSE
    133 892 CGPG3084 19656 SENSE
    134 893 CGPG309 10217 ANTI-SENSE
    135 894 CGPG3094 18874 SENSE
    136 895 CGPG3095 18875 SENSE
    137 896 CGPG3137 19256 SENSE
    138 897 CGPG3156 19537 SENSE
    139 898 CGPG3157 74201 SENSE
    140 899 CGPG3205 74233 SENSE
    141 900 CGPG3236 18644 SENSE
    142 901 CGPG3248 18827 SENSE
    143 902 CGPG3255 18220 SENSE
    144 903 CGPG3258 18830 SENSE
    145 904 CGPG3261 19205 SENSE
    146 905 CGPG3269 18226 SENSE
    147 906 CGPG3270 18227 SENSE
    148 907 CGPG3283 18239 SENSE
    149 908 CGPG3302 70415 SENSE
    150 909 CGPG3334 18329 SENSE
    151 910 CGPG3361 72606 SENSE
    152 911 CGPG337 10230 ANTI-SENSE
    153 912 CGPG3400 19608 SENSE
    154 913 CGPG3410 18271 SENSE
    155 914 CGPG3424 18347 SENSE
    156 915 CGPG3428 18403 SENSE
    157 916 CGPG3465 74206 SENSE
    158 917 CGPG347 10234 ANTI-SENSE
    159 918 CGPG351 71115 SENSE
    160 919 CGPG3567 18406 SENSE
    161 920 CGPG3575 19619 SENSE
    162 921 CGPG3579 19623 SENSE
    163 922 CGPG3605 18381 SENSE
    164 923 CGPG3612 18408 SENSE
    165 924 CGPG3616 18720 SENSE
    166 925 CGPG3631 77537 SENSE
    167 926 CGPG365 70833 SENSE
    168 927 CGPG3665 19328 SENSE
    169 928 CGPG3684 19312 SENSE
    170 929 CGPG3690 70538 SENSE
    171 930 CGPG3717 70440 SENSE
    172 931 CGPG372 11319 ANTI-SENSE
    173 932 CGPG3724 70443 SENSE
    174 933 CGPG375 72357 SENSE
    175 934 CGPG3781 70466 SENSE
    176 935 CGPG380 70241 SENSE
    177 936 CGPG3821 70476 SENSE
    178 937 CGPG3824 70477 SENSE
    179 938 CGPG3901 19713 SENSE
    180 939 CGPG391 12601 SENSE
    181 940 CGPG3931 19747 SENSE
    182 941 CGPG394 11117 ANTI-SENSE
    183 942 CGPG3964 70965 SENSE
    184 943 CGPG397 10366 ANTI-SENSE
    184 943 CGPG397 13404 SENSE
    185 944 CGPG3975 70935 SENSE
    186 945 CGPG3983 77717 SENSE
    187 946 CGPG3986 19966 SENSE
    188 947 CGPG3991 70909 SENSE
    189 948 CGPG4050 19906 SENSE
    190 949 CGPG4070 70974 SENSE
    191 950 CGPG4071 19802 SENSE
    192 951 CGPG4099 19746 SENSE
    193 952 CGPG4138 70902 SENSE
    194 953 CGPG4152 19933 SENSE
    195 954 CGPG4153 19927 SENSE
    196 955 CGPG4164 70976 SENSE
    197 956 CGPG4169 71440 SENSE
    198 957 CGPG421 10413 ANTI-SENSE
    199 958 CGPG422 11119 ANTI-SENSE
    200 959 CGPG4223 78659 SENSE
    201 960 CGPG4240 78665 SENSE
    202 961 CGPG4242 78969 SENSE
    203 962 CGPG4248 78970 SENSE
    204 963 CGPG425 71250 SENSE
    205 964 CGPG4265 78972 SENSE
    206 965 CGPG4283 78677 SENSE
    207 966 CGPG4297 70632 SENSE
    208 967 CGPG43 75205 SENSE
    209 968 CGPG430 10359 ANTI-SENSE
    209 968 CGPG430 11408 SENSE
    210 969 CGPG4305 73616 SENSE
    211 970 CGPG4307 78358 SENSE
    212 971 CGPG4315 71839 SENSE
    213 972 CGPG4320 78417 SENSE
    214 973 CGPG4344 71952 SENSE
    215 974 CGPG4346 78717 SENSE
    216 975 CGPG4349 75040 SENSE
    217 976 CGPG4365 71843 SENSE
    218 977 CGPG4383 70666 SENSE
    219 978 CGPG4389 71846 SENSE
    220 979 CGPG4404 71314 SENSE
    221 980 CGPG4405 76410 SENSE
    222 981 CGPG4419 71322 SENSE
    223 982 CGPG4432 73214 SENSE
    224 983 CGPG4437 71963 SENSE
    225 984 CGPG4443 71326 SENSE
    226 985 CGPG445 70834 SENSE
    227 986 CGPG4453 73215 SENSE
    228 987 CGPG4481 71334 SENSE
    229 988 CGPG4490 71335 SENSE
    230 989 CGPG4498 71347 SENSE
    231 990 CGPG4506 71820 SENSE
    232 991 CGPG4553 70764 SENSE
    233 992 CGPG4583 70680 SENSE
    234 993 CGPG4643 72375 SENSE
    235 994 CGPG4650 72469 SENSE
    236 995 CGPG4660 73951 SENSE
    237 996 CGPG468 11003 ANTI-SENSE
    238 997 CGPG4684 71613 SENSE
    239 998 CGPG4689 78203 SENSE
    240 999 CGPG4691 71638 SENSE
    241 1000 CGPG4702 71631 SENSE
    242 1001 CGPG4703 72368 SENSE
    243 1002 CGPG4710 78202 SENSE
    244 1003 CGPG4713 78207 SENSE
    245 1004 CGPG4730 75209 SENSE
    246 1005 CGPG4747 72457 SENSE
    247 1006 CGPG4755 73639 SENSE
    248 1007 CGPG4772 72526 SENSE
    249 1008 CGPG4779 72531 SENSE
    250 1009 CGPG4848 73336 SENSE
    251 1010 CGPG4879 73722 SENSE
    252 1011 CGPG4882 72650 SENSE
    253 1012 CGPG4892 73686 SENSE
    254 1013 CGPG4903 78353 SENSE
    255 1014 CGPG4925 73726 SENSE
    256 1015 CGPG4937 74715 SENSE
    257 1016 CGPG4949 73230 SENSE
    258 1017 CGPG4971 72663 SENSE
    259 1018 CGPG499 70822 SENSE
    260 1019 CGPG5004 72827 SENSE
    261 1020 CGPG5028 78339 SENSE
    262 1021 CGPG5032 73309 SENSE
    263 1022 CGPG5038 78725 SENSE
    264 1023 CGPG5045 74222 SENSE
    265 1024 CGPG5048 78341 SENSE
    266 1025 CGPG5051 78342 SENSE
    267 1026 CGPG5061 78349 SENSE
    268 1027 CGPG5062 73683 SENSE
    269 1028 CGPG5069 73280 SENSE
    270 1029 CGPG5070 73281 SENSE
    271 1030 CGPG5097 73313 SENSE
    272 1031 CGPG510 12772 ANTI-SENSE
    273 1032 CGPG5100 73314 SENSE
    274 1033 CGPG5117 73861 SENSE
    275 1034 CGPG5151 73676 SENSE
    276 1035 CGPG5155 74212 SENSE
    277 1036 CGPG5159 74218 SENSE
    278 1037 CGPG516 71218 SENSE
    279 1038 CGPG5161 73731 SENSE
    280 1039 CGPG5186 73251 SENSE
    281 1040 CGPG519 12773 ANTI-SENSE
    282 1041 CGPG5190 73254 SENSE
    283 1042 CGPG5191 73255 SENSE
    284 1043 CGPG5196 73257 SENSE
    285 1044 CGPG521 11049 SENSE
    286 1045 CGPG5211 74231 SENSE
    287 1046 CGPG5212 73266 SENSE
    288 1047 CGPG5213 75823 SENSE
    289 1048 CGPG522 11353 SENSE
    290 1049 CGPG5223 72025 SENSE
    291 1050 CGPG5224 72037 SENSE
    292 1051 CGPG5225 72049 SENSE
    293 1052 CGPG5254 78213 SENSE
    294 1053 CGPG5257 72007 SENSE
    295 1054 CGPG5262 72067 SENSE
    296 1055 CGPG5265 72008 SENSE
    297 1056 CGPG5282 72022 SENSE
    298 1057 CGPG5304 72096 SENSE
    299 1058 CGPG532 10811 ANTI-SENSE
    300 1059 CGPG5336 72138 SENSE
    301 1060 CGPG5350 74261 SENSE
    302 1061 CGPG5355 74264 SENSE
    303 1062 CGPG5376 74271 SENSE
    304 1063 CGPG5377 74272 SENSE
    305 1064 CGPG5382 78442 SENSE
    306 1065 CGPG5385 76709 SENSE
    307 1066 CGPG539 75002 SENSE
    308 1067 CGPG5437 78361 SENSE
    309 1068 CGPG5450 74238 SENSE
    310 1069 CGPG5473 78434 SENSE
    311 1070 CGPG55 73932 SENSE
    312 1071 CGPG5505 72713 SENSE
    313 1072 CGPG5510 72773 SENSE
    314 1073 CGPG5514 72678 SENSE
    315 1074 CGPG5541 72765 SENSE
    316 1075 CGPG5546 72730 SENSE
    317 1076 CGPG5552 72707 SENSE
    318 1077 CGPG5556 72755 SENSE
    319 1078 CGPG557 10610 ANTI-SENSE
    320 1079 CGPG5576 73953 SENSE
    321 1080 CGPG5596 73173 SENSE
    322 1081 CGPG5605 73979 SENSE
    323 1082 CGPG5606 73966 SENSE
    324 1083 CGPG561 12776 ANTI-SENSE
    325 1084 CGPG5618 72960 SENSE
    326 1085 CGPG5642 73021 SENSE
    327 1086 CGPG5644 73163 SENSE
    328 1087 CGPG5647 73187 SENSE
    329 1088 CGPG5655 73188 SENSE
    330 1089 CGPG5660 73153 SENSE
    331 1090 CGPG5662 73983 SENSE
    332 1091 CGPG568 11516 ANTI-SENSE
    333 1092 CGPG5686 73179 SENSE
    334 1093 CGPG5702 73009 SENSE
    335 1094 CGPG5712 73109 SENSE
    336 1095 CGPG5713 73121 SENSE
    337 1096 CGPG5715 73157 SENSE
    338 1097 CGPG5723 73158 SENSE
    339 1098 CGPG5729 73088 SENSE
    340 1099 CGPG5730 73135 SENSE
    341 1100 CGPG5732 73005 SENSE
    342 1101 CGPG5741 73171 SENSE
    343 1102 CGPG5752 73042 SENSE
    344 1103 CGPG5771 73067 SENSE
    345 1104 CGPG5778 73148 SENSE
    346 1105 CGPG5782 72933 SENSE
    347 1106 CGPG5785 77723 SENSE
    348 1107 CGPG5797 73048 SENSE
    349 1108 CGPG580 10616 ANTI-SENSE
    350 1109 CGPG5805 72923 SENSE
    351 1110 CGPG5810 78501 SENSE
    352 1111 CGPG5822 78371 SENSE
    353 1112 CGPG5837 74332 SENSE
    354 1113 CGPG5855 74738 SENSE
    355 1114 CGPG5868 75225 SENSE
    356 1115 CGPG587 11149 SENSE
    357 1116 CGPG5889 74739 SENSE
    358 1117 CGPG5893 74748 SENSE
    359 1118 CGPG5909 78113 SENSE
    360 1119 CGPG5914 75233 SENSE
    361 1120 CGPG5921 77311 SENSE
    362 1121 CGPG5925 77008 SENSE
    363 1122 CGPG5926 77321 SENSE
    364 1123 CGPG5930 76214 SENSE
    365 1124 CGPG5945 75238 SENSE
    366 1125 CGPG5958 76118 SENSE
    367 1126 CGPG5977 75243 SENSE
    368 1127 CGPG598 72602 SENSE
    369 1128 CGPG5986 75810 SENSE
    370 1129 CGPG5994 75094 SENSE
    371 1130 CGPG5996 75818 SENSE
    372 1131 CGPG6021 75248 SENSE
    373 1132 CGPG6027 74605 SENSE
    374 1133 CGPG6035 75252 SENSE
    375 1134 CGPG604 10620 ANTI-SENSE
    376 1135 CGPG6049 74611 SENSE
    377 1136 CGPG606 11152 SENSE
    378 1137 CGPG6069 76610 SENSE
    379 1138 CGPG608 70243 SENSE
    380 1139 CGPG6080 74371 SENSE
    381 1140 CGPG6082 74373 SENSE
    382 1141 CGPG6089 74615 SENSE
    383 1142 CGPG6120 74620 SENSE
    384 1143 CGPG6128 74626 SENSE
    385 1144 CGPG614 10622 ANTI-SENSE
    386 1145 CGPG6149 74636 SENSE
    387 1146 CGPG6172 74656 SENSE
    388 1147 CGPG6174 74658 SENSE
    389 1148 CGPG6176 74659 SENSE
    390 1149 CGPG6197 74673 SENSE
    391 1150 CGPG620 13518 ANTI-SENSE
    391 1150 CGPG620 70824 SENSE
    392 1151 CGPG6201 75267 SENSE
    393 1152 CGPG6204 75283 SENSE
    394 1153 CGPG621 13805 SENSE
    395 1154 CGPG6210 76221 SENSE
    396 1155 CGPG6211 76226 SENSE
    397 1156 CGPG6214 76222 SENSE
    398 1157 CGPG6215 76611 SENSE
    399 1158 CGPG6222 76228 SENSE
    400 1159 CGPG6229 76435 SENSE
    401 1160 CGPG6233 76436 SENSE
    402 1161 CGPG6237 78743 SENSE
    403 1162 CGPG6243 75814 SENSE
    404 1163 CGPG6248 77016 SENSE
    405 1164 CGPG6252 78734 SENSE
    406 1165 CGPG6267 75274 SENSE
    407 1166 CGPG6272 76233 SENSE
    408 1167 CGPG6294 74674 SENSE
    409 1168 CGPG63 70225 SENSE
    410 1169 CGPG6311 75291 SENSE
    411 1170 CGPG6317 75292 SENSE
    412 1171 CGPG6328 78607 SENSE
    413 1172 CGPG6334 78367 SENSE
    414 1173 CGPG6336 76528 SENSE
    415 1174 CGPG6349 77319 SENSE
    416 1175 CGPG6352 74677 SENSE
    417 1176 CGPG6353 78109 SENSE
    418 1177 CGPG6364 77725 SENSE
    419 1178 CGPG6366 73437 SENSE
    420 1179 CGPG6375 73450 SENSE
    421 1180 CGPG6388 73416 SENSE
    422 1181 CGPG6391 73452 SENSE
    423 1182 CGPG6399 73453 SENSE
    424 1183 CGPG6407 73454 SENSE
    425 1184 CGPG6418 73491 SENSE
    426 1185 CGPG6430 73445 SENSE
    427 1186 CGPG6432 73469 SENSE
    428 1187 CGPG6437 73434 SENSE
    429 1188 CGPG6445 73471 SENSE
    430 1189 CGPG6450 73436 SENSE
    431 1190 CGPG6458 73525 SENSE
    432 1191 CGPG6465 73514 SENSE
    433 1192 CGPG6476 73551 SENSE
    434 1193 CGPG6505 73519 SENSE
    435 1194 CGPG6507 73543 SENSE
    436 1195 CGPG6509 73567 SENSE
    437 1196 CGPG6510 73579 SENSE
    438 1197 CGPG6515 73556 SENSE
    439 1198 CGPG6520 73545 SENSE
    440 1199 CGPG6531 73511 SENSE
    441 1200 CGPG6553 74138 SENSE
    442 1201 CGPG6557 74186 SENSE
    443 1202 CGPG6563 74163 SENSE
    444 1203 CGPG6564 74175 SENSE
    445 1204 CGPG6572 74176 SENSE
    446 1205 CGPG6577 74141 SENSE
    447 1206 CGPG6588 74178 SENSE
    448 1207 CGPG6596 74179 SENSE
    449 1208 CGPG6614 74110 SENSE
    450 1209 CGPG6619 74170 SENSE
    451 1210 CGPG6623 74123 SENSE
    452 1211 CGPG6626 74159 SENSE
    453 1212 CGPG663 10633 ANTI-SENSE
    454 1213 CGPG6635 74172 SENSE
    455 1214 CGPG6636 74184 SENSE
    456 1215 CGPG6641 74582 SENSE
    457 1216 CGPG6642 74584 SENSE
    458 1217 CGPG6645 74687 SENSE
    459 1218 CGPG6660 74461 SENSE
    460 1219 CGPG6671 74403 SENSE
    461 1220 CGPG6697 74430 SENSE
    462 1221 CGPG6706 74443 SENSE
    463 1222 CGPG6723 74457 SENSE
    464 1223 CGPG6729 74434 SENSE
    465 1224 CGPG6738 74447 SENSE
    466 1225 CGPG6742 74495 SENSE
    467 1226 CGPG6752 74513 SENSE
    468 1227 CGPG6760 74514 SENSE
    469 1228 CGPG6768 74515 SENSE
    470 1229 CGPG6779 74552 SENSE
    471 1230 CGPG6785 74529 SENSE
    472 1231 CGPG6800 74519 SENSE
    473 1232 CGPG686 10638 ANTI-SENSE
    474 1233 CGPG6898 76547 SENSE
    475 1234 CGPG6900 76548 SENSE
    476 1235 CGPG691 14703 SENSE
    477 1236 CGPG6920 75856 SENSE
    478 1237 CGPG6921 76642 SENSE
    479 1238 CGPG6930 77522 SENSE
    480 1239 CGPG6934 77516 SENSE
    481 1240 CGPG6945 75864 SENSE
    482 1241 CGPG6946 76275 SENSE
    483 1242 CGPG6948 76276 SENSE
    484 1243 CGPG6974 75869 SENSE
    485 1244 CGPG6976 76558 SENSE
    486 1245 CGPG6996 75876 SENSE
    487 1246 CGPG7002 75878 SENSE
    488 1247 CGPG7013 75881 SENSE
    489 1248 CGPG7021 77525 SENSE
    490 1249 CGPG7056 76454 SENSE
    491 1250 CGPG7071 75895 SENSE
    492 1251 CGPG7075 78377 SENSE
    493 1252 CGPG7080 75896 SENSE
    494 1253 CGPG7094 77527 SENSE
    495 1254 CGPG7095 78984 SENSE
    496 1255 CGPG7104 77528 SENSE
    497 1256 CGPG7118 76752 SENSE
    498 1257 CGPG7122 78106 SENSE
    499 1258 CGPG713 11720 ANTI-SENSE
    500 1259 CGPG7130 78740 SENSE
    501 1260 CGPG7145 76157 SENSE
    502 1261 CGPG7166 77530 SENSE
    503 1262 CGPG7179 76755 SENSE
    504 1263 CGPG7184 76166 SENSE
    505 1264 CGPG7185 76756 SENSE
    506 1265 CGPG7192 78990 SENSE
    507 1266 CGPG7199 78460 SENSE
    508 1267 CGPG72 11022 ANTI-SENSE
    509 1268 CGPG7231 77533 SENSE
    510 1269 CGPG7241 76572 SENSE
    511 1270 CGPG7243 76186 SENSE
    512 1271 CGPG7258 76190 SENSE
    513 1272 CGPG7265 77071 SENSE
    514 1273 CGPG7274 76194 SENSE
    515 1274 CGPG7291 78112 SENSE
    516 1275 CGPG7303 74802 SENSE
    517 1276 CGPG7315 74851 SENSE
    518 1277 CGPG7324 74864 SENSE
    519 1278 CGPG7327 74805 SENSE
    520 1279 CGPG7338 74842 SENSE
    521 1280 CGPG7347 78231 SENSE
    522 1281 CGPG7348 74867 SENSE
    523 1282 CGPG7352 74820 SENSE
    524 1283 CGPG7356 74868 SENSE
    525 1284 CGPG7359 74809 SENSE
    526 1285 CGPG7362 74845 SENSE
    527 1286 CGPG7372 74870 SENSE
    528 1287 CGPG7379 74859 SENSE
    529 1288 CGPG7398 74985 SENSE
    530 1289 CGPG7403 74950 SENSE
    531 1290 CGPG7404 74962 SENSE
    532 1291 CGPG7410 74939 SENSE
    533 1292 CGPG7417 74928 SENSE
    534 1293 CGPG7423 74905 SENSE
    535 1294 CGPG7424 74917 SENSE
    536 1295 CGPG7430 74989 SENSE
    537 1296 CGPG7438 74990 SENSE
    538 1297 CGPG7443 74955 SENSE
    539 1298 CGPG7449 74932 SENSE
    540 1299 CGPG7450 74944 SENSE
    541 1300 CGPG7452 74968 SENSE
    542 1301 CGPG7459 74957 SENSE
    543 1302 CGPG7480 75374 SENSE
    544 1303 CGPG7481 75386 SENSE
    545 1304 CGPG7483 77807 SENSE
    546 1305 CGPG7497 75388 SENSE
    547 1306 CGPG7503 75365 SENSE
    548 1307 CGPG7504 75377 SENSE
    549 1308 CGPG7510 75354 SENSE
    550 1309 CGPG7516 75331 SENSE
    551 1310 CGPG7517 75343 SENSE
    552 1311 CGPG7523 77809 SENSE
    553 1312 CGPG7524 75332 SENSE
    554 1313 CGPG7525 75344 SENSE
    555 1314 CGPG7532 75333 SENSE
    556 1315 CGPG7537 75393 SENSE
    557 1316 CGPG7548 75335 SENSE
    558 1317 CGPG7575 75462 SENSE
    559 1318 CGPG7577 75486 SENSE
    560 1319 CGPG7590 75452 SENSE
    561 1320 CGPG7599 75465 SENSE
    562 1321 CGPG7601 75489 SENSE
    563 1322 CGPG7605 75442 SENSE
    564 1323 CGPG7607 75466 SENSE
    565 1324 CGPG7616 75479 SENSE
    566 1325 CGPG7632 75481 SENSE
    567 1326 CGPG7673 78233 SENSE
    568 1327 CGPG7683 75539 SENSE
    569 1328 CGPG773 11919 ANTI-SENSE
    570 1329 CGPG7776 75603 SENSE
    571 1330 CGPG7781 75663 SENSE
    572 1331 CGPG7785 75616 SENSE
    573 1332 CGPG7787 75640 SENSE
    574 1333 CGPG7793 75617 SENSE
    575 1334 CGPG7796 75653 SENSE
    576 1335 CGPG7797 75665 SENSE
    577 1336 CGPG7801 75618 SENSE
    578 1337 CGPG7813 78238 SENSE
    579 1338 CGPG7816 75608 SENSE
    580 1339 CGPG7826 75633 SENSE
    581 1340 CGPG7861 75761 SENSE
    582 1341 CGPG7863 75785 SENSE
    583 1342 CGPG7868 75750 SENSE
    584 1343 CGPG7881 75716 SENSE
    585 1344 CGPG7887 78129 SENSE
    586 1345 CGPG7899 77539 SENSE
    587 1346 CGPG7901 77540 SENSE
    588 1347 CGPG7909 77542 SENSE
    589 1348 CGPG7911 77543 SENSE
    590 1349 CGPG7919 77545 SENSE
    591 1350 CGPG7935 77550 SENSE
    592 1351 CGPG7940 77552 SENSE
    593 1352 CGPG7959 77556 SENSE
    594 1353 CGPG7967 77559 SENSE
    595 1354 CGPG7975 77957 SENSE
    596 1355 CGPG7996 77565 SENSE
    597 1356 CGPG8006 78508 SENSE
    598 1357 CGPG801 11748 ANTI-SENSE
    599 1358 CGPG8023 77920 SENSE
    600 1359 CGPG8025 77573 SENSE
    601 1360 CGPG8038 77961 SENSE
    602 1361 CGPG8053 77922 SENSE
    603 1362 CGPG8054 77337 SENSE
    604 1363 CGPG8059 77924 SENSE
    605 1364 CGPG8070 77926 SENSE
    606 1365 CGPG8073 77964 SENSE
    607 1366 CGPG8076 77346 SENSE
    608 1367 CGPG8084 77350 SENSE
    609 1368 CGPG8093 77929 SENSE
    610 1369 CGPG8095 77586 SENSE
    611 1370 CGPG8096 78510 SENSE
    612 1371 CGPG8097 77930 SENSE
    613 1372 CGPG8112 77590 SENSE
    614 1373 CGPG8120 77592 SENSE
    615 1374 CGPG8129 77361 SENSE
    616 1375 CGPG8140 77934 SENSE
    617 1376 CGPG8157 77367 SENSE
    618 1377 CGPG8158 78121 SENSE
    619 1378 CGPG8165 77370 SENSE
    620 1379 CGPG8169 78117 SENSE
    621 1380 CGPG8203 77950 SENSE
    622 1381 CGPG8205 78905 SENSE
    623 1382 CGPG8212 75913 SENSE
    624 1383 CGPG8213 75925 SENSE
    625 1384 CGPG8225 75974 SENSE
    626 1385 CGPG8227 75903 SENSE
    627 1386 CGPG8235 75904 SENSE
    628 1387 CGPG8236 75916 SENSE
    629 1388 CGPG8244 75917 SENSE
    630 1389 CGPG8254 75942 SENSE
    631 1390 CGPG8255 75954 SENSE
    632 1391 CGPG8262 75943 SENSE
    633 1392 CGPG8264 75967 SENSE
    634 1393 CGPG8269 75932 SENSE
    635 1394 CGPG8271 75956 SENSE
    636 1395 CGPG8305 78135 SENSE
    637 1396 CGPG8320 78612 SENSE
    638 1397 CGPG8326 77969 SENSE
    639 1398 CGPG8344 78136 SENSE
    640 1399 CGPG8347 77627 SENSE
    641 1400 CGPG8359 78142 SENSE
    642 1401 CGPG8370 77973 SENSE
    643 1402 CGPG8371 78141 SENSE
    644 1403 CGPG8375 78963 SENSE
    645 1404 CGPG8378 78153 SENSE
    646 1405 CGPG8383 78156 SENSE
    647 1406 CGPG841 11807 ANTI-SENSE
    648 1407 CGPG8436 78528 SENSE
    649 1408 CGPG8438 78530 SENSE
    650 1409 CGPG8450 78618 SENSE
    651 1410 CGPG8451 78919 SENSE
    652 1411 CGPG8459 77974 SENSE
    653 1412 CGPG8461 77630 SENSE
    654 1413 CGPG8463 78921 SENSE
    655 1414 CGPG8471 78620 SENSE
    656 1415 CGPG8474 77975 SENSE
    657 1416 CGPG8475 78536 SENSE
    658 1417 CGPG8476 78537 SENSE
    659 1418 CGPG8490 78540 SENSE
    660 1419 CGPG8510 77993 SENSE
    661 1420 CGPG8530 78924 SENSE
    662 1421 CGPG8533 78009 SENSE
    663 1422 CGPG8544 78014 SENSE
    664 1423 CGPG8546 78015 SENSE
    665 1424 CGPG8549 78018 SENSE
    666 1425 CGPG8555 78021 SENSE
    667 1426 CGPG8561 78158 SENSE
    668 1427 CGPG8569 78026 SENSE
    669 1428 CGPG8573 78028 SENSE
    670 1429 CGPG8588 78032 SENSE
    671 1430 CGPG8597 78388 SENSE
    672 1431 CGPG8607 78044 SENSE
    673 1432 CGPG8611 78047 SENSE
    674 1433 CGPG8629 78055 SENSE
    675 1434 CGPG8632 78057 SENSE
    676 1435 CGPG8634 78059 SENSE
    677 1436 CGPG8635 78553 SENSE
    678 1437 CGPG8636 78163 SENSE
    679 1438 CGPG8640 78060 SENSE
    680 1439 CGPG8642 78062 SENSE
    681 1440 CGPG8646 78065 SENSE
    682 1441 CGPG8666 78590 SENSE
    683 1442 CGPG8677 78177 SENSE
    684 1443 CGPG8688 78952 SENSE
    685 1444 CGPG8689 78559 SENSE
    686 1445 CGPG8704 78169 SENSE
    687 1446 CGPG8716 78178 SENSE
    688 1447 CGPG8754 78932 SENSE
    689 1448 CGPG8769 78185 SENSE
    690 1449 CGPG8774 78186 SENSE
    691 1450 CGPG8778 78572 SENSE
    692 1451 CGPG8784 78631 SENSE
    693 1452 CGPG879 12425 ANTI-SENSE
    694 1453 CGPG8797 78938 SENSE
    695 1454 CGPG8810 78961 SENSE
    696 1455 CGPG8827 78584 SENSE
    697 1456 CGPG8853 78589 SENSE
    698 1457 CGPG8873 78252 SENSE
    699 1458 CGPG8877 76314 SENSE
    700 1459 CGPG8878 76326 SENSE
    701 1460 CGPG8881 76362 SENSE
    702 1461 CGPG8895 76340 SENSE
    703 1462 CGPG8906 76377 SENSE
    704 1463 CGPG8917 76319 SENSE
    705 1464 CGPG8919 76343 SENSE
    706 1465 CGPG8925 76320 SENSE
    707 1466 CGPG8930 76380 SENSE
    708 1467 CGPG8937 77831 SENSE
    709 1468 CGPG8942 76334 SENSE
    710 1469 CGPG8946 76382 SENSE
    711 1470 CGPG8990 76838 SENSE
    712 1471 CGPG9001 77841 SENSE
    713 1472 CGPG9008 77838 SENSE
    714 1473 CGPG9016 76865 SENSE
    715 1474 CGPG9036 77834 SENSE
    716 1475 CGPG9060 76823 SENSE
    717 1476 CGPG9069 76836 SENSE
    718 1477 CGPG908 14133 ANTI-SENSE
    719 1478 CGPG9093 76927 SENSE
    720 1479 CGPG9096 76963 SENSE
    721 1480 CGPG9097 76975 SENSE
    722 1481 CGPG9106 76988 SENSE
    723 1482 CGPG9111 76953 SENSE
    724 1483 CGPG9112 76965 SENSE
    725 1484 CGPG9123 77161 SENSE
    726 1485 CGPG9124 77852 SENSE
    727 1486 CGPG9138 77151 SENSE
    728 1487 CGPG9143 77116 SENSE
    729 1488 CGPG9150 77105 SENSE
    730 1489 CGPG9152 77129 SENSE
    731 1490 CGPG9162 77154 SENSE
    732 1491 CGPG9165 77190 SENSE
    733 1492 CGPG9166 77107 SENSE
    734 1493 CGPG9171 77167 SENSE
    735 1494 CGPG9177 77144 SENSE
    736 1495 CGPG9178 77156 SENSE
    737 1496 CGPG9179 77168 SENSE
    738 1497 CGPG9181 77192 SENSE
    739 1498 CGPG9188 77181 SENSE
    740 1499 CGPG9189 77193 SENSE
    741 1500 CGPG9201 77147 SENSE
    742 1501 CGPG9222 77853 SENSE
    743 1502 CGPG9234 77854 SENSE
    744 1503 CGPG9237 77287 SENSE
    745 1504 CGPG9244 77276 SENSE
    746 1505 CGPG9248 77229 SENSE
    747 1506 CGPG9249 77241 SENSE
    748 1507 CGPG9251 77265 SENSE
    749 1508 CGPG9280 77233 SENSE
    750 1509 CGPG9285 77293 SENSE
    751 1510 CGPG9302 77473 SENSE
    752 1511 CGPG931 76402 SENSE
    753 1512 CGPG9313 77428 SENSE
    754 1513 CGPG9315 77429 SENSE
    755 1514 CGPG9327 78277 SENSE
    756 1515 CGPG933 11935 ANTI-SENSE
    757 1516 CGPG9334 78259 SENSE
    758 1517 CGPG967 12276 ANTI-SENSE
    759 1518 CGPG988 12365 SENSE
    / / / / /
    • Recombinant DNA
  • DNA for use in the present invention to improve traits in plants have a nucleotide sequence of SEQ ID NO:1 through SEQ ID NO:759, as well as the homologs of such DNA molecules. A subset of the DNA for gene suppression aspects of the invention includes fragments of the disclosed full polynucleotides consisting of oligonucleotides of 21 or more consecutive nucleotides. Oligonucleotides the larger molecules having a sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 759 are useful as probes and primers for detection of the polynucleotides used in the invention. Also useful in this invention are variants of the DNA. Such variants may be naturally occurring, including DNA from homologous genes from the same or a different species, or may be non-natural variants, for example DNA synthesized using chemical synthesis methods, or generated using recombinant DNA techniques. Degeneracy of the genetic code provides the possibility to substitute at least one base of the protein encoding sequence of a gene with a different base without causing the amino acid sequence of the polypeptide produced from the gene to be changed. Hence, a DNA useful in the present invention may have any base sequence that has been changed from the sequences provided herein by substitution in accordance with degeneracy of the genetic code.
  • Homologs of the genes providing DNA demonstrated as useful in improving traits in model plants disclosed herein will generally have significant identity with the DNA disclosed herein. DNA is substantially identical to a reference DNA it when the sequences of the polynucleotides are optimally aligned there is about 60% nucleotide equivalence; more preferably 70%; more preferably 80% equivalence; more preferably 85% equivalence; more preferably 90%; more preferably 95%; and/or more preferably 98% or 99% equivalence over a comparison window. A comparison window is preferably at least 50-100 nucleotides, and more preferably is the entire length of the polynucleotide provided herein. Optimal alignment of sequences for aligning a comparison window may be conducted by algorithms; preferably by computerized implementations of these algorithms (for example, the Wisconsin Genetics Software Package Release 7.0-10.0, Genetics Computer Group, 575 Science Dr., Madison, Wis.). The reference polynucleotide may be a full-length molecule or a portion of a longer molecule. Preferentially, the window of comparison for determining polynucleotide identity of protein encoding sequences is the entire coding region.
  • Proteins useful for imparting enhanced traits are entire proteins or at least a sufficient portion of the entire protein to impart the relevant biological activity of the protein. Proteins useful for generation of transgenic plants having enhanced traits include the proteins with an amino acid sequence provided herein as SEQ ID NO: 760 through SEQ ID NO: 1518, as well as homologs of such proteins.
  • Homologs of the proteins useful in the invention are identified by comparison of the amino acid sequence of the protein to amino acid sequences of proteins from the same or different plant sources, e.g. manually or by using known homology-based search algorithms such as those commonly known and referred to as BLAST, FASTA, and Smith-Waterman. As used herein, a homolog is a protein from the same or a different organism that performs the same biological function as the polypeptide to which it is compared. An orthologous relation between two organisms is not necessarily manifest as a one-to-one correspondence between two genes, because a gene can be duplicated or deleted after organism phylogenetic separation, such as speciation. For a given protein, there may be no ortholog or more than one ortholog. Other complicating factors include alternatively spliced transcripts from the same gene, limited gene identification, redundant copies of the same gene with different sequence lengths or corrected sequence. A local sequence alignment program, e.g., BLAST, can be used to search a database of sequences to find similar sequences, and the summary Expectation value (E-value) used to measure the sequence base similarity. As a protein hit with the best E-value for a particular organism may not necessarily be an ortholog or the only ortholog, a reciprocal BLAST search is used in the present invention to filter hit sequences with significant E-values for ortholog identification. The reciprocal BLAST entails search of the significant hits against a database of amino acid sequences from the base organism that are similar to the sequence of the query protein. A hit is a likely ortholog, when the reciprocal BLAST's best hit is the query protein itself or a protein encoded by a duplicated gene after speciation. Thus, homolog is used herein to describe proteins that are assumed to have functional similarity by inference from sequence base similarity. The relationship of homologs with amino acid sequences of SEQ ID NO: 1519 to SEQ ID NO: 67778 to the proteins with amino acid sequences of SEQ ID NO: to 760 to SEQ ID NO: 1518 are found in the listing of Table 16.
  • Other functional homolog proteins differ in one or more amino acids from those of a trait-improving protein disclosed herein as the result of one or more of the well-known conservative amino acid substitutions, e.g., valine is a conservative substitute for alanine and threonine is a conservative substitute for serine. Conservative substitutions for an amino acid within the native sequence can be selected from other members of a class to which the naturally occurring amino acid belongs. Representative amino acids within these various classes include, but are not limited to: (1) acidic (negatively charged) amino acids such as aspartic acid and glutamic acid; (2) basic (positively charged) amino acids such as arginine, histidine, and lysine; (3) neutral polar amino acids such as glycine, serine, threonine, cysteine, tyrosine, asparagine, and glutamine; and (4) neutral nonpolar (hydrophobic) amino acids such as alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan, and methionine. Conserved substitutes for an amino acid within a native amino acid sequence can be selected from other members of the group to which the naturally occurring amino acid belongs. For example, a group of amino acids having aliphatic side chains is glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having aliphatic-hydroxyl side chains is serine and threonine; a group of amino acids having amide-containing side chains is asparagine and glutamine; a group of amino acids having aromatic side chains is phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic side chains is lysine, arginine, and histidine; and a group of amino acids having sulfur-containing side chains is cysteine and methionine. Naturally conservative amino acids substitution groups are: valine-leucine, valine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, aspartic acid-glutamic acid, and asparagine-glutamine. A further aspect of the invention comprises proteins that differ in one or more amino acids from those of a described protein sequence as the result of deletion or insertion of one or more amino acids in a native sequence.
  • Homologs of the trait-improving proteins provided herein will generally demonstrate significant sequence identity. Of particular interest are proteins having at least 50% sequence identity, more preferably at least about 70% sequence identity or higher, e.g., at least about 80% sequence identity with an amino acid sequence of SEQ ID NO:760 through SEQ ID NO: 1518. Of course useful proteins also include those with higher identity, e.g., 90% to 99% identity. Identity of protein homologs is determined by optimally aligning the amino acid sequence of a putative protein homolog with a defined amino acid sequence and by calculating the percentage of identical and conservatively substituted amino acids over the window of comparison. The window of comparison for determining identity can be the entire amino acid sequence disclosed herein, e.g., the full sequence of any of SEQ ID NO: 760 through SEQ ID NO: 1518.
  • Genes that are homologous to each other can be grouped into families and included in multiple sequence alignments. Then a consensus sequence for each group can be derived. This analysis enables the derivation of conserved and class-(family) specific residues or motifs that are functionally important. These conserved residues and motifs can be further validated with 3D protein structure if available. The consensus sequence can be used to define the full scope of the invention, e.g., to identify proteins with a homolog relationship. Thus, the present invention contemplates that protein homologs include proteins with an amino acid sequence that has at least 90% identity to such a consensus amino acid sequence sequences.
    • Gene Stacking
  • The present invention also contemplates that the trait-improving recombinant DNA provided herein can be used in combination with other recombinant DNA to create plants with multiple desired traits or a further enhanced trait. The combinations generated can include multiple copies of any one or more of the recombinant DNA constructs. These stacked combinations can be created by any method, including but not limited to cross breeding of transgenic plants, or multiple genetic transformation.
    • Transformation Methods
  • Numerous methods for transforming chromosomes in a plant cell nucleus with recombinant DNA are known in the art and are used in methods of preparing a transgenic plant cell nucleus cell, and plant. Two effective methods for such transformation are Agrobacterium-mediated transformation and microprojectile bombardment. Microprojectile bombardment methods are illustrated in U.S. Pat. Nos. 5,015,580 (soybean); 5,550,318 (corn); 5,538,880 (corn); 5,914,451 (soybean); 6,160,208 (corn); 6,399,861 (corn); 6,153,812 (wheat) and 6,365,807 (rice) and Agrobacterium-mediated transformation is described in U.S. Pat. Nos. 5,159,135 (cotton); 5,824,877 (soybean); 5,463,174 (canola); 5,591,616 (corn); 6,384,301 (soybean), 7,026,528 (wheat) and 6,329,571 (rice), all of which are incorporated herein by reference. Transformation of plant material is practiced in tissue culture on a nutrient media, i.e. a mixture of nutrients that will allow cells to grow in vitro. Recipient cell targets include, but are not limited to, meristem cells, hypocotyls, calli, immature embryos and gametic cells such as microspores, pollen, sperm and egg cells. Callus may be initiated from tissue sources including, but not limited to, immature embryos, hypocotyls, seedling apical meristems, microspores and the like. Cells containing a transgenic nucleus are grown into transgenic plants.
  • In addition to direct transformation of a plant material with a recombinant DNA, a transgenic plant cell nucleus can be prepared by crossing a first plant having cells with a transgenic nucleus with recombinant DNA with a second plant lacking the trangenci nucleus. For example, recombinant DNA can be introduced into a nucleus from a first plant line that is amenable to transformation to transgenic nucleus in cells that are grown into a transgenic plant which can be crossed with a second plant line to introgress the recombinant DNA into the second plant line. A transgenic plant with recombinant DNA providing an enhanced trait, e.g. enhanced yield, can be crossed with transgenic plant line having other recombinant DNA that confers another trait, for example herbicide resistance or pest resistance, to produce progeny plants having recombinant DNA that confers both traits. Typically, in such breeding for combining traits the transgenic plant donating the additional trait is a male line and the transgenic plant carrying the base traits is the female line. The progeny of this cross will segregate such that some of the plants will carry the DNA for both parental traits and some will carry DNA for one parental trait; such plants can be identified by markers associated with parental recombinant DNA, e.g. marker identification by analysis for recombinant DNA or, in the case where a selectable marker is linked to the recombinant, by application of the selecting agent such as a herbicide for use with a herbicide tolerance marker, or by selection for the enhanced trait. Progeny plants carrying DNA for both parental traits can be crossed back into the female parent line multiple times, for example usually 6 to 8 generations, to produce a progeny plant with substantially the same genotype as one original transgenic parental line but for the recombinant DNA of the other transgenic parental line
  • In the practice of transformation DNA is typically introduced into only a small percentage of target plant cells in any one transformation experiment. Marker genes are used to provide an efficient system for identification of those cells that are stably transformed by, receiving and integrating a recombinant DNA molecule into their genomes. Preferred marker genes provide selective markers which confer resistance to a selective agent, such as an antibiotic or a herbicide. Any of the herbicides to which plants of this invention may be resistant are useful agents for selective markers. Potentially transformed cells are exposed to the selective agent. In the population of surviving cells will be those cells where, generally, the resistance-conferring gene is integrated and expressed at sufficient levels to permit cell survival. Cells may be tested further to confirm stable integration of the exogenous DNA. Commonly used selective marker genes include those conferring resistance to antibiotics such as kanamycin and paromomycin (nptlI), hygromycin B (aph IV), spectinomycin (aadA) and gentamycin (aac3 and aacC4) or resistance to herbicides such as glufosinate (bar or pat), dicamba (DMO) and glyphosate (aroA or EPSPS). Examples of such selectable markers are illustrated in U.S. Pat. Nos. 5,550,318; 5,633,435; 5,780,708 and 6,118,047, all of which are incorporated herein by reference. Selectable markers which provide an ability to visually identify transformants can also be employed, for example, a gene expressing a colored or fluorescent protein such as a luciferase or green fluorescent protein (GFP) or a gene expressing a beta-glucuronidase or uidA gene (GUS) for which various chromogenic substrates are known.
  • Plant cells that survive exposure to the selective agent, or plant cells that have been scored positive in a screening assay, may be cultured in regeneration media and allowed to mature into plants. Developing plantlets regenerated from transformed plant cells can be transferred to plant growth mix, and hardened off, for example, in an environmentally controlled chamber at about 85% relative humidity, 600 ppm CO2, and 25-250 microeinsteins m−2 s−1 of light, prior to transfer to a greenhouse or growth chamber for maturation. Plants are regenerated from about 6 weeks to 10 months after a transformant is identified, depending on the initial tissue, and plant species. Plants may be pollinated using conventional plant breeding methods known to those of skill in the art and seed produced, for example self-pollination is commonly used with transgenic corn. The regenerated transformed plant or its progeny seed or plants can be tested for expression of the recombinant DNA and selected for the presence of enhanced agronomic trait.
    • Transgenic Plants and Seeds
  • Transgenic plants derived from transgenic plant cells having a transgenic nucleus of this invention are grown to generate transgenic plants having an enhanced trait as compared to a control plant and produce transgenic seed and haploid pollen of this invention. Such plants with enhanced traits are identified by selection of transformed plants or progeny seed for the enhanced trait. For efficiency a selection method is designed to evaluate multiple transgenic plants (events) comprising the recombinant DNA, for example multiple plants from 2 to 20 or more transgenic events. Transgenic plants grown from transgenic seed provided herein demonstrate improved agronomic traits that contribute to increased yield or other trait that provides increased plant value, including, for example, improved seed quality. Of particular interest are plants having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
    • Discovery of Trait-Improving Recombinant DNA
  • To identify nuclei with recombinant DNA that confer enhanced traits to plants, Arabidopsis thaliana was transformed with a candidate recombinant DNA construct and screened for an enhanced trait.
  • Arabidopsis thaliana is used a model for genetics and metabolism in plants. Arabidopsis has a small genome, and well-documented studies are available. It is easy to grow in large numbers and mutants defining important genetically controlled mechanisms are either available, or can readily be obtained. Various methods to introduce and express isolated homologous genes are available (see Koncz, e.g., Methods in Arabidopsis Research e.g., (1992), World Scientific, New Jersey, New Jersey, in “Preface”).
  • A two-step screening process was employed which comprised two passes of trait characterization to ensure that the trait modification was dependent on expression of the recombinant DNA, but not due to the chromosomal location of the integration of the transgene. Twelve independent transgenic lines for each recombinant DNA construct were established and assayed for the transgene expression levels. Five transgenic lines with high transgene expression levels were used in the first pass screen to evaluate the transgene's function in T2 transgenic plants. Subsequently, three transgenic events, which had been shown to have one or more enhanced traits, were further evaluated in the second pass screen to confirm the transgene's ability to impart an enhanced trait. The following Table 3 summarizes the enhanced traits that have been confirmed as provided by a recombinant DNA construct.
  • In particular, Table 3 reports:
  • “PEP SEQ ID” which is the amino acid sequence of the protein cognate to the DNA in the recombinant DNA construct corresponding to a protein sequence of a SEQ ID NO. in the Sequence Listing.
  • “construct_id” is an arbitrary name for the recombinant DNA describe more particularly in Table 1.
  • “annotation” refers to a description of the top hit protein obtained from an amino acid sequence query of each PEP SEQ ID NO to GenBank database of the National Center for Biotechnology Information (ncbi). More particularly, “gi” is the GenBank ID number for the top BLAST hit.
  • “description” refers to the description of the top BLAST hit.
  • “e-value” provides the expectation value for the BLAST hit.
  • “% id” refers to the percentage of identically matched amino acid residues along the length of the portion of the sequences which is aligned by BLAST between the sequence of interest provided herein and the hit sequence in GenBank.
  • “traits” identify by two letter codes the confirmed enhancement in a transgenic plant provided by the recombinant DNA. The codes for enhanced traits are:
  • “CK” which indicates cold tolerance enhancement identified under a cold shock tolerance screen;
  • “CS” which indicates cold tolerance enhancement identified by a cold germination tolerance screen;
  • “DS” which indicates drought tolerance enhancement identified by a soil drought stress tolerance screen;
  • “PEG” which indicates osmotic stress tolerance enhancement identified by a PEG induced osmotic stress tolerance screen;
  • “HS” which indicates heat stress tolerance enhancement identified by a heat stress tolerance screen;
  • “SS” which indicates high salinity stress tolerance enhancement identified bra salt stress tolerance screen;
  • “LN” which indicates nitrogen use efficiency enhancement identified by a limited nitrogen tolerance screen;
  • “LL” which indicates attenuated shade avoidance response identified by a shade tolerance screen under a low light condition;
  • “PP” which indicates enhanced growth and development at early stages identified by an early plant growth and development screen;
  • “SP” which indicates enhanced growth and development at late stages identified by a late plant growth and development screen provided herein.
  • TABLE 3
    PEP Seq Construct Annotation
    ID No. ID E-value % id Description Trait
    760 12792 1.00E−107 73 ref|NP_198588.2|nucleic acid binding [Arabidopsis thaliana] DS
    761 13673 0 94 ref|NP_850412.1|peptidase [Arabidopsis thaliana] SS
    762 12020 6.00E−50 100 gb|AAF70854.1|AC003113_21F24O1.1 [Arabidopsis thaliana] SP
    763 10174 1.00E−111 90 ref|NP_567720.1|DREB1A (DEHYDRATION RESPONSE HS PEG
    ELEMENT B1A); DNA binding/transcription factor/
    transcriptional activator [Arabidopsis thaliana]
    764 11827 2.00E−83 89 ref|NP_565558.1|unknown protein [Arabidopsis thaliana] LN
    765 12435 3.00E−53 100 ref|NP_565280.1|NADH dehydrogenase (ubiquinone)/NADH LN
    dehydrogenase [Arabidopsis thaliana]
    766 12015 0 94 ref|NP_197429.1|KAPP; protein phosphatase type 2C LN
    [Arabidopsis thaliana]
    767 11836 1.00E−146 97 ref|NP_566060.1|unknown protein [Arabidopsis thaliana] LN
    768 12141 1.00E−134 94 ref|NP_192755.1|unknown protein [Arabidopsis thaliana] LN
    769 12040 5.00E−97 91 ref|NP_567673.1|unknown protein [Arabidopsis thaliana] DS
    770 12437 7.00E−35 85 ref|NP_190335.1|unknown protein [Arabidopsis thaliana] LN
    771 12156 6.00E−55 100 ref|NP_179093.1|RNA binding/nucleic acid binding [Arabidopsis DS
    thaliana]
    772 11853 1.00E−81 94 ref|NP_565677.1|unknown protein [Arabidopsis thaliana] SS
    gb|AAC79591.1|
    773 12224 1.00E−145 82 ref|NP_565860.1|unknown protein [Arabidopsis thaliana] LL
    gb|AAC98059.1|
    774 11856 1.00E−103 100 ref|NP_565273.1|hydrolase [Arabidopsis thaliana] LN
    775 12065 9.00E−20 78 ref|NP_179185.1|unknown protein [Arabidopsis thaliana] LN
    776 12419 1.00E−148 100 ref|NP_186847.1|oxidoreductase [Arabidopsis thaliana] LN
    777 12208 0 100 ref|NP_565169.1|unknown protein [Arabidopsis thaliana] LN
    778 14803 2.00E−82 79 ref|NP_187893.1|unknown protein [Arabidopsis thaliana] HS
    779 10176 0 100 ref|NP_178313.1|ATPTR2-B (NITRATE TRANSPORTER 1); LN
    transporter [Arabidopsis thaliana]
    780 18011 1.00E−109 82 ref|NP_172517.1|ARR4 (RESPONSE REGULATOR 4); CS
    transcription regulator/two-component response regulator
    [Arabidopsis thaliana]
    781 12714 5.00E−53 100 ref|NP_566217.1|RNA binding/rRNA binding [Arabidopsis CK
    thaliana]
    782 10507 9.00E−99 100 ref|NP_201097.1|ARR6 (RESPONSE REGULATOR 6); LN
    transcription regulator/two-component response regulator
    [Arabidopsis thaliana]
    783 15039 0 99 dbj|BAF02191.1|hypothetical protein [Arabidopsis thaliana] LN
    784 12733 1.00E−137 94 ref|NP_194298.1|unknown protein [Arabidopsis thaliana] DS
    785 13237 1.00E−52 100 ref|NP_180192.1|unknown protein [Arabidopsis thaliana] LN
    786 13504 1.00E−137 100 ref|NP_177643.1|unknown protein [Arabidopsis thaliana] DS
    787 12932 1.00E−174 94 ref|NP_564618.1|unknown protein [Arabidopsis thaliana] SP
    788 75935 0 93 ref|NP_565242.1|protein binding [Arabidopsis thaliana] CS
    789 73333 0 95 ref|NP_198718.1|ATP binding/kinase/protein kinase/protein SS
    serine/threonine kinase/protein-tyrosine kinase [Arabidopsis
    thaliana]
    790 75993 0 93 ref|NP_171661.1|ATP binding/kinase/protein kinase/protein LL
    serine/threonine kinase/protein-tyrosine kinase [Arabidopsis
    thaliana]
    791 19401 0 94 ref|NP_195275.1|ATP binding/kinase/protein kinase/protein LN
    serine/threonine kinase/protein-tyrosine kinase [Arabidopsis
    thaliana]
    792 12766 5.00E−74 100 ref|NP_565233.1|unknown protein [Arabidopsis thaliana] SS
    793 76025 0 95 ref|NP_179580.1|malic enzyme/oxidoreductase, acting on NADH PEG
    or NADPH, NAD or NADP as acceptor [Arabidopsis thaliana]
    794 13708 0 100 ref|NP_181187.1|fructose-bisphosphate aldolase [Arabidopsis LN
    thaliana]
    795 13305 0 94 ref|NP_180287.1|PAP1 (PURPLE ACID PHOSPHATASE 1); LN
    hydrolase/protein serine/threonine phosphatase [Arabidopsis
    thaliana]
    796 15806 0 97 ref|NP_174089.1|APL2 [Arabidopsis thaliana] SS
    797 14712 0 92 ref|NP_171617.1|PDH-E1 ALPHA (PYRUVATE LN
    DEHYDROGENASE E1 ALPHA); oxidoreductase, acting on the
    aldehyde or oxo group of donors, disulfide as acceptor/pyruvate
    dehydrogenase (acetyl-transferring) [Arabidopsis thaliana]
    798 76013 0 92 ref|NP_194141.2|ATP binding/kinase/protein kinase/protein DS
    serine/threonine kinase/protein-tyrosine kinase [Arabidopsis
    thaliana]
    799 10192 0 99 ref|NP_180997.1|CYP710A1; heme binding/iron ion binding/ CS PP SS
    monooxygenase/oxygen binding [Arabidopsis thaliana]
    800 74775 0 96 ref|NP_175812.1|ALDH7B4; aldehyde dehydrogenase/ DS
    oxidoreductase [Arabidopsis thaliana] r
    801 13841 2.00E−33 100 ref|NP_194401.1|hydrogen-transporting ATP synthase, rotational LN
    mechanism/hydrogen-transporting ATPase, rotational
    mechanism [Arabidopsis thaliana]
    802 15805 0 100 ref|NP_567620.1|ZAC; ARF GTPase activator [Arabidopsis LN
    thaliana]
    803 14253 1.00E−167 87 ref|NP_195499.1|unknown protein [Arabidopsis thaliana] LN
    804 13650 1.00E−151 91 ref|NP_196069.1|phosphatidate cytidylyltransferase [Arabidopsis LN
    thaliana]
    805 13855 1.00E−94 86 ref|NP_567531.1|structural constituent of ribosome [Arabidopsis LN
    thaliana]
    806 76049 0 99 ref|NP_182198.2|unknown protein [Arabidopsis thaliana] DS HS
    807 14271 0 82 ref|NP_181342.1|unknown protein [Arabidopsis thaliana] DS
    808 73927 0 100 ref|NP_189059.1|FAD binding/disulfide oxidoreductase/ CS
    glutathione-disulfide reductase/oxidoreductase [Arabidopsis
    thaliana]
    809 13657 6.00E−76 72 ref|NP_565661.2|HDT4 [Arabidopsis thaliana] LN
    810 13938 2.00E−90 77 gb|AAL67123.1|AT3g06760/F3E22_10 [Arabidopsis thaliana] SP
    810 14730 2.00E−90 77 gb|AAL67123.1|AT3g06760/F3E22_10 [Arabidopsis thaliana] SP
    811 73948 0 97 ref|NP_176185.1|ATP binding/ATP-dependent helicase/ CS
    helicase/nucleic acid binding [Arabidopsis thaliana]
    812 18116 0 100 ref|NP_182144.1|oxidoreductase [Arabidopsis thaliana] CS
    813 14341 0 100 ref|NP_176646.1|unknown protein [Arabidopsis thaliana] SS
    814 13960 1.00E−179 100 ref|NP_565875.1|unknown protein [Arabidopsis thaliana] SP
    814 74391 1.00E−179 100 ref|NP_565875.1|unknown protein [Arabidopsis thaliana] SP
    815 75957 0 95 gb|ABK28258.1|unknown [Arabidopsis thaliana] LL
    816 70240 0 100 ref|NP_172751.1|AN11; nucleotide binding [Arabidopsis thaliana] CS
    817 70748 0 97 ref|NP_173077.1|ATP binding/protein kinase/protein CK
    serine/threonine kinase/protein-tyrosine kinase [Arabidopsis
    thaliana]
    818 70807 0 93 ref|NP_188160.2|protein binding [Arabidopsis thaliana] CS
    819 73986 0 87 ref|NP_974833.1|unknown protein [Arabidopsis thaliana] DS
    820 77005 0 97 ref|NP_566580.1|CIPK1 (CBL-INTERACTING PROTEIN KINASE CS
    1); ATP binding/kinase/protein kinase/protein serine/threonine
    kinase/protein-tyrosine kinase [Arabidopsis thaliana]
    821 70410 5.00E−34 86 ref|NP_850158.1|CLE5 (CLAVATA3/ESR-RELATED 5); receptor SP
    binding [Arabidopsis thaliana]
    822 14827 1.00E−153 88 ref|NP_564658.2|unknown protein [Arabidopsis thaliana] DS
    823 19122 0 93 ref|NP_566009.1|unknown protein [Arabidopsis thaliana] LL
    824 16446 0 94 ref|NP_566277.2|unknown protein [Arabidopsis thaliana] SP
    825 15143 6.00E−84 100 ref|NP_194152.1|SLY1 (SLEEPY1) [Arabidopsis thaliana] LN
    826 70401 0 93 sp|Q9SMZ3|FBX13_ARATHF-box only protein 13 PEG
    emb|CAB36790.1|putative protein [Arabidopsis thaliana]
    827 16182 0 100 emb|CAB44691.1|putative protein [Arabidopsis thaliana] DS
    828 15126 1.00E−138 95 ref|NP_198741.1|unknown protein [Arabidopsis thaliana] CS
    829 15628 0 100 ref|NP_567421.1|unknown protein [Arabidopsis thaliana] CS
    830 78355 0 90 gb|AAD10665.1|Hypothetical protein [Arabidopsis thaliana] SS
    831 70560 0 100 gb|AAB81879.1|putative zinc finger protein [Arabidopsis thaliana] CS
    832 19133 0 97 ref|NP_194117.3|protein binding/ubiquitin-protein ligase/zinc ion DS
    binding [Arabidopsis thaliana]
    833 73602 0 74 gb|AAR28013.1|mutant TFIIF-alpha [Arabidopsis thaliana] CS
    834 71702 1.00E−169 100 pir||T49271CELL DIVISION CONTROL PROTEIN 2 HOMOLOG LL
    A—Arabidopsis thaliana
    835 14909 0 98 gb|AAC39477.1|respiratory burst oxidase protein C [Arabidopsis CS PP HS SS PEG
    thaliana]
    836 14927 1.00E−88 65 ref|NP_568285.1|unknown protein [Arabidopsis thaliana] LN
    837 75945 0 94 ref|NP_563899.1|NRT1.1; transporter [Arabidopsis thaliana] SP
    838 16553 0 100 ref|NP_567083.1|nucleotide-sugar transporter/sugar porter SS
    [Arabidopsis thaliana]
    839 75221 0 87 ref|NP_195567.2|unknown protein [Arabidopsis thaliana] CS HS
    840 70746 5.00E−60 79 gb|AAM64668.1|unknown [Arabidopsis thaliana] PEG
    841 70403 1.00E−137 85 gb|AAK26011.1|AF360301_1unknown protein [Arabidopsis PP
    thaliana]
    842 15966 2.00E−73 71 ref|NP_568974.1|ATFP3; metal ion binding [Arabidopsis thaliana] CK
    843 76076 4.00E−34 100 ref|NP_179357.1|unknown protein [Arabidopsis thaliana] PP
    844 17014 2.00E−57 76 ref|NP_564008.1|unknown protein [Arabidopsis thaliana] SS PEG
    845 16007 0 100 ref|NP_564729.1|ZW9 [Arabidopsis thaliana] DS
    846 16208 1.00E−06 100 gb|AAF79580.1|AC022464_38F22G5.2 [Arabidopsis thaliana] CS
    847 17310 0 96 ref|NP_188117.1|catalytic [Arabidopsis thaliana] HS
    848 15716 1.00E−164 96 ref|NP_563630.1|BPS1 (BYPASS 1) [Arabidopsis thaliana] LN
    849 15627 0 89 ref|NP_565533.1|heat shock protein binding/unfolded protein SS
    binding [Arabidopsis thaliana]
    850 15409 0 95 ref|NP_188010.1|unknown protein [Arabidopsis thaliana] CK PEG
    850 17201 0 95 ref|NP_188010.1|unknown protein [Arabidopsis thaliana] PEG
    851 15903 0 86 ref|NP_199280.1|unknown protein [Arabidopsis thaliana] CK
    852 10332 0 96 ref|NP_188080.1|CYP72A8; heme binding/iron ion binding/ SP
    monooxygenase/oxygen binding [Arabidopsis thaliana]
    853 73968 0 90 ref|NP_565477.1|unknown protein [Arabidopsis thaliana] LN
    854 17003 1.00E−171 95 ref|NP_174746.1|PHI-1 (PHOSPHATE-INDUCED 1) [Arabidopsis DS SS
    thaliana]
    855 73847 0 97 ref|NP_849912.1|ATP binding/kinase [Arabidopsis thaliana] LN
    856 76041 0 97 ref|NP_566284.1|transferase, transferring glycosyl groups/ CS LL
    transferase, transferring hexosyl groups [Arabidopsis thaliana]
    857 74567 0 75 ref|NP_566917.1|calmodulin binding [Arabidopsis thaliana] CS LL
    ref|NP_974405.1|calmodulin binding [Arabidopsis thaliana]
    858 15809 0 97 ref|NP_568150.1|unknown protein [Arabidopsis thaliana] PP
    859 70110 0 92 ref|NP_014814.1|Lcb4p [Saccharomyces cerevisiae] LN
    860 70123 1.00E−180 100 ref|NP_014392.1|Lst8p [Saccharomyces cerevisiae] CK SS
    861 74702 0 87 ref|NP_850390.1|unknown protein [Arabidopsis thaliana] SP
    862 75936 0 95 ref|NP_187671.1|CAT7 (CATIONIC AMINO ACID CS
    TRANSPORTER 7); cationic amino acid transporter [Arabidopsis
    thaliana]
    863 10462 1.00E−136 100 ref|NP_565895.1|catalytic/hydrolase [Arabidopsis thaliana] DS
    864 17402 1.00E−60 100 ref|NP_190775.1|unknown protein [Arabidopsis thaliana] CS
    865 73707 0 94 ref|NP_564272.1|unknown protein [Arabidopsis thaliana] CS
    866 17129 3.00E−61 100 ref|NP_564630.1|unknown protein [Arabidopsis thaliana] LN
    867 72665 3.00E−54 89 ref|NP_564090.1|unknown protein [Arabidopsis thaliana] LL
    868 18206 0 100 ref|NP_564983.1|transferase, transferring glycosyl groups/ LN
    transferase, transferring hexosyl groups [Arabidopsis thaliana]
    869 17151 1.00E−155 100 ref|NP_171882.1|ATPHB2 (PROHIBITIN 2) [Arabidopsis thaliana] LN
    870 17813 5.00E−98 100 ref|NP_199762.1|protein binding [Arabidopsis thaliana] SS
    871 70845 0 100 ref|NP_173920.1|RCN1 (ROOTS CURL IN NPA); protein CS
    phosphatase type 2A regulator [Arabidopsis thaliana]
    872 16607 1.00E−171 95 ref|NP_355455.1|hypothetical protein AGR_C_4560 SP
    [Agrobacterium tumefaciens str. C58]
    873 72675 1.00E−179 78 ref|NP_200890.1|protein binding/ubiquitin-protein ligase/zinc ion LL LN
    binding [Arabidopsis thaliana]
    874 72677 0 86 sp|Q5EAE9|ATL5C_ARATHRING-H2 finger protein ATL5C LL
    precursor dbj|BAB09675.1|unnamed protein product [Arabidopsis
    thaliana]
    875 74534 0 95 ref|NP_196233.1|CYC1BAT; cyclin-dependent protein kinase PP
    regulator [Arabidopsis thaliana]
    876 74535 0 85 ref|NP_564978.1|NTL1; calcium ion binding/transporter CS
    [Arabidopsis thaliana]
    877 10204 0 89 ref|NP_179544.1|nucleotide binding [Arabidopsis thaliana] PP LL
    878 10472 1.00E−157 100 ref|NP_565480.1|catalytic/protein phosphatase type 2C LN
    [Arabidopsis thaliana]
    879 10431 1.00E−118 88 ref|NP_850625.1|imidazoleglycerol-phosphate dehydratase LN
    [Arabidopsis thaliana]
    880 72906 0 92 ref|NP_200387.1|DNA binding [Arabidopsis thaliana] PP
    881 78362 0 95 ref|NP_176118.2|DNA binding/transcription factor [Arabidopsis CS
    thaliana]
    882 17930 1.00E−11 60 ref|NP_173425.2|unknown protein [Arabidopsis thaliana] SS
    883 18442 0 92 ref|NP_198690.1|transcription factor [Arabidopsis thaliana] SS
    884 73207 0 94 ref|NP_173148.2|dimethylallyltranstransferase [Arabidopsis CS
    thaliana]
    885 19166 4.00E−99 91 emb|CAB45503.1|hypothetical protein [Arabidopsis thaliana] DS
    886 10469 1.00E−137 95 ref|NP_191762.1|ROC4; peptidyl-prolyl cis-trans isomerase LN
    [Arabidopsis thaliana]
    887 18415 1.00E−111 71 emb|CAB85519.1|putative protein [Arabidopsis thaliana] CS
    888 18418 1.00E−113 100 ref|NP_200034.1|ATGB1 [Arabidopsis thaliana] CK SS
    889 19532 1.00E−179 100 ref|NP_190986.1|CDC2B (CDC2-LIKE GENE); kinase CS
    [Arabidopsis thaliana]
    890 18423 1.00E−151 100 ref|NP_180496.1|SAG13; oxidoreductase [Arabidopsis thaliana] LN
    891 77909 0 92 ref|NP_191785.1|catalytic/protein phosphatase type 2C CK DS
    892 19656 4.00E−48 77 ref|NP_200260.1|PBP1 (PINOID-BINDING PROTEIN 1); calcium CS SS
    ion binding [Arabidopsis thaliana]
    893 10217 1.00E−135 94 ref|NP_199674.1|cyclin-dependent protein kinase [Arabidopsis LN
    thaliana]
    894 18874 2.00E−81 100 ref|NP_176511.1|unknown protein [Arabidopsis thaliana] SS
    895 18875 0 96 ref|NP_198127.1|unknown protein [Arabidopsis thaliana] SS
    896 19256 0 96 ref|NP_568785.1|SPDS3 (SPERMIDINE SYNTHASE 3) DS
    [Arabidopsis thaliana]
    897 19537 0 100 ref|NP_568931.1|ATP binding/ATP-dependent helicase/ LL
    helicase/nucleic acid binding [Arabidopsis thaliana]
    898 74201 0 90 ref|NP_567067.1|ATP binding/ATP-dependent helicase/ LN
    helicase/nucleic acid binding [Arabidopsis thaliana]
    899 74233 0 97 ref|NP_199051.1|unknown protein [Arabidopsis thaliana] SS
    900 18644 7.00E−62 100 ref|NP_172620.1|electron transporter/thiol-disulfide exchange DS
    intermediate [Arabidopsis thaliana]
    901 18827 0 91 ref|NP_565206.1|ubiquitin-protein ligase/zinc ion binding CS
    [Arabidopsis thaliana]
    902 18220 0 100 ref|NP_177629.1|nucleotidyltransferase [Arabidopsis thaliana] SP
    903 18830 0 96 ref|NP_188813.1|UDP-glycosyltransferase/transferase, PEG
    transferring glycosyl groups [Arabidopsis thaliana]
    904 19205 1.00E−161 84 gb|ABF55664.2|double MYC-tagged mitogen activated protein LN
    kinase kinase 4 [synthetic construct]
    905 18226 7.00E−99 92 ref|NP_197890.1|unknown protein [Arabidopsis thaliana] CS
    906 18227 1.00E−62 73 ref|NP_564432.3|OHP2 (ONE-HELIX PROTEIN 2) [Arabidopsis LN
    thaliana]
    907 18239 0 100 ref|NP_193460.1|unknown protein [Arabidopsis thaliana] SP
    908 70415 1.00E−136 96 ref|NP_849930.1|AGL3 (AGAMOUS-LIKE 3); DNA binding/ CK
    transcription factor [Arabidopsis thaliana]
    909 18329 7.00E−06 70 ref|NP_178619.1|unknown protein [Arabidopsis thaliana] LN
    910 72606 1.00E−166 79 ref|NP_566784.1|unknown protein [Arabidopsis thaliana] CS
    911 10230 0 96 ref|NP_172406.1|transferase, transferring glycosyl groups/ LN
    transferase, transferring hexosyl groups [Arabidopsis thaliana]
    912 19608 0 82 ref|NP_201045.1|calmodulin binding [Arabidopsis thaliana] CS
    913 18271 3.00E−97 82 gb|AAA21820.1|alpha-subunit; putative LN
    914 18347 2.00E−65 100 ref|NP_566786.1|DNA binding/transcription factor [Arabidopsis SP
    thaliana]
    915 18403 0 89 ref|NP_187364.1|unknown protein [Arabidopsis thaliana] CK
    916 74206 0 91 ref|NP_201348.1|cysteine-type endopeptidase/ubiquitin CS
    thiolesterase [Arabidopsis thaliana]
    917 10234 2.00E−60 72 ref|NP_193759.1|unknown protein [Arabidopsis thaliana] LN
    918 71115 1.00E−167 87 ref|NP_189058.1|PMP (PUTATIVE TYPE 1 MEMBRANE DS
    PROTEIN) [Arabidopsis thaliana]
    919 18406 8.00E−79 100 ref|NP_564160.1|unknown protein [Arabidopsis thaliana] SS
    920 19619 2.00E−87 83 ref|NP_563890.1|unknown protein [Arabidopsis thaliana] HS
    921 19623 1.00E−125 100 ref|NP_563994.1|SYP51 (SYNTAXIN OF PLANTS 51) DS
    [Arabidopsis thaliana]
    922 18381 9.00E−96 84 ref|NP_564601.1|unknown protein [Arabidopsis thaliana] SS
    923 18408 8.00E−69 91 ref|NP_564808.1|unknown protein [Arabidopsis thaliana] DS
    924 18720 1.00E−175 89 ref|NP_564840.1|unknown protein [Arabidopsis thaliana] CK
    925 77537 1.00E−122 81 ref|NP_565125.1|unknown protein [Arabidopsis thaliana] CS
    926 70833 0 90 ref|NP_566212.2|ATBPM4; protein binding [Arabidopsis thaliana] LL
    927 19328 0 93 ref|NP_638257.1|hypothetical protein XCC2909 [Xanthomonas DS
    campestris pv. campestris str. ATCC 33913]
    928 19312 0 100 ref|NP_013243.1|Proline oxidase, nuclear-encoded mitochondrial SS
    protein involved in utilization of proline as sole nitrogen source;
    PUT1 transcription is induced by Put3p in the presence of proline
    and the absence of a preferred nitrogen source [Saccharomyces
    cerevisiae]
    929 70538 1.00E−146 93 ref|NP_199892.1|unknown protein [Arabidopsis thaliana] SS
    930 70440 0 88 ref|NP_195953.1|cysteine-type peptidase [Arabidopsis thaliana] CK LN
    931 11319 0 97 ref|NP_177797.2|unknown protein [Arabidopsis thaliana] LN
    932 70443 1.00E−151 81 ref|NP_173841.1|unknown protein [Arabidopsis thaliana] CS
    933 72357 1.00E−141 100 ref|NP_190300.1|ubiquitin-protein ligase/zinc ion binding PP
    [Arabidopsis thaliana]
    934 70466 1.00E−172 94 ref|NP_196084.1|DNA binding/transcription factor [Arabidopsis LL
    thaliana]
    935 70241 5.00E−39 100 gb|EAZ44836.1|hypothetical protein OsJ_028319 [Oryza sativa SP
    (japonica cultivar-group)]
    936 70476 1.00E−153 95 ref|NP_176240.1|unknown protein [Arabidopsis thaliana] LN
    937 70477 1.00E−150 100 ref|NP_564877.1|WRKY67; transcription factor [Arabidopsis SS
    thaliana]
    938 19713 0 100 ref|NP_637886.1|oxidoreductase [Xanthomonas campestris pv. PP
    campestris str. ATCC 33913]
    939 12601 3.00E−70 100 ref|NP_195713.1|DNA binding [Arabidopsis thaliana] CK
    ref|NP_001050276.1|Os03g0390600 [Oryza sativa (japonica
    cultivar-group)] gb|AAB36494.1|histone H3.2 [Medicago sativa]
    940 19747 0 69 emb|CAB54847.1|hydroperoxide lyase [Medicago sativa] CS
    941 11117 1.00E−174 91 ref|NP_973592.1|ATPUP2 [Arabidopsis thaliana] LN
    942 70965 3.00E−95 46 gb|EAY82507.1|hypothetical protein OsI_036466 [Oryza sativa CS
    (indica cultivar-group)]
    943 10366 1.00E−153 92 ref|NP_181358.1|unknown protein [Arabidopsis thaliana] CK
    943 13404 1.00E−153 92 ref|NP_181358.1|unknown protein [Arabidopsis thaliana] LN
    944 70935 0 77 gb|ABE91638.1|hypothetical protein MtrDRAFT_AC142394g9v2 CS
    [Medicago truncatula]
    945 77717 1.00E−136 69 ref|NP_565111.1|unknown protein [Arabidopsis thaliana] CS
    946 19966 1.00E−163 80 gb|AAF27919.1|AF220203_1Ttg1-like protein [Malus x SS
    domestica]
    947 70909 1.00E−116 74 ref|NP_192696.3|unknown protein [Arabidopsis thaliana] SP
    948 19906 0 79 gb|AAD11430.1|protein phosphatase 2C homolog CK
    [Mesembryanthemum crystallinum]
    949 70974 0 72 gb|ABN09819.1|Not CCR4-Not complex component, N-terminal; SP
    tRNA-binding arm [Medicago truncatula]
    950 19802 0 90 gb|AAK11734.1|serine/threonine/tyrosine kinase [Arachis CS
    hypogaea]
    951 19746 1.00E−127 92 sp|Q96450|1433A_SOYBN14-3-3-like protein A (SGF14A) CS
    gb|AAB09580.1|SGF14A [Glycine max]
    952 70902 1.00E−135 81 gb|ABE77803.1|oxidoreductase, short chain PEG
    dehydrogenase/reductase family, putative [Medicago truncatula]
    953 19933 2.00E−92 68 gb|ABE81369.1|RNA-binding region RNP-1 (RNA recognition SP
    motif) [Medicago truncatula]
    954 19927 0 76 gb|ABE88827.1|Hydroxymethylglutaryl-coenzyme A reductase, CS SS
    putative [Medicago truncatula]
    955 70976 1.00E−164 79 ref|NP_194914.1|catalytic/protein phosphatase type 2C PEG
    [Arabidopsis thaliana]
    956 71440 0 60 ref|NP_196473.1|nucleotide binding [Arabidopsis thaliana] CS
    957 10413 0 93 ref|NP_197748.1|CDPK9 (CALCIUM-DEPENDENT PROTEIN LN
    KINASE 9); ATP binding/calcium ion binding/calcium- and
    calmodulin-dependent protein kinase/kinase/protein kinase/
    protein serine/threonine kinase/protein-tyrosine kinase
    [Arabidopsis thaliana]
    958 11119 1.00E−172 89 ref|NP_196779.1|CPK17; ATP binding/calcium ion binding/ LN
    calcium- and calmodulin-dependent protein kinase/kinase/
    protein kinase/protein serine/threonine kinase/protein-tyrosine
    kinase [Arabidopsis thaliana]
    959 78659 1.00E−164 90 ref|NP_175249.1|DNA binding/transcription factor [Arabidopsis LN
    thaliana]
    960 78665 0 100 ref|NP_567343.1|ubiquitin-protein ligase [Arabidopsis thaliana] DS
    961 78969 0 100 ref|NP_194509.1|catalytic/protein phosphatase type 2C LN
    [Arabidopsis thaliana]
    962 78970 7.00E−86 100 ref|NP_564143.1|calcium ion binding [Arabidopsis thaliana] HS
    963 71250 1.00E−160 100 ref|NP_567676.1|ATP binding/protein kinase/protein SS LN
    serine/threonine kinase/protein-tyrosine kinase/signal transducer
    [Arabidopsis thaliana]
    964 78972 0 94 ref|NP_176647.1|catalytic [Arabidopsis thaliana] LN
    965 78677 2.00E−25 43 gb|AAG40050.2|AF324699_1At1g76180 [Arabidopsis thaliana] SS
    966 70632 3.00E−85 100 ref|NP_187663.1|AHB2 [Arabidopsis thaliana] DS
    967 75205 0 92 ref|NP_196484.1|AAP2 (AMINO ACID PERMEASE 2); amino SS
    acid permease [Arabidopsis thaliana]
    968 10359 1.00E−156 100 gb|AAR10436.1|YDA [Arabidopsis thaliana] DS
    968 11408 1.00E−156 100 gb|AAR10436.1|YDA [Arabidopsis thaliana] LL
    969 73616 1.00E−163 100 ref|NP_199265.1|ribose-5-phosphate isomerase [Arabidopsis LN
    thaliana]
    970 78358 0 100 ref|NP_188056.1|diaminopimelate decarboxylase [Arabidopsis LL
    thaliana]
    971 71839 0 96 ref|NP_200945.1|unknown protein [Arabidopsis thaliana] LN PEG
    972 78417 0 91 ref|NP_191221.1|unknown protein [Arabidopsis thaliana] LN
    973 71952 1.00E−169 100 ref|NP_197477.1|binding/oxidative phosphorylation uncoupler LL
    [Arabidopsis thaliana]
    974 78717 0 85 ref|NP_566301.1|unknown protein [Arabidopsis thaliana] LN PEG
    975 75040 0 92 ref|NP_566410.1|unknown protein [Arabidopsis thaliana] LL
    976 71843 1.00E−134 94 ref|NP_194519.1|unknown protein [Arabidopsis thaliana] LN
    977 70666 3.00E−79 91 ref|NP_565742.1|unknown protein [Arabidopsis thaliana] LN
    978 71846 0 100 ref|NP_177890.1|1-aminocyclopropane-1-carboxylate synthase/ SP
    transaminase/transferase, transferring nitrogenous groups
    [Arabidopsis thaliana]
    979 71314 0 96 ref|NP_172774.1|CYP86C4; heme binding/iron ion binding/ SP
    monooxygenase/oxygen binding [Arabidopsis thaliana]
    980 76410 0 99 ref|NP_188081.1|CYP72A9; heme binding/iron ion binding/ LL LN
    monooxygenase/oxygen binding [Arabidopsis thaliana]
    981 71322 0 93 ref|NP_680111.1|CYP71A21; heme binding/iron ion binding/ LN
    monooxygenase/oxygen binding [Arabidopsis thaliana]
    982 73214 0 97 ref|NP_196559.1|CYP78A7; heme binding/iron ion binding/ DS
    monooxygenase/oxygen binding [Arabidopsis thaliana]
    983 71963 0 97 ref|NP_199079.1|AOS (ALLENE OXIDE SYNTHASE); hydrolyase/ SP PP
    oxygen binding [Arabidopsis thaliana]
    984 71326 0 83 pir||T00605probable cytochrome P450 At2g02580 [imported]- LN
    Arabidopsis thaliana
    985 70834 0 95 ref|NP_175900.1|LOX1; lipoxygenase [Arabidopsis thaliana] CS
    986 73215 0 97 gb|AAF97287.1|AC010164_9Putative cytochrome P450 CS
    [Arabidopsis thaliana]
    987 71334 0 97 ref|NP_193568.2|hydrolase, hydrolyzing O-glycosyl compounds SP LN
    [Arabidopsis thaliana]
    988 71335 0 96 ref|NP_173573.1|catalytic [Arabidopsis thaliana] LN
    989 71347 0 100 ref|NP_568479.1|TGG2 (GLUCOSIDE GLUCOHYDROLASE 2); CK
    hydrolase, hydrolyzing O-glycosyl compounds [Arabidopsis
    thaliana]
    990 71820 3.00E−55 75 emb|CAC03600.1|splicing factor SC35 [Arabidopsis thaliana] LL
    991 70764 1.00E−164 94 ref|NP_172084.2|unknown protein [Arabidopsis thaliana] LL
    992 70680 8.00E−79 100 ref|NP_567038.1|protein kinase C binding/zinc ion binding LL
    [Arabidopsis thaliana]
    993 72375 0 73 gb|ABE85332.1|Protein kinase [Medicago truncatula] SP
    994 72469 0 90 dbj|BAD95891.1|Ser/Thr protein kinase [Lotus japonicus] CK
    995 73951 0 81 gb|AAR15466.1|WD-repeat protein [Capsella rubella] CS
    996 11003 1.00E−118 94 ref|NP_178022.1|NADH dehydrogenase (ubiquinone)/electron LN
    transporter/iron ion binding [Arabidopsis thaliana]
    997 71613 1.00E−110 85 ref|NP_199556.1|AtTIP2; 3; water channel [Arabidopsis thaliana] LL
    998 78203 0 93 gb|AAF27063.1|AC008262_12F4N2.23 [Arabidopsis thaliana] CS
    999 71638 0 90 ref|NP_174210.1|ATS9 (19S PROTEOSOME SUBUNIT 9) CS
    [Arabidopsis thaliana]
    1000 71631 0 96 ref|NP_564785.1|antiporter/glucose-6-phosphate transporter LL
    [Arabidopsis thaliana]
    1001 72368 0 98 ref|NP_187640.1|organic anion transporter [Arabidopsis thaliana] SP
    1002 78202 0 98 ref|NP_564338.1|CARB (CARBAMOYL PHOSPHATE CK
    SYNTHETASE B); ATP binding/carbamoyl-phosphate synthase/
    ligase [Arabidopsis thaliana]
    1003 78207 0 96 ref|NP_030560.1|unknown protein [Arabidopsis thaliana] CS HS
    1004 75209 0 92 ref|NP_187286.1|EMB3004; 3-dehydroquinate dehydratase/ LN
    shikimate 5-dehydrogenase [Arabidopsis thaliana]
    1005 72457 7.00E−86 100 ref|NP_568956.1|ubiquitin conjugating enzyme/ubiquitin-like CS
    activating enzyme [Arabidopsis thaliana]
    1006 73639 0 98 ref|NP_197589.1|ATP binding/protein binding [Arabidopsis CS
    thaliana]
    1007 72526 1.00E−55 81 ref|NP_567335.1|unknown protein [Arabidopsis thaliana] CK
    1008 72531 0 100 ref|NP_194003.1|O-sialoglycoprotein endopeptidase [Arabidopsis CS
    thaliana]
    1009 73336 1.00E−167 100 ref|NP_201090.1|catalytic [Arabidopsis thaliana] LL
    1010 73722 0 94 ref|NP_191029.1|sugar binding [Arabidopsis thaliana] CS
    1011 72650 1.00E−168 85 ref|NP_568218.1|unknown protein [Arabidopsis thaliana] DS
    1012 73686 5.00E−67 100 ref|NP_189296.1|unknown protein [Arabidopsis thaliana] CK LL
    1013 78353 1.00E−119 86 sp|Q9SLB6|LBD17_ARATHLOB domain-containing protein 17 LL LN
    gb|AAD23726.1|hypothetical protein [Arabidopsis thaliana]
    1014 73726 0 100 ref|NP_179795.1|nucleotide binding [Arabidopsis thaliana] LN
    1015 74715 0 97 ref|NP_197059.1|nucleotide binding [Arabidopsis thaliana] CS
    1016 73230 0 96 ref|NP_191164.1|ATP binding/kinase/protein kinase/protein CS
    serine/threonine kinase/protein-tyrosine kinase [Arabidopsis
    thaliana]
    1017 72663 2.00E−97 100 ref|NP_565393.1|ATP binding/kinase/shikimate kinase LN
    [Arabidopsis thaliana]
    1018 70822 0 94 ref|NP_198905.1|ATCLC-A (CHLORIDE CHANNEL A); anion HS
    channel/voltage-gated chloride channel [Arabidopsis thaliana]
    1019 72827 1.00E−164 95 ref|NP_173856.1|oxidoreductase [Arabidopsis thaliana] LN
    1020 78339 0 96 ref|NP_197098.1|oxidoreductase [Arabidopsis thaliana] LL
    1021 73309 1.00E−171 100 dbj|BAA96982.1|11-beta-hydroxysteroid dehydrogenase-like LL
    [Arabidopsis thaliana]
    1022 78725 0 94 ref|NP_192359.1|kinase [Arabidopsis thaliana] LN
    1023 74222 0 93 ref|NP_174039.1|ATP binding/kinase/protein serine/threonine LL LN
    kinase [Arabidopsis thaliana]
    1024 78341 0 93 ref|NP_176603.1|ATP binding/kinase/protein serine/threonine LN PEG
    kinase [Arabidopsis thaliana]
    1025 78342 1.00E−178 93 ref|NP_188875.1|AOX1B; alternative oxidase [Arabidopsis LL LN
    thaliana]
    1026 78349 2.00E−55 100 ref|NP_568772.3|FIB1 (FIBRILLARIN 1) [Arabidopsis thaliana] CS
    1027 73683 7.00E−90 100 ref|NP_564105.1|ASK4; ubiquitin-protein ligase [Arabidopsis DS
    thaliana]
    1028 73280 7.00E−86 94 ref|NP_565297.1|ASK16 (ARABIDOPSIS SKP1-LIKE 16); SP
    ubiquitin-protein ligase [Arabidopsis thaliana]
    1029 73281 3.00E−77 96 ref|NP_565467.1|MEO (MEIDOS); ubiquitin-protein ligase LN
    [Arabidopsis thaliana]
    1030 73313 0 95 ref|NP_172572.1|kinase [Arabidopsis thaliana] CS
    1031 12772 1.00E−117 94 ref|NP_176435.1|Rho GDP-dissociation inhibitor [Arabidopsis SS
    thaliana]
    1032 73314 0 89 ref|NP_186833.1|ATP binding/kinase/protein kinase/protein DS
    serine/threonine kinase/protein-tyrosine kinase [Arabidopsis
    thaliana]
    1033 73861 0 97 ref|NP_195565.2|ATPLC1; phospholipase C [Arabidopsis PEG
    thaliana]
    1034 73676 1.00E−164 100 ref|NP_201532.2|CYP81G1; heme binding/iron ion binding/ PEG
    monooxygenase/oxygen binding [Arabidopsis thaliana]
    1035 74212 0 100 ref|NP_176086.1|heme binding/iron ion binding/ LL
    monooxygenase/oxygen binding [Arabidopsis thaliana]
    1036 74218 0 98 gb|AAG60111.1|AC073178_22cytochrome P450, putative CK DS
    [Arabidopsis thaliana]
    1037 71218 0 91 ref|NP_188021.1|RSH2 (RELA-SPOT HOMOLOG); catalytic PP
    [Arabidopsis thaliana]
    1038 73731 0 94 ref|NP_179782.1|CYP96A5; heme binding/iron ion binding/ CS
    monooxygenase/oxygen binding [Arabidopsis thaliana]
    1039 73251 1.00E−98 100 ref|NP_186922.1|electron transporter/thiol-disulfide exchange CS
    intermediate [Arabidopsis thaliana]
    1040 12773 0 100 ref|NP_565903.1|catalytic/hydrolase [Arabidopsis thaliana] PEG
    1041 73254 8.00E−50 80 ref|NP_566150.1|unknown protein [Arabidopsis thaliana] CS
    1042 73255 1.00E−169 100 ref|NP_850995.1|unknown protein [Arabidopsis thaliana] SP
    1043 73257 6.00E−39 85 gb|AAF01528.1|AC009991_24hypothetical protein [Arabidopsis LN
    thaliana]
    1044 11049 0 100 ref|NP_181474.2|catalytic/hydrolase [Arabidopsis thaliana] LN
    1045 74231 0 84 ref|NP_190740.1|unknown protein [Arabidopsis thaliana] CS
    1046 73266 2.00E−89 79 ref|NP_190816.1|unknown protein [Arabidopsis thaliana] PP
    1047 75823 1.00E−101 70 ref|NP_566967.1|unknown protein [Arabidopsis thaliana] LL
    1048 11353 1.00E−155 85 ref|NP_565721.1|ADS2; iron ion binding/oxidoreductase/ LN
    stearoyl-CoA 9-desaturase [Arabidopsis thaliana]
    1049 72025 0 95 ref|NP_199995.1|PGM (PHOSPHOGLUCOMUTASE) CS
    [Arabidopsis thaliana]
    1050 72037 0 91 ref|NP_179336.1|protein binding [Arabidopsis thaliana] SS
    1051 72049 0 100 emb|CAA16713.1|cytochrome P450 [Arabidopsis thaliana] SP
    1052 78213 1.00E−151 93 ref|NP_181836.1|AT-P4H-1; oxidoreductase, acting on paired CS
    donors, with incorporation or reduction of molecular oxygen, 2-
    oxoglutarate as one donor, and incorporation of one atom each of
    oxygen into both donors/procollagen-proline 4-dioxygenase
    [Arabidopsis thaliana]
    1053 72007 0 100 ref|NP_011943.1|Mitochondrially localized type 2C protein CK
    phosphatase; expression induced by growth on ethanol and by
    sustained osmotic stress; possible role in carbon source
    utilization in low oxygen environments [Saccharomyces
    cerevisiae]
    1054 72067 1.00E−171 83 ref|NP_011043.1|Sho1p [Saccharomyces cerevisiae] DS
    1055 72008 4.00E−71 100 sp|P40001|YEA8_YEASTHypothetical 14.0 kDa protein in GCN4- LL
    WBP1 intergenic region gb|AAB64485.1|Yel008wp
    [Saccharomyces cerevisiae]
    1056 72022 1.00E−127 72 ref|NP_564894.1|unknown protein [Arabidopsis thaliana] CK
    1057 72096 3.00E−64 66 ref|NP_001051798.1|Os03g0831900 [Oryza sativa (japonica CS
    cultivar-group)]
    1058 10811 0 96 ref|NP_175947.1|BCDH BETA1 (BRANCHED-CHAIN ALPHA- LN
    KETO ACID DECARBOXYLASE E1 BETA SUBUNIT); 3-methyl-
    2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)
    [Arabidopsis thaliana]
    1059 72138 4.00E−89 65 ref|NP_180496.1|SAG13; oxidoreductase [Arabidopsis thaliana] CK
    1060 74261 0 98 ref|NP_566923.1|branched-chain-amino-acid transaminase/ LL
    catalytic [Arabidopsis thaliana]
    1061 74264 1.00E−122 100 ref|NP_196452.1|unknown protein [Arabidopsis thaliana] CS
    1062 74271 0 93 ref|NP_195096.2|unknown protein [Arabidopsis thaliana] CS
    1063 74272 1.00E−112 90 ref|NP_195409.1|unknown protein [Arabidopsis thaliana] SS
    1064 78442 0 91 ref|NP_189231.1|protein phosphatase type 2A regulator LL
    [Arabidopsis thaliana]
    1065 76709 0 96 ref|NP_174119.1|carboxy-lyase [Arabidopsis thaliana] CK
    1066 75002 0 94 ref|NP_566016.1|ATCS; citrate (SI)-synthase [Arabidopsis CS PP
    thaliana]
    1067 78361 0 82 gb|AAL09767.1|AT5g03040/F15A17_70 [Arabidopsis thaliana] SS
    1068 74238 0 92 ref|NP_850730.1|dihydrodipicolinate synthase [Arabidopsis SS
    thaliana]
    1069 78434 0 100 ref|NP_180966.1|permease [Arabidopsis thaliana] DS
    1070 73932 0 85 ref|NP_173508.1|carbohydrate transporter/nucleoside SS
    transporter/sugar porter [Arabidopsis thaliana]
    1071 72713 0 97 ref|NP_567914.1|LKR [Arabidopsis thaliana] ref|NP_849486.1| SS
    LKR [Arabidopsis thaliana]
    1072 72773 1.00E−149 93 ref|NP_013180.1|Inhibitor of Cdc28-Clb kinase complexes that PP
    controls G1/S phase transition, preventing premature S phase
    and ensuring genomic integrity; phosphorylation targets Sic1p for
    SCF(CDC4)-dependent turnover; functional homolog of
    mammalian Kip1 [Saccharomyces cerevisiae]
    1073 72678 0 91 ref|NP_015445.1|B-type cyclin involved in DNA replication during PEG
    S phase; activates Cdc28p to promote initiation of DNA synthesis;
    functions in formation of mitotic spindles along with Clb3p and
    Clb4p; most abundant during late G1 phase [Saccharomyces
    cerevisiae]
    1074 72765 0 88 ref|NP_009934.1|Sat4p [Saccharomyces cerevisiae] PP PEG
    1075 72730 1.00E−146 92 ref|NP_012214.1|Pcl7p [Saccharomyces cerevisiae] CS
    1076 72707 5.00E−66 90 ref|NP_011461.1|Erv14p [Saccharomyces cerevisiae] CK
    1077 72755 1.00E−134 89 ref|NP_116710.1|Rpn12p [Saccharomyces cerevisiae] PP PEG
    1078 10610 1.00E−110 89 ref|NP_187123.1|PR4 (PATHOGENESIS-RELATED 4) LN
    [Arabidopsis thaliana]
    1079 73953 0 92 ref|NP_850165.1|DNA binding/NAD+ ADP-ribosyltransferase LL
    [Arabidopsis thaliana]
    1080 73173 1.00E−113 91 ref|NP_191263.1|ARR9 (RESPONSE REACTOR 4); transcription HS
    regulator [Arabidopsis thaliana]
    1081 73979 0 96 sp|O49289|RH29_ARATHPutative DEAD-box ATP-dependent SS PEG
    RNA helicase 29 gb|AAC00620.1|Similar ATP-dependent RNA
    Helicase [Arabidopsis thaliana]
    1082 73966 0 94 ref|NP_194578.1|HAESA (RECEPTOR-LIKE PROTEIN KINASE LN
    5); ATP binding/kinase/protein serine/threonine kinase
    [Arabidopsis thaliana]
    1083 12776 0 100 ref|NP_178421.1|FT1 (FUCOSYLTRANSFERASE 1); PP
    fucosyltransferase/transferase, transferring glycosyl groups
    [Arabidopsis thaliana]
    1084 72960 0 87 ref|NP_190906.1|carbohydrate binding/kinase [Arabidopsis PEG
    thaliana]
    1085 73021 0 100 ref|NP_243103.1|NADP-dependent glyceraldehyde-3-phosphate CS PP PEG
    dehydrogenase [Bacillus halodurans C-125]
    1086 73163 0 99 ref|NP_243584.1|glutamate dehydrogenase [Bacillus halodurans CS SS
    C-125]
    1087 73187 0 93 ref|NP_244808.1|1-pyrroline-5-carboxylate dehydrogenase CK
    [Bacillus halodurans C-125]
    1088 73188 1.00E−173 100 ref|NP_389366.1|glutaminase [Bacillus subtilis subsp. subtilis str. PEG
    168]
    1089 73153 1.00E−159 92 ref|NP_415018.1|predicted glutaminase [Escherichia coli K12] CK
    1090 73983 0 99 ref|ZP_00107721.1|COG0160: 4-aminobutyrate aminotransferase CK
    and related aminotransferases [Nostoc punctiforme PCC 73102]
    1091 11516 0 98 ref|NP_564571.1|THFS (10-FORMYLTETRAHYDROFOLATE LN
    SYNTHETASE); ATP binding/formate-tetrahydrofolate ligase
    [Arabidopsis thaliana]
    1092 73179 0 97 ref|NP_387399.1|beta alanine-pyruvate transaminase LL
    [Sinorhizobium meliloti 1021]
    1093 73009 0 87 ref|NP_927600.1|glutamine synthetase [Photorhabdus SS
    luminescens subsp. laumondii TTO1]
    1094 73109 4.00E−95 100 ref|NP_840275.1|adenine phosphoribosyltransferase PEG
    [Nitrosomonas europaea ATCC 19718]
    1095 73121 1.00E−117 94 ref|ZP_00109456.1|COG0120: Ribose 5-phosphate isomerase PEG
    [Nostoc punctiforme PCC 73102]
    1096 73157 1.00E−98 100 ref|NP_791813.1|adenine phosphoribosyltransferase CS
    [Pseudomonas syringae pv. tomato str. DC3000]
    1097 73158 5.00E−71 93 ref|NP_928672.1|nucleoside diphosphate kinase [Photorhabdus SS
    luminescens subsp. laumondii TTO1]
    1098 73088 0 100 ref|NP_013311.1|B-type cyclin involved in cell cycle progression; DS
    activates Cdc28p to promote the G2/M transition; may be
    involved in DNA replication and spindle assembly; accumulates
    during S phase and G2, then targeted for ubiquitin-mediated
    degradation [Saccharomyces cerevisiae]
    1099 73135 0 91 ref|NP_011846.1|Putative protein of unknown function; green PP
    fluorescent protein (GFP)-fusion protein co-localizes with clathrin-
    coated vesicles [Saccharomyces cerevisiae]
    1100 73005 2.00E−63 90 ref|NP_014508.1|Hrt1p [Saccharomyces cerevisiae] CS
    1101 73171 0 87 ref|NP_015262.1|Constituent of the mitochondrial inner CK
    membrane presequence translocase (TIM23 complex); may
    promote binding of incoming precursor proteins to the
    intermembrane space domain of Tom22p during translocation
    [Saccharomyces cerevisiae]
    1102 73042 0 88 ref|NP_014450.1|Pop2p [Saccharomyces cerevisiae] SS
    1103 73067 0 100 ref|NP_010301.1|Probable membrane protein with three CS
    predicted transmembrane domains; homologous to Ybr042cp,
    similar to C. elegans F55A11.5 and maize 1-acyl-glycerol-3-
    phosphate acyltransferase; null exhibits no apparent phenotype
    [Saccharomyces cerevisiae]
    1104 73148 0 100 emb|CAA56013.1|A-509 protein [Saccharomyces cerevisiae] CS
    1105 72933 0 94 ref|NP_010632.1|Hxt3p [Saccharomyces cerevisiae] LN
    1106 77723 0 90 ref|NP_012321.1|Hxt8p [Saccharomyces cerevisiae] CK CS
    1107 73048 0 93 ref|NP_010331.1|Amino acid permease involved in the uptake of CS
    cysteine, leucine, isoleucine and valine [Saccharomyces
    cerevisiae]
    1108 10616 0 100 ref|NP_194906.1|MGD1 LN
    (MONOGALACTOSYLDIACYLGLYCEROL SYNTHASE 1); 1,2-
    diacylglycerol 3-beta-galactosyltransferase [Arabidopsis thaliana]
    1109 72923 0 98 ref|NP_116600.1|Agp3p [Saccharomyces cerevisiae] SP
    1110 78501 0 100 gb|AAD32292.1|putative protein kinase [Arabidopsis thaliana] SP
    1111 78371 0 94 gb|AAF27112.1|AC011809_21Putative protein kinase LL
    [Arabidopsis thaliana]
    1112 74332 1.00E−174 95 ref|NP_178581.1|ATP binding/kinase/protein kinase/protein LL
    serine/threonine kinase/protein-tyrosine kinase [Arabidopsis
    thaliana]
    1113 74738 0 94 ref|NP_850311.1|ATP binding/kinase/protein kinase/protein SS LN
    serine/threonine kinase/protein-tyrosine kinase [Arabidopsis
    thaliana]
    1114 75225 0 100 ref|NP_849998.1|ATP binding/kinase/protein kinase/protein CS
    serine/threonine kinase/protein-tyrosine kinase [Arabidopsis
    thaliana]
    1115 11149 1.00E−110 91 ref|NP_568067.1|FK506 binding/peptidyl-prolyl cis-trans DS
    isomerase [Arabidopsis thaliana]
    1116 74739 0 87 ref|NP_564844.1|ATP binding/protein kinase [Arabidopsis CS
    thaliana]
    1117 74748 1.00E−172 92 ref|NP_179308.1|ATP binding/kinase/protein kinase/protein LL
    serine/threonine kinase/protein-tyrosine kinase [Arabidopsis
    thaliana]
    1118 78113 0 100 ref|NP_198610.1|oxidoreductase/zinc ion binding [Arabidopsis PEG
    thaliana]
    1119 75233 0 96 ref|NP_851257.1|oxidoreductase/zinc ion binding [Arabidopsis CS
    thaliana]
    1120 77311 0 83 ref|NP_850553.1|ATP binding/nucleoside-triphosphatase/ LN
    nucleotide binding [Arabidopsis thaliana]
    1121 77008 0 89 ref|NP_177460.2|ATP binding/ATP-dependent peptidase/ CS
    nucleoside-triphosphatase/nucleotide binding/serine-type
    endopeptidase [Arabidopsis thaliana]
    1122 77321 0 98 ref|NP_565299.1|ATP binding/ATP-dependent helicase/DNA CS
    binding/nucleoside-triphosphatase/nucleotide binding
    [Arabidopsis thaliana]
    1123 76214 0 100 ref|NP_564533.1|unknown protein [Arabidopsis thaliana] DS
    1124 75238 0 96 ref|NP_566361.1|disulfide oxidoreductase/oxidoreductase PEG
    [Arabidopsis thaliana]
    1125 76118 0 92 ref|NP_568125.1|disulfide oxidoreductase/oxidoreductase PP HS
    [Arabidopsis thaliana]
    1126 75243 0 91 ref|NP_567074.2|ATP binding/kinase/protein kinase/protein CS
    serine/threonine kinase/protein-tyrosine kinase [Arabidopsis
    thaliana]
    1127 72602 0 91 ref|NP_178198.1|NRAMP1; manganese ion transporter/metal ion LN
    transporter [Arabidopsis thaliana]
    1128 75810 0 100 gb|ABG54332.1|double HA-tagged mitogen activated protein SS
    kinase 5 [synthetic construct]
    1129 75094 0 89 ref|NP_199951.1|unknown protein [Arabidopsis thaliana] CS
    1130 75818 1.00E−150 91 ref|NP_566411.2|unknown protein [Arabidopsis thaliana] CS
    1131 75248 0 88 ref|NP_568685.1|RNA binding/nucleic acid binding [Arabidopsis LL
    thaliana]
    1132 74605 6.00E−60 86 ref|NP_200911.1|RNA binding/nucleic acid binding [Arabidopsis LL
    thaliana]
    1133 75252 0 97 ref|NP_567801.1|NADH dehydrogenase/disulfide oxidoreductase LL
    [Arabidopsis thaliana]
    1134 10620 2.00E−56 77 ref|NP_175633.1|unknown protein [Arabidopsis thaliana] LN
    1135 74611 4.00E−57 63 ref|NP_683304.1|unknown protein [Arabidopsis thaliana] LL LN
    1136 11152 0 91 ref|NP_199220.1|CAD1 (CADMIUM SENSITIVE 1) [Arabidopsis LL
    thaliana]
    1137 76610 0 100 ref|NP_176261.1|ATRPAC43; DNA binding/DNA-directed RNA CS
    polymerase [Arabidopsis thaliana]
    1138 70243 1.00E−107 100 ref|NP_177128.1|ATHVA22C [Arabidopsis thaliana] SS
    1139 74371 1.00E−170 100 ref|NP_177541.1|strictosidine synthase [Arabidopsis thaliana] LN
    1140 74373 1.00E−100 93 ref|NP_177712.1|ATROP4 (RHO-LIKE GTP BINDING PROTEIN CS SS LN
    4); GTP binding [Arabidopsis thaliana]
    1141 74615 1.00E−177 87 ref|NP_565394.1|nickel ion transporter [Arabidopsis thaliana] SS
    1142 74620 6.00E−77 100 ref|NP_188045.1|unknown protein [Arabidopsis thaliana] LN
    1143 74626 5.00E−93 88 ref|NP_566635.1|unknown protein [Arabidopsis thaliana] LL
    1144 10622 1.00E−147 100 ref|NP_001031481.1|UREG; metal ion binding/nickel ion binding/ LN
    nucleotide binding [Arabidopsis thaliana]
    1145 74636 2.00E−89 94 gb|AAO19647.1|CAXIP1 protein [Arabidopsis thaliana] LL
    1146 74656 1.00E−107 93 ref|NP_195699.1|GTP binding [Arabidopsis thaliana] CS
    1147 74658 1.00E−115 100 ref|NP_195709.1|ATGB3 (GTP-BINDING PROTEIN 3); GTP HS
    binding [Arabidopsis thaliana]
    1148 74659 4.00E−99 88 ref|NP_568121.1|ATRAB ALPHA; GTP binding [Arabidopsis CS
    thaliana]
    1149 74673 0 92 gb|AAL24269.1|AT5g51550/K17N15_10 [Arabidopsis thaliana] SS
    1150 13518 0 94 ref|NP_191100.1|ATP binding/methionine-tRNA ligase/tRNA DS
    ligase [Arabidopsis thaliana]
    1150 70824 0 94 ref|NP_191100.1|ATP binding/methionine-tRNA ligase/tRNA CK
    ligase [Arabidopsis thaliana]
    1151 75267 0 90 ref|NP_200758.1|unknown protein [Arabidopsis thaliana] LL
    1152 75283 0 93 ref|NP_201300.1|unknown protein [Arabidopsis thaliana] LN
    1153 13805 0 94 ref|NP_186764.1|PTB (POLYPYRIMIDINE TRACT-BINDING); LN
    RNA binding/nucleic acid binding [Arabidopsis thaliana]
    1154 76221 0 97 ref|NP_187191.2|carbohydrate transporter/sugar porter SP PP
    [Arabidopsis thaliana]
    1155 76226 0 93 ref|NP_187247.1|carbohydrate transporter/sugar porter DS
    [Arabidopsis thaliana]
    1156 76222 0 95 ref|NP_188627.1|STP4 (SUGAR TRANSPORTER); carbohydrate LL
    transporter/sugar porter [Arabidopsis thaliana]
    1157 76611 0 97 ref|NP_190157.2|transporter [Arabidopsis thaliana] LL
    1158 76228 0 92 ref|NP_197718.1|carbohydrate transporter/sugar porter LL
    [Arabidopsis thaliana]
    1159 76435 0 93 ref|NP_175449.1|carbohydrate transporter/sugar porter LL
    [Arabidopsis thaliana]
    1160 76436 0 91 ref|NP_178054.1|carbohydrate transporter/sugar porter DS
    [Arabidopsis thaliana]
    1161 78743 0 90 ref|NP_179438.1|carbohydrate transporter/sugar porter LN
    [Arabidopsis thaliana]
    1162 75814 0 91 ref|NP_201166.1|HEN3 (HUA ENHANCER 3); ATP binding/ CS PP
    kinase/protein kinase/protein serine/threonine kinase/protein-
    tyrosine kinase [Arabidopsis thaliana]
    1163 77016 0 93 ref|NP_195802.1|ATSR1 (SERINE/THREONINE PROTEIN CS
    KINASE 1); ATP binding/kinase/protein kinase/protein
    serine/threonine kinase/protein-tyrosine kinase [Arabidopsis
    thaliana]
    1164 78734 0 98 ref|NP_199394.1|CIPK20 (CBL-INTERACTING PROTEIN PEG
    KINASE 20); kinase [Arabidopsis thaliana]
    1165 75274 0 100 ref|NP_200709.2|ATP binding/protein kinase/protein CS
    serine/threonine kinase/protein-tyrosine kinase [Arabidopsis
    thaliana]
    1166 76233 0 89 ref|NP_197154.2|ATP binding/kinase/protein kinase/protein SP
    serine/threonine kinase/protein-tyrosine kinase [Arabidopsis
    thaliana]
    1167 74674 0 100 ref|NP_191331.2|ATP binding/kinase/protein kinase/protein PEG
    serine/threonine kinase/protein-tyrosine kinase [Arabidopsis
    thaliana]
    1168 70225 0 94 ref|NP_187668.1|CYP77A6; heme binding/iron ion binding/ CS
    monooxygenase/oxygen binding [Arabidopsis thaliana]
    1169 75291 0 98 ref|NP_201303.1|unknown protein [Arabidopsis thaliana] CS
    dbj|BAA97310.1|unnamed protein product [Arabidopsis thaliana]
    1170 75292 0 91 gb|AAL57662.1|At1g72120/F28P5_2 [Arabidopsis thaliana] SS
    1171 78607 0 96 gb|AAC39370.1|trehalose-6-phosphate phosphatase [Arabidopsis LN
    thaliana]
    1172 78367 1.00E−172 100 ref|NP_186907.1|STE1 (STEROL 1); C-5 sterol desaturase CK DS
    [Arabidopsis thaliana]
    1173 76528 1.00E−165 93 gb|AAM64961.1|putative C-4 sterol methyl oxidase [Arabidopsis DS LL
    thaliana]
    1174 77319 0 77 ref|NP_568416.1|protein binding [Arabidopsis thaliana] CS
    1175 74677 2.00E−73 87 gb|AAM67086.1|unknown [Arabidopsis thaliana] SS
    1176 78109 1.00E−149 87 ref|NP_182332.1|PAC (PALE CRESS) [Arabidopsis thaliana] CS
    1177 77725 0 100 ref|NP_391274.1|glyceraldehyde-3-phosphate dehydrogenase HS
    [Bacillus subtilis subsp. subtilis str. 168]
    1178 73437 0 99 ref|YP_517842.1|glyceraldehyde 3-phosphate dehydrogenase SS
    [Desulfitobacterium hafniense Y51]
    1179 73450 0 100 ref|YP_350062.1|hypothetical protein Pfl_4334 [Pseudomonas CS
    fluorescens PfO-1]
    1180 73416 0 100 ref|NP_443010.1|glucose-1-phosphate adenylyltransferase HS
    [Synechocystis sp. PCC 6803]
    1181 73452 0 97 ref|NP_388496.1|sorbitol dehydrogenase [Bacillus subtilis subsp. SS LN
    subtilis str. 168]
    1182 73453 0 95 ref|NP_414890.1|alcohol dehydrogenase class III/glutathione- CK
    dependent formaldehyde dehydrogenase [Escherichia coli K12]
    1183 73454 0 95 ref|ZP_00110545.1|COG0837: Glucokinase [Nostoc punctiforme PP SS
    PCC 73102]
    1184 73491 0 91 ref|NP_791383.1|alcohol dehydrogenase, class III [Pseudomonas CS
    syringae pv. tomato str. DC3000]
    1185 73445 1.00E−176 83 ref|ZP_00709024.1|COG0473: Isocitrate/isopropylmalate SP
    dehydrogenase [Escherichia coli B171]
    1186 73469 1.00E−131 65 ref|YP_958498.1|Alcohol dehydrogenase GroES domain protein CS
    [Marinobacter aquaeolei VT8]
    1187 73434 0 94 ref|NP_012342.1|Putative protein of unknown function, predicted CS
    to encode a triose phosphate transporter subfamily member
    based on phylogenetic analysis; similar to YOR307C/SLY41;
    deletion mutant has a respiratory growth defect [Saccharomyces
    cerevisiae]
    1188 73471 0 93 ref|NP_391658.1|pyrroline-5 carboxylate dehydrogenase [Bacillus CS
    subtilis subsp. subtilis str. 168]
    1189 73436 0 91 ref|YP_355035.1|Aldehyde dehydrogenase family protein SP SS
    [Rhodobacter sphaeroides 2.4.1]
    1190 73525 0 95 ref|NP_790108.1|succinate-semialdehyde dehydrogenase PP
    [Pseudomonas syringae pv. tomato str. DC3000]
    1191 73514 1.00E−174 100 ref|NP_242723.1|fructokinase [Bacillus halodurans C-125] SP
    dbj|BAB05576.1|fructokinase [Bacillus halodurans C-125]
    1192 73551 1.00E−171 95 ref|YP_690914.1|6-phosphofructokinase I [Shigella flexneri 5 str. LL
    8401]
    1193 73519 0 95 ref|NP_414696.1|glutamate-1-semialdehyde aminotransferase CS
    [Escherichia coli K12]
    1194 73543 0 99 ref|NP_389628.1|glutamine synthetase [Bacillus subtilis subsp. CS
    subtilis str. 168]
    1195 73567 1.00E−159 92 ref|NP_415018.1|predicted glutaminase [Escherichia coli K12] CS DS
    1196 73579 0 96 ref|NP_792487.1|succinate-semialdehyde dehydrogenase PP
    [Pseudomonas syringae pv. tomato str. DC3000]
    1197 73556 0 97 ref|NP_790150.1|succinate-semialdehyde dehydrogenase SP
    [Pseudomonas syringae pv. tomato str. DC3000]
    1198 73545 0 99 ref|NP_792858.1|aldehyde dehydrogenase family protein PEG
    [Pseudomonas syringae pv. tomato str. DC3000]
    1199 73511 1.00E−161 66 ref|YP_546017.1|Phosphopyruvate hydratase [Methylobacillus LL
    flagellatus KT]
    1200 74138 0 97 ref|NP_415933.1|aldehyde dehydrogenase A, NAD-linked PEG
    [Escherichia coli K12]
    1201 74186 0 100 ref|NP_416275.1|glutamate dehydrogenase [Escherichia coli CS
    K12]
    1202 74163 0 95 ref|NP_391649.1|hypothetical protein BSU37690 [Bacillus subtilis PP
    subsp. subtilis str. 168]
    1203 74175 0 96 ref|NP_244424.1|phosphoglyceromutase [Bacillus halodurans C- LN
    125]
    1204 74176 0 99 ref|YP_517842.1|glyceraldehyde 3-phosphate dehydrogenase LN
    [Desulfitobacterium hafniense Y51]
    1205 74141 0 99 ref|YP_543116.1|2,3-bisphosphoglycerate-independent LN
    phosphoglycerate mutase [Escherichia coli UTI89]
    1206 74178 0 98 ref|NP_387154.1|dihydrolipoamide dehydrogenase LN
    [Sinorhizobium meliloti 1021]
    1207 74179 0 83 ref|NP_441936.1|dihydrolipoamide acetyltransferase CS
    [Synechocystis sp. PCC 6803]
    1208 74110 0 92 ref|NP_930835.1|pyruvate dehydrogenase E1 component SP
    [Photorhabdus luminescens subsp. laumondii TTO1]
    1209 74170 0 98 ref|ZP_00106110.1|COG0021: Transketolase [Nostoc CS
    punctiforme PCC 73102]
    1210 74123 1.00E−174 100 ref|NP_014585.1|Gpm3p [Saccharomyces cerevisiae] LL
    1211 74159 1.00E−71 88 ref|NP_440036.1|hypothetical protein slr0250 [Synechocystis sp. PP
    PCC 6803]
    1212 10633 1.00E−150 81 ref|NP_850491.1|CA1 (CARBONIC ANHYDRASE 1); carbonate LN
    dehydratase/zinc ion binding [Arabidopsis thaliana]
    1213 74172 2.00E−62 99 ref|NP_440674.1|cytochrome c553 [Synechocystis sp. PCC 6803] SS
    1214 74184 7.00E−47 98 ref|NP_440475.1|hypothetical protein ssr1698 [Synechocystis sp. CS PP SS
    PCC 6803]
    1215 74582 1.00E−164 99 ref|NP_440558.1|aspartoacylase [Synechocystis sp. PCC 6803] CS
    1216 74584 0 99 ref|NP_009780.1|E1 beta subunit of the pyruvate dehydrogenase CS
    (PDH) complex, which is an evolutionarily-conserved multi-protein
    complex found in mitochondria [Saccharomyces cerevisiae]
    1217 74687 1.00E−142 99 ref|NP_385544.1|PROBABLE TRIOSEPHOSPHATE LL
    ISOMERASE PROTEIN [Sinorhizobium meliloti 1021]
    1218 74461 3.00E−70 99 ref|NP_638210.1|hypothetical protein XCC2862 [Xanthomonas SS
    campestris pv. campestris str. ATCC 33913]
    1219 74403 0 98 ref|NP_356568.1|glucose-1-phosphate adenylyltransferase LL
    [Agrobacterium tumefaciens str. C58]
    1220 74430 1.00E−178 99 ref|NP_289016.1|transaldolase [Escherichia coli O157:H7 SS
    EDL933]
    1221 74443 0 97 ref|NP_391271.1|phosphoglyceromutase [Bacillus subtilis subsp. LL
    subtilis str. 168]
    1222 74457 0 100 ref|YP_350062.1|hypothetical protein Pfl_4334 [Pseudomonas LL
    fluorescens PfO-1]
    1223 74434 0 99 ref|NP_790208.1|glutamine synthetase, type I [Pseudomonas CS
    syringae pv. tomato str. DC3000]
    1224 74447 0 91 ref|NP_385430.1|PUTATIVE AMINOTRANSFERASE PROTEIN LN
    [Sinorhizobium meliloti 1021]
    1225 74495 0 94 ref|NP_386611.1|PUTATIVE ALDEHYDE DEHYDROGENASE PEG
    PROTEIN [Sinorhizobium meliloti 1021]
    1226 74513 1.00E−115 87 ref|YP_052359.1|triosephosphate isomerase [Erwinia carotovora LL
    subsp. atroseptica SCRI1043]
    1227 74514 0 100 ref|NP_242374.11|asparagine synthetase [Bacillus halodurans C- PEG
    125]
    1228 74515 0 98 ref|YP_350541.1|glucose-6-phosphate isomerase [Pseudomonas CS LL
    fluorescens PfO-1]
    1229 74552 0 98 ref|NP_390871.1|pullulanase [Bacillus subtilis subsp. subtilis str. PEG
    168]
    1230 74529 0 96 ref|NP_418330.1|formate dehydrogenase-O, large subunit CS
    [Escherichia coli K12]
    1231 74519 0 86 ref|NP_931552.1|glucose-6-phosphate isomerase [Photorhabdus CS
    luminescens subsp. laumondii TTO1]
    1232 10638 1.00E−70 58 ref|NP_189273.1|ARRZ-1A; RNA binding/nucleotide binding LN
    [Arabidopsis thaliana]
    1233 76547 5.00E−89 89 ref|NP_190024.1|unknown protein [Arabidopsis thaliana] PP
    1234 76548 0 94 ref|NP_190153.1|ATP binding/kinase/protein kinase/protein SS
    serine/threonine kinase/protein-tyrosine kinase [Arabidopsis
    thaliana]
    1235 14703 1.00E−56 87 gb|ABK28584.1|unknown [Arabidopsis thaliana] LN
    1236 75856 8.00E−18 42 ref|NP_190667.2|unknown protein [Arabidopsis thaliana] CS
    1237 76642 0 92 ref|NP_563988.1|metal ion transporter [Arabidopsis thaliana] LL
    1238 77522 0 83 ref|NP_190912.1|unknown protein [Arabidopsis thaliana] CK
    1239 77516 0 90 ref|NP_191095.1|unknown protein [Arabidopsis thaliana] CS
    1240 75864 3.00E−63 100 ref|NP_191376.1|ATBS14A; protein transporter [Arabidopsis LL
    thaliana]
    1241 76275 1.00E−157 84 ref|NP_191386.1|unknown protein [Arabidopsis thaliana] CS
    1242 76276 0 100 ref|NP_191408.1|phosphoric ester hydrolase [Arabidopsis SP
    thaliana]
    1243 75869 1.00E−85 100 ref|NP_192145.1|unknown protein [Arabidopsis thaliana] DS
    1244 76558 2.00E−77 73 ref|NP_192181.2|unknown protein [Arabidopsis thaliana] PP
    1245 75876 1.00E−101 100 pdb|1FSI|AChain A, Crystal Structure Of Cyclic Nucleotide HS
    Phosphodiesterase Of Appr>p From Arabidopsis Thaliana
    1246 75878 2.00E−82 78 emb|CAA20466.1|putative protein [Arabidopsis thaliana] CS
    1247 75881 7.00E−91 89 ref|NP_194766.1|protein binding/ubiquitin-protein ligase/zinc ion LL
    binding [Arabidopsis thaliana]
    1248 77525 0 95 ref|NP_195212.1|beta-fructofuranosidase [Arabidopsis thaliana] CS
    1249 76454 1.00E−176 88 ref|NP_196814.1|unknown protein [Arabidopsis thaliana] LL
    1250 75895 2.00E−27 78 ref|NP_197316.1|unknown protein [Arabidopsis thaliana] LL
    1251 78377 1.00E−154 85 ref|NP_197406.1|catalytic [Arabidopsis thaliana] HS
    1252 75896 7.00E−70 100 ref|NP_197550.1|arsenate reductase (glutaredoxin)/electron CS
    transporter/thiol-disulfide exchange intermediate [Arabidopsis
    thaliana]
    1253 77527 0 85 ref|NP_850871.1|unknown protein [Arabidopsis thaliana] CS
    1254 78984 0 100 ref|NP_198084.1|catalytic [Arabidopsis thaliana] SS
    1255 77528 0 92 ref|NP_568564.1|unknown protein [Arabidopsis thaliana] SS
    1256 76752 0 84 ref|NP_199429.1|unknown protein [Arabidopsis thaliana] LL
    1257 78106 0 100 gb|ABK06440.1|flag-tagged protein kinase domain of putative SS
    mitogen-activated protein kinase kinase kinase [synthetic
    construct]
    1258 11720 0 89 ref|NP_565622.1|RCY1; cyclin-dependent protein kinase LN
    regulator [Arabidopsis thaliana]
    1259 78740 1.00E−121 75 ref|NP_200152.1|unknown protein [Arabidopsis thaliana] PP
    1260 76157 1.00E−154 88 ref|NP_001032094.1|carrier/steroid binding [Arabidopsis LN
    thaliana]
    1261 77530 0 83 ref|NP_201241.1|heat shock protein binding/unfolded protein SP CS
    binding [Arabidopsis thaliana]
    1262 76755 0 87 gb|AAM14093.1|putative bystin [Arabidopsis thaliana] PEG
    1263 76166 4.00E−99 82 ref|NP_171940.1|RIC3 (ROP-INTERACTIVE CRIB MOTIF- PEG
    CONTAINING PROTEIN 3) [Arabidopsis thaliana]
    1264 76756 0 90 ref|NP_171927.1|ERS2 (ETHYLENE RESPONSE SENSOR 2); LN
    receptor [Arabidopsis thaliana]
    1265 78990 0 100 ref|NP_175364.1|oxidoreductase, acting on paired donors, with CS
    incorporation or reduction of molecular oxygen, 2-oxoglutarate as
    one donor, and incorporation of one atom each of oxygen into
    both donors [Arabidopsis thaliana]
    1266 78460 9.00E−97 75 ref|NP_175584.1|unknown protein [Arabidopsis thaliana] LN
    1267 11022 0 95 ref|NP_192078.1|PPOX; protoporphyrinogen oxidase LN
    [Arabidopsis thaliana]
    1268 77533 0 96 ref|NP_177399.1|ATP binding/phenylalanine-tRNA ligase PEG
    [Arabidopsis thaliana]
    1269 76572 0 100 ref|NP_177988.1|gamma-glutamyl hydrolase [Arabidopsis PEG
    thaliana]
    1270 76186 7.00E−48 84 ref|NP_172210.1|unknown protein [Arabidopsis thaliana] LL
    1271 76190 7.00E−35 63 ref|NP_565499.1|unknown protein [Arabidopsis thaliana] LL
    1272 77071 1.00E−160 96 ref|NP_565626.1|unknown protein [Arabidopsis thaliana] SP
    1273 76194 3.00E−94 79 ref|NP_565716.1|unknown protein [Arabidopsis thaliana] LN
    1274 78112 1.00E−83 91 ref|NP_181610.1|RNA binding/translation initiation factor CS
    [Arabidopsis thaliana]
    1275 74802 0 80 gb|AAO17183.1|Orf17 [Photorhabdus luminescens] SS
    1276 74851 1.00E−163 100 ref|NP_014366.1|Siw14p [Saccharomyces cerevisiae] CK
    1277 74864 6.00E−61 95 ref|NP_014486.1|Hxt11p [Saccharomyces cerevisiae] CK
    1278 74805 0 97 ref|NP_015359.1|Actin-related protein involved in transcriptional HS
    regulation; subunit of the chromatin remodeling Snf/Swi complex
    [Saccharomyces cerevisiae]
    1279 74842 2.00E−61 65 ref|NP_001044880.1|Os01g0862200 [Oryza sativa (japonica SS PEG
    cultivar-group)]
    1280 78231 0 66 gb|EAY94228.1|hypothetical protein OsI_015461 [Oryza sativa LL
    (indica cultivar-group)]
    1281 74867 1.00E−154 65 gb|EAZ43471.1|hypothetical protein OsJ_026954 [Oryza sativa SS
    (japonica cultivar-group)]
    1282 74820 1.00E−136 48 gb|EAY97430.1|hypothetical protein OsI_018663 [Oryza sativa LN
    (indica cultivar-group)]
    1283 74868 1.00E−101 94 ref|NP_001046499.1|Os02g0265400 [Oryza sativa (japonica PP
    cultivar-group)]
    1284 74809 1.00E−122 80 gb|EAZ13333.1|hypothetical protein OsJ_003158 [Oryza sativa LN
    (japonica cultivar-group)]
    1285 74845 7.00E−43 83 ref|NP_001050930.1|Os03g0685900 [Oryza sativa (japonica CS PP
    cultivar-group)]
    1286 74870 6.00E−91 48 sp|Q5XF85|ATL4J_ARATHRING-H2 finger protein ATL4J LN
    precursor emb|CAB43903.1|putative protein [Arabidopsis
    thaliana]
    1287 74859 1.00E−109 55 gb|ABD32420.1|Zinc finger, RING-type [Medicago truncatula] CS
    1288 74985 3.00E−75 94 ref|NP_001045113.1|Os01g0901800 [Oryza sativa (japonica PEG
    cultivar-group)]
    1289 74950 1.00E−159 75 gb|EAZ00193.1|hypothetical protein OsI_021425 [Oryza sativa LN
    (indica cultivar-group)]
    1290 74962 3.00E−89 91 gb|ABB99414.1|FT-like protein [Hordeum vulgare subsp. vulgare] CS
    1291 74939 5.00E−42 65 ref|NP_563746.1|transcription factor [Arabidopsis thaliana] LL
    1292 74928 1.00E−134 87 ref|NP_001044154.1|Os01g0732200 [Oryza sativa (japonica SP CS
    cultivar-group)]
    1293 74905 0 87 ref|NP_927600.1|glutamine synthetase [Photorhabdus SP
    luminescens subsp. laumondii TTO1]
    1294 74917 0 99 ref|YP_346085.1|Inositol phosphatase/fructose-1,6- CS
    bisphosphatase [Pseudomonas fluorescens PfO-1]
    1295 74989 4.00E−69 89 ref|NP_439999.1|hypothetical protein slr0732 [Synechocystis sp. CS
    PCC 6803]
    1296 74990 1.00E−92 95 ref|NP_441647.1|hypothetical protein slr1160 [Synechocystis sp. LL
    PCC 6803]
    1297 74955 1.00E−110 99 ref|NP_441787.1|hypothetical protein slr1649 [Synechocystis sp. CS PP
    PCC 6803]
    1298 74932 1.00E−123 83 ref|NP_441624.1|hypothetical protein slr1530 [Synechocystis sp. CS
    PCC 6803]
    1299 74944 8.00E−76 99 ref|NP_440928.1|hypothetical protein sll0871 [Synechocystis sp. SS
    PCC 6803]
    1300 74968 6.00E−76 99 ref|NP_441307.1|hypothetical protein sll1979 [Synechocystis sp. CS
    PCC 6803]
    1301 74957 1.00E−161 100 ref|NP_440540.1|hypothetical protein slr1699 [Synechocystis sp. LL
    PCC 6803]
    1302 75374 0 72 ref|NP_001067247.1|Os12g0610500 [Oryza sativa (japonica CK LN
    cultivar-group)]
    1303 75386 1.00E−147 74 emb|CAH67158.1|H0717B12.5 [Oryza sativa (indica cultivar- CS
    group)]
    1304 77807 0 85 ref|NP_001044268.1|Os01g0752700 [Oryza sativa (japonica SP
    cultivar-group)]
    1305 75388 0 76 gb|EAZ29806.1|hypothetical protein OsJ_013289 [Oryza sativa SS
    (japonica cultivar-group)]
    1306 75365 1.00E−82 81 ref|NP_001057701.1|Os06g0498800 [Oryza sativa (japonica DS LL LN
    cultivar-group)]
    1307 75377 3.00E−81 77 gb|EAZ24403.1|hypothetical protein OsJ_007886 [Oryza sativa CK
    (japonica cultivar-group)]
    1308 75354 8.00E−77 82 ref|NP_001062977.1|Os09g0360400 [Oryza sativa (japonica LL
    cultivar-group)]
    1309 75331 1.00E−108 84 ref|NP_001061046.1|Os08g0160000 [Oryza sativa (japonica CS
    cultivar-group)]
    1310 75343 1.00E−122 59 ref|NP_001053728.1|Os04g0594500 [Oryza sativa (japonica CS PEG
    cultivar-group)]
    1311 77809 1.00E−27 75 ref|NP_001059709.1|Os07g0498300 [Oryza sativa (japonica LL
    cultivar-group)]
    1312 75332 1.00E−119 72 dbj|BAD19345.1|2 coiled coil domains of eukaryotic origin (31.3 kD)- SP
    like protein [Oryza sativa (japonica cultivar-group)]
    1313 75344 1.00E−146 81 gb|EAZ31718.1|hypothetical protein OsJ_015201 [Oryza sativa PP
    (japonica cultivar-group)]
    1314 75333 2.00E−78 58 gb|EAZ32939.1|hypothetical protein OsJ_016422 [Oryza sativa LL
    (japonica cultivar-group)]
    1315 75393 1.00E−136 79 gb|EAT82167.1|hypothetical protein SNOG_10773 CS
    [Phaeosphaeria nodorum SN15]
    1316 75335 2.00E−63 79 ref|NP_001046956.1|Os02g0515600 [Oryza sativa (japonica CS
    cultivar-group)]
    1317 75462 1.00E−85 90 dbj|BAD36027.1|putative calcineurin B subunit [Oryza sativa CS
    (japonica cultivar-group)]
    1318 75486 1.00E−139 89 ref|NP_001050137.1|Os03g0355800 [Oryza sativa (japonica HS
    cultivar-group)]
    1319 75452 1.00E−61 91 ref|NP_001059781.1|Os07g0516200 [Oryza sativa (japonica CS
    cultivar-group)]
    1320 75465 2.00E−82 29 ref|NP_974032.1|unknown protein [Arabidopsis thaliana] HS
    1321 75489 1.00E−115 73 gb|ABE82748.1|CCT [Medicago truncatula] PP LN
    1322 75442 3.00E−51 51 emb|CAG26903.1|ALY protein [Nicotiana benthamiana] CS
    1323 75466 1.00E−147 84 ref|NP_001052646.1|Os04g0391900 [Oryza sativa (japonica SP CS
    cultivar-group)]
    1324 75479 1.00E−118 87 ref|NP_001044439.1|Os01g0780800 [Oryza sativa (japonica LL
    cultivar-group)]
    1325 75481 7.00E−35 87 gb|ABE89387.1|Zinc finger, Tim10/DDP-type [Medicago CS
    truncatula]
    1326 78233 0 70 gb|ABE91310.1|F20D23.20 protein - Arabidopsis thaliana-related CK CS
    [Medicago truncatula]
    1327 75539 2.00E−51 79 ref|NP_564405.1|LOL1 (LSD ONE LIKE 1) [Arabidopsis thaliana] LL
    1328 11919 0 91 ref|NP_565195.1|AVP2 [Arabidopsis thaliana] PP
    1329 75603 1.00E−162 64 ref|NP_001067658.1|Os11g0265200 [Oryza sativa (japonica LN
    cultivar-group)]
    1330 75663 7.00E−87 70 gb|AAW57783.1|unknown protein [Oryza sativa (japonica cultivar- SS
    group)]
    1331 75616 0 96 ref|NP_194004.1|ATP binding/protein kinase/protein CK
    serine/threonine kinase/protein-tyrosine kinase [Arabidopsis
    thaliana]
    1332 75640 1.00E−153 81 ref|NP_001043765.1|Os01g0658700 [Oryza sativa (japonica LL LN
    cultivar-group)]
    1333 75617 4.00E−40 88 ref|NP_001054686.1|Os05g0154900 [Oryza sativa (japonica SS
    cultivar-group)]
    1334 75653 0 92 ref|NP_568338.2|TOZ (TORMOZEMBRYO DEFECTIVE); LN
    nucleotide binding [Arabidopsis thaliana]
    1335 75665 2.00E−95 77 gb|EAY76352.1|hypothetical protein OsI_004199 [Oryza sativa SS
    (indica cultivar-group)]
    1336 75618 0 85 ref|NP_178381.2|ATP binding/protein kinase/protein HS
    serine/threonine kinase [Arabidopsis thaliana]
    1337 78238 0 95 ref|NP_172998.1|nucleotide binding [Arabidopsis thaliana] DS
    1338 75608 9.00E−72 70 gb|EAZ21409.1|hypothetical protein OsJ_004892 [Oryza sativa LL
    (japonica cultivar-group)]
    1339 75633 6.00E−89 64 ref|NP_001046704.1|Os02g0326000 [Oryza sativa (japonica HS
    cultivar-group)]
    1340 75761 5.00E−50 54 ref|NP_174505.1|unknown protein [Arabidopsis thaliana] PEG
    1341 75785 1.00E−74 53 gb|AAK40310.1|putative methyl-binding domain protein MBD111 CS
    [Zea mays]
    1342 75750 2.00E−47 45 ref|NP_001042916.1|Os01g0328500 [Oryza sativa (japonica PEG
    cultivar-group)]
    1343 75716 0 96 ref|NP_386374.1|PUTATIVE ALDEHYDE DEHYDROGENASE DS LN
    PROTEIN [Sinorhizobium meliloti 1021]
    1344 78129 0 98 ref|NP_182096.1|unknown protein [Arabidopsis thaliana] CK
    1345 77539 1.00E−147 88 ref|NP_187983.1|RNA binding/nucleic acid binding [Arabidopsis SP
    thaliana]
    1346 77540 0 86 ref|NP_188270.1|calmodulin binding [Arabidopsis thaliana] LN
    1347 77542 1.00E−170 92 ref|NP_172882.1|unknown protein [Arabidopsis thaliana] SP
    1348 77543 0 83 ref|NP_189492.1|ATP binding/ATPase/nucleoside- LL
    triphosphatase/nucleotide binding [Arabidopsis thaliana]
    1349 77545 1.00E−141 100 ref|NP_190275.1|unknown protein [Arabidopsis thaliana] SS
    1350 77550 1.00E−163 81 ref|NP_173191.2|calmodulin binding [Arabidopsis thaliana] SP
    1351 77552 1.00E−104 89 emb|CAB78029.1|putative protein [Arabidopsis thaliana] CK
    1352 77556 0 94 ref|NP_173485.1|CYCB2; 3; cyclin-dependent protein kinase PP SS
    regulator [Arabidopsis thaliana]
    1353 77559 1.00E−174 78 ref|NP_196341.1|calmodulin binding [Arabidopsis thaliana] CS
    1354 77957 1.00E−168 97 ref|NP_196955.1|unknown protein [Arabidopsis thaliana] CK
    1355 77565 1.00E−138 100 gb|AAO00857.1|putative protein [Arabidopsis thaliana] DS LN
    1356 78508 0 97 ref|NP_175058.1|ATP binding/ATPase/nucleoside- LL LN
    triphosphatase/nucleotide binding [Arabidopsis thaliana]
    1357 11748 1.00E−105 88 ref|NP_200037.1|MSBP1 [Arabidopsis thaliana] LN
    1358 77920 0 89 ref|NP_177325.2|RNA binding/nucleic acid binding [Arabidopsis CS DS
    thaliana]
    1359 77573 0 81 ref|NP_177411.1|calmodulin binding [Arabidopsis thaliana] LN
    1360 77961 0 94 gb|AAD25685.1|putative membrane transporter [Arabidopsis CS
    thaliana]
    1361 77922 0 100 ref|NP_181978.1|unknown protein [Arabidopsis thaliana] LL
    1362 77337 1.00E−121 93 ref|NP_186871.1|unknown protein [Arabidopsis thaliana] PEG
    1363 77924 4.00E−44 100 ref|NP_566521.1|unknown protein [Arabidopsis thaliana] CK
    1364 77926 1.00E−136 100 ref|NP_193032.1|catalytic [Arabidopsis thaliana] SS
    1365 77964 5.00E−91 88 ref|NP_194100.1|unknown protein [Arabidopsis thaliana] CS
    1366 77346 4.00E−62 100 emb|CAA20568.1|putative protein [Arabidopsis thaliana] CS
    1367 77350 1.00E−51 88 ref|NP_564175.2|unknown protein [Arabidopsis thaliana] CS
    1368 77929 0 84 ref|NP_174029.1|unknown protein [Arabidopsis thaliana] CS
    1369 77586 1.00E−175 100 ref|NP_200984.1|ATIPK2BETA; inositol or phosphatidylinositol PEG
    kinase [Arabidopsis thaliana]
    1370 78510 0 93 ref|NP_201011.1|OXA1; protein translocase [Arabidopsis LN
    thaliana]
    1371 77930 1.00E−170 92 ref|NP_201115.1|S-adenosylmethionine-dependent CS
    methyltransferase [Arabidopsis thaliana]
    1372 77590 1.00E−113 84 ref|NP_172126.1|unknown protein [Arabidopsis thaliana] SS
    1373 77592 0 97 ref|NP_172535.1|unknown protein [Arabidopsis thaliana] PEG
    1374 77361 5.00E−99 84 ref|NP_193650.2|protein binding [Arabidopsis thaliana] CK SS
    1375 77934 0 91 ref|NP_195066.1|unknown protein [Arabidopsis thaliana] PEG
    1376 77367 2.00E−74 66 ref|NP_196973.1|unknown protein [Arabidopsis thaliana] CS
    1377 78121 0 100 emb|CAC01785.1|Carboxylesterase-like protein [Arabidopsis LL
    thaliana]
    1378 77370 7.00E−70 100 ref|NP_197550.1|arsenate reductase (glutaredoxin)/electron CS
    transporter/thiol-disulfide exchange intermediate [Arabidopsis
    thaliana]
    1379 78117 0 96 ref|NP_851079.1|unknown protein [Arabidopsis thaliana] CS
    1380 77950 1.00E−177 100 ref|NP_180191.1|urate oxidase [Arabidopsis thaliana] PP
    1381 78905 1.00E−155 75 ref|NP_565809.1|unknown protein [Arabidopsis thaliana] CK
    1382 75913 2.00E−73 80 ref|NP_001052968.1|Os04g0456700 [Oryza sativa (japonica LL
    cultivar-group)]
    1383 75925 0 80 gb|EAY77273.1|hypothetical protein OsI_005120 [Oryza sativa SP
    (indica cultivar-group)]
    1384 75974 0 100 ref|NP_488061.1|fructose-1,6-bisphosphatase [Nostoc sp. PCC PP
    7120]
    1385 75903 0 95 ref|NP_385577.1|PUTATIVE NITRITE REDUCTASE PROTEIN SS
    [Sinorhizobium meliloti 1021]
    1386 75904 0 97 ref|NP_244182.1|succinate-semialdehyde dehydrogenase CS LN
    [Bacillus halodurans C-125] dbj|BAB07035.1]
    1387 75916 0 100 ref|NP_792120.1|nitrate reductase [Pseudomonas syringae pv. SP SS
    tomato str. DC3000]
    1388 75917 0 98 ref|NP_487197.1|phytochrome A, two-component sensor protein SS
    [Nostoc sp. PCC 7120]
    1389 75942 0 100 ref|NP_485391.1|ferredoxin-sulfite reductase [Nostoc sp. PCC CS
    7120]
    1390 75954 0 100 ref|NP_662565.1|pyruvate phosphate dikinase [Chlorobium CS
    tepidum TLS] gb|AAM72907.1|
    1391 75943 0 99 ref|NP_442685.1|glutamate dehydrogenase (NADP+) CS PEG
    [Synechocystis sp. PCC 6803]
    1392 75967 0 96 ref|ZP_00768095.1|Aldehyde dehydrogenase [Chloroflexus CK LN
    aurantiacus J-10-fl]
    1393 75932 0 96 ref|ZP_00767023.1|Phosphoglycerate kinase [Chloroflexus CS HS
    aurantiacus J-10-fl]
    1394 75956 0 99 ref|NP_440375.1|glutamate-ammonia ligase [Synechocystis sp. HS
    PCC 6803]
    1395 78135 1.00E−170 85 ref|NP_172800.2|sulfotransferase [Arabidopsis thaliana] LL
    1396 78612 0 75 ref|NP_188602.1|unknown protein [Arabidopsis thaliana] DS
    1397 77969 0 90 ref|NP_188797.1|unknown protein [Arabidopsis thaliana] PP
    1398 78136 0 93 ref|NP_171739.1|unknown protein [Arabidopsis thaliana] CS
    1399 77627 6.00E−69 100 ref|NP_190190.1|structural constituent of ribosome [Arabidopsis SS
    thaliana]
    1400 78142 4.00E−43 58 ref|NP_192985.1|PEARLI 1 1; lipid binding [Arabidopsis thaliana] LN
    1401 77973 1.00E−103 92 emb|CAB36513.1|putative protein [Arabidopsis thaliana] LL
    1402 78141 0 100 ref|NP_564112.1|pseudouridylate synthase/tRNA-pseudouridine PEG
    synthase [Arabidopsis thaliana]
    1403 78963 1.00E−102 100 ref|NP_195300.1|unknown protein [Arabidopsis thaliana] LN
    1404 78153 0 92 emb|CAB93721.1|hypothetical protein [Arabidopsis thaliana] CS
    1405 78156 1.00E−160 83 ref|NP_564205.1|unknown protein [Arabidopsis thaliana] LL
    1406 11807 0 83 ref|NP_181291.1|ASP1 (PDE1 SUPPRESSOR 1); DNA binding LN
    [Arabidopsis thaliana]
    1407 78528 0 90 ref|NP_177234.1|unknown protein [Arabidopsis thaliana] LN
    1408 78530 0 100 ref|NP_177212.2|unknown protein [Arabidopsis thaliana] CK
    1409 78618 0 91 ref|NP_565086.1|unknown protein [Arabidopsis thaliana] LL
    1410 78919 0 95 gb|AAG52386.1|AC011765_38unknown protein; 120049-117988 PP
    [Arabidopsis thaliana]
    1411 77974 1.00E−174 86 gb|AAF68123.1|AC010793_18F20B17.8 [Arabidopsis thaliana] CK
    1412 77630 7.00E−69 100 ref|NP_172256.1|RPS15A (RIBOSOMAL PROTEIN S15A); PP
    structural constituent of ribosome [Arabidopsis thaliana]
    1413 78921 0 95 ref|NP_565307.1|inositol or phosphatidylinositol kinase/ LN
    phosphotransferase, alcohol group as acceptor [Arabidopsis
    thaliana]
    1414 78620 0 100 gb|AAD03575.1|unknown protein [Arabidopsis thaliana] DS
    1415 77975 4.00E−40 100 ref|NP_179905.1|zinc ion binding [Arabidopsis thaliana] CS
    1416 78536 0 95 ref|NP_180034.1|sarcosine oxidase [Arabidopsis thaliana] CS
    1417 78537 1.00E−179 79 ref|NP_180187.1|calmodulin binding [Arabidopsis thaliana] PEG
    1418 78540 0 100 ref|NP_565908.1|amino acid binding [Arabidopsis thaliana] SS LL
    1419 77993 3.00E−86 100 gb|AAF02163.1|AC009853_23unknown protein [Arabidopsis PEG
    thaliana]
    1420 78924 0 95 ref|NP_188597.1|catalytic/iron ion binding [Arabidopsis thaliana] LL
    1421 78009 5.00E−63 79 ref|NP_188798.2|unknown protein [Arabidopsis thaliana] LL
    1422 78014 1.00E−136 88 ref|NP_189478.2|unknown protein [Arabidopsis thaliana] CS
    1423 78015 1.00E−165 96 ref|NP_190352.1|DNA binding [Arabidopsis thaliana] CS
    1424 78018 1.00E−132 100 ref|NP_563661.1|unknown protein [Arabidopsis thaliana] PEG
    1425 78021 1.00E−108 93 ref|NP_173266.1|hydrolase [Arabidopsis thaliana] CK
    1426 78158 5.00E−90 87 emb|CAA16775.1|hypothetical protein [Arabidopsis thaliana] CK
    1427 78026 1.00E−154 93 ref|NP_564109.1|oxidoreductase, acting on paired donors, with LL
    incorporation or reduction of molecular oxygen, 2-oxoglutarate as
    one donor, and incorporation of one atom each of oxygen into
    both donors [Arabidopsis thaliana]
    1428 78028 1.00E−102 80 ref|NP_564130.1|unknown protein [Arabidopsis thaliana] CS
    gb|ABD19644.1|
    1429 78032 5.00E−78 91 gb|ABK28138.1|unknown [Arabidopsis thaliana] PEG
    1430 78388 2.00E−68 100 ref|NP_171877.1|unknown protein [Arabidopsis thaliana] LL
    1431 78044 1.00E−156 94 gb|AAF99798.1|AC012463_15T2E6.19 [Arabidopsis thaliana] LL
    1432 78047 5.00E−78 88 ref|NP_175487.1|unknown protein [Arabidopsis thaliana] CS
    1433 78055 1.00E−167 95 ref|NP_176410.1|unknown protein [Arabidopsis thaliana] SS
    1434 78057 1.00E−168 100 ref|NP_176835.1|ubiquitin-protein ligase/zinc ion binding CK
    [Arabidopsis thaliana]
    1435 78059 1.00E−167 90 ref|NP_172124.2|iron ion binding/oxidoreductase/stearoyl-CoA CS
    9-desaturase [Arabidopsis thaliana]
    1436 78553 3.00E−77 92 ref|NP_176998.1|unknown protein [Arabidopsis thaliana] SS
    1437 78163 1.00E−108 80 gb|AAG52601.1|AC016447_10hypothetical protein; 95246-97368 LN
    [Arabidopsis thaliana]
    1438 78060 1.00E−118 100 gb|AAD55282.1|AC008263_13ESTs gb|T04387, gb|R84022 and DS PEG
    gb|T42239 come from this gene. [Arabidopsis thaliana]
    1439 78062 1.00E−173 100 ref|NP_177653.1|transporter [Arabidopsis thaliana] CS PP
    1440 78065 1.00E−113 100 gb|AAG52095.1|AC012680_6unknown protein; 48924-49705 CS LL
    [Arabidopsis thaliana]
    1441 78590 4.00E−63 100 ref|NP_565623.1|plastoquinol-plastocyanin reductase LL
    [Arabidopsis thaliana]
    1442 78177 2.00E−70 72 ref|NP_180909.2|unknown protein [Arabidopsis thaliana] DS
    1443 78952 1.00E−107 95 ref|NP_565887.1|unknown protein [Arabidopsis thaliana] LL
    1444 78559 1.00E−155 89 ref|NP_973636.1|unknown protein [Arabidopsis thaliana] LN
    1445 78169 1.00E−151 100 gb|AAF01548.1|AC009325_18unknown protein [Arabidopsis PP
    thaliana]
    1446 78178 1.00E−157 100 ref|NP_187462.1|unknown protein [Arabidopsis thaliana] CS
    1447 78932 0 75 emb|CAB80914.1|hypothetical protein [Arabidopsis thaliana] CK
    1448 78185 2.00E−87 100 ref|NP_196768.1|unknown protein [Arabidopsis thaliana] PEG
    1449 78186 1.00E−99 92 ref|NP_199091.2|unknown protein [Arabidopsis thaliana] CS
    1450 78572 0 96 ref|NP_171850.1|unknown protein [Arabidopsis thaliana] LL
    1451 78631 1.00E−98 91 gb|AAD10675.1|Similar to human BC-2 protein, [Arabidopsis LL
    thaliana]
    1452 12425 0 93 gb|AAD39650.1|AC007591_15Similar to gb|Z70524 PDR5-like LN
    ABC transporter from Spirodela polyrrhiza and is a member of the
    PF|00005 ABC transporter family. ESTs gb|N97039 and
    gb|T43169 come from this gene. [Arabidopsis thaliana]
    1453 78938 0 95 ref|NP_175579.1|4CL1 (4-COUMARATE:COA LIGASE 1); 4- PP
    coumarate-CoA ligase [Arabidopsis thaliana]
    1454 78961 1.00E−127 84 ref|NP_564988.1|unknown protein [Arabidopsis thaliana] LN
    1455 78584 1.00E−117 75 ref|NP_178114.1|unknown protein [Arabidopsis thaliana] PP
    1456 78589 1.00E−106 90 ref|NP_180437.2|unknown protein [Arabidopsis thaliana] CS
    1457 78252 0 61 ref|NP_001043638.1|Os01g0628900 [Oryza sativa (japonica LN
    cultivar-group)]
    1458 76314 1.00E−134 76 gb|AAR01658.1|putative inositol polyphosphate 5-phosphatase CK
    [Oryza sativa (japonica cultivar-group)]
    1459 76326 0 78 ref|NP_001048842.1|Os03g0128700 [Oryza sativa (japonica CK
    cultivar-group)]
    1460 76362 1.00E−47 80 gb|AAR87161.1|hypothetical protein [Oryza sativa (japonica PEG
    cultivar-group)]
    1461 76340 7.00E−64 92 ref|NP_010440.1|RNA polymerase I subunit A14 [Saccharomyces LN
    cerevisiae]
    1462 76377 0 98 ref|NP_199440.1|ATP binding/DNA binding/DNA-dependent CK
    ATPase/nucleoside-triphosphatase/nucleotide binding
    [Arabidopsis thaliana]
    1463 76319 0 93 ref|NP_850426.1|kinase [Arabidopsis thaliana] LL LN
    1464 76343 0 90 ref|NP_173578.2|ATP binding/kinase/protein kinase/protein LN
    serine/threonine kinase/protein-tyrosine kinase [Arabidopsis
    thaliana]
    1465 76320 1.00E−109 84 ref|NP_001063406.1|Os09g0463600 [Oryza sativa (japonica LL
    cultivar-group)]
    1466 76380 0 76 ref|NP_001044432.1|Os01g0779300 [Oryza sativa (japonica LN
    cultivar-group)]
    1467 77831 0 80 gb|ABA91110.1|leucine-rich repeat family protein, putative, SS
    expressed [Oryza sativa (japonica cultivar-group)]
    1468 76334 8.00E−21 56 ref|NP_190188.1|RNA binding/nucleic acid binding [Arabidopsis LN
    thaliana]
    1469 76382 0 78 emb|CAH66974.1|H0714H04.1 [Oryza sativa (indica cultivar- LN
    group)]
    1470 76838 3.00E−98 81 gb|EAY84304.1|hypothetical protein OsI_005537 [Oryza sativa LL LN
    (indica cultivar-group)]
    1471 77841 1.00E−102 85 ref|NP_001067006.1|Os12g0557400 [Oryza sativa (japonica LL
    cultivar-group)]
    1472 77838 1.00E−134 86 ref|NP_001043004.1|Os01g0356500 [Oryza sativa (japonica SS
    cultivar-group)]
    1473 76865 2.00E−79 91 ref|NP_001060126.1|Os07g0585800 [Oryza sativa (japonica SP
    cultivar-group)]
    1474 77834 1.00E−166 89 ref|NP_001043134.1|Os01g0501800 [Oryza sativa (japonica PEG
    cultivar-group)]
    1475 76823 4.00E−46 100 gb|EAY97498.1|hypothetical protein OsI_018731 [Oryza sativa CS
    (indica cultivar-group)]
    1476 76836 1.00E−46 65 ref|NP_001049532.1|Os03g0244000 [Oryza sativa (japonica PP
    cultivar-group)]
    1477 14133 0 89 pir||G71435hypothetical protein - Arabidopsis thaliana LN
    1478 76927 5.00E−58 74 gb|EAY75504.1|hypothetical protein OsI_003351 [Oryza sativa LL
    (indica cultivar-group)]
    1479 76963 1.00E−107 90 gb|EAY84610.1|hypothetical protein OsI_005843 [Oryza sativa LN
    (indica cultivar-group)]
    1480 76975 3.00E−32 62 ref|NP_001055878.1|Os05g0486200 [Oryza sativa (japonica SS
    cultivar-group)]
    1481 76988 4.00E−44 81 ref|NP_001053850.1|Os04g0612900 [Oryza sativa (japonica DS
    cultivar-group)] dbj|BAF15764.1|
    1482 76953 7.00E−43 75 sp|Q07764|HVA22_HORVUProtein HVA22 gb|AAA16094.1|A22 CS
    1483 76965 3.00E−89 75 gb|EAZ28929.1|hypothetical protein OsJ_012412 [Oryza sativa SP
    (japonica cultivar-group)]
    1484 77161 1.00E−123 77 emb|CAH66750.1|H0409D10.8 [Oryza sativa (indica cultivar- CS
    group)
    1485 77852 0 87 ref|NP_001064303.1|Os10g0203000 [Oryza sativa (japonica CK
    cultivar-group)]
    1486 77151 0 91 ref|NP_001050897.1|Os03g0679700 [Oryza sativa (japonica SS
    cultivar-group)]
    1487 77116 1.00E−133 84 gb|EAY87341.1|hypothetical protein OsI_008574 [Oryza sativa SP
    (indica cultivar-group)]
    1488 77105 0 81 gb|EAZ26357.1|hypothetical protein OsJ_009840 [Oryza sativa CK PP
    (japonica cultivar-group)]
    1489 77129 0 73 dbj|BAD19332.1|putative eukaryotic translation initiation factor 2A CS
    [Oryza sativa (japonica cultivar-group)]
    1490 77154 0 98 ref|NP_001056944.1|Os06g0173100 [Oryza sativa (japonica PEG
    cultivar-group)]
    1491 77190 0 100 ref|NP_417002.1|bifunctional GMP synthase/glutamine LL
    amidotransferase protein [Escherichia coli K12]
    1492 77107 0 100 ref|NP_486886.1|bifunctional GMP synthase/glutamine SP CS
    amidotransferase protein [Nostoc sp. PCC 7120]
    1493 77167 1.00E−141 92 gb|AAZ20768.1|branchy [Setaria italica] PP
    1494 77144 0 100 ref|NP_416789.1|NADH:ubiquinone oxidoreductase, chain C, D CK
    [Escherichia coli K12]
    1495 77156 1.00E−132 100 ref|NP_443063.1|bifunctional phosphoribosyl-AMP CS
    cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein
    [Synechocystis sp. PCC 6803]
    1496 77168 0 83 ref|NP_001047841.1|Os02g0700600 [Oryza sativa (japonica SP
    cultivar-group)]
    1497 77192 7.00E−77 84 dbj|BAD27669.1|putative actin related protein 2/3 complex, 21 kDa PEG
    subunit [Oryza sativa (japonica cultivar-group)]
    1498 77181 8.00E−29 84 ref|NP_001049737.1|Os03g0280400 [Oryza sativa (japonica LL
    cultivar-group)]
    1499 77193 1.00E−111 87 ref|NP_001049175.1|Os03g0182700 [Oryza sativa (japonica PP PEG
    cultivar-group)]
    1500 77147 1.00E−124 64 emb|CAE04316.1|OSJNBb0016D16.7 [Oryza sativa (japonica DS LL
    cultivar-group)]
    1501 77853 0 91 ref|NP_418588.1|predicted carbohydrate kinase [Escherichia coli LN
    K12]
    1502 77854 4.00E−68 86 ref|NP_001042156.1|Os01g0173000 [Oryza sativa (japonica SS
    cultivar-group)]
    1503 77287 1.00E−46 63 ref|NP_001054446.1|Os05g0111200 [Oryza sativa (japonica CS LL
    cultivar-group)]
    1504 77276 2.00E−73 66 ref|NP_001045229.1|Os01g0921600 [Oryza sativa (japonica LN
    cultivar-group)]
    1505 77229 1.00E−53 90 gb|AAL67582.1|AC018929_4unknown protein [Oryza sativa] CS SS
    1506 77241 1.00E−159 73 ref|NP_001045995.1|Os02g0165100 [Oryza sativa (japonica SS
    cultivar-group)]
    1507 77265 1.00E−115 60 gb|EAZ04741.1|hypothetical protein OsI_025973 [Oryza sativa LN
    (indica cultivar-group)]
    1508 77233 1.00E−113 96 ref|NP_001043339.1|Os01g0559000 [Oryza sativa (japonica CS
    cultivar-group)]
    1509 77293 1.00E−102 81 ref|NP_001056330.1|Os05g0564100 [Oryza sativa (japonica PEG
    cultivar-group)]
    1510 77473 0 75 ref|NP_001067661.1|Os11g0265600 [Oryza sativa (japonica CK
    cultivar-group)]
    1511 76402 0 95 ref|NP_199899.1|ATP binding/protein kinase/protein CK PEG
    serine/threonine kinase/protein-tyrosine kinase [Arabidopsis
    thaliana]
    1512 77428 0 86 dbj|BAC07390.1|putative NAD synthetase [Oryza sativa (japonica SS
    cultivar-group)]
    1513 77429 3.00E−93 73 ref|NP_001044830.1|Os01g0853000 [Oryza sativa (japonica CS
    cultivar-group)]
    1514 78277 0 95 ref|NP_192815.1|ATOPT7; oligopeptide transporter [Arabidopsis DS
    thaliana]
    1515 11935 0 97 ref|NP_188434.2|nucleotide binding [Arabidopsis thaliana] SP
    1516 78259 0 93 ref|NP_190717.1|carbohydrate transporter/nucleoside LN
    transporter/sugar porter [Arabidopsis thaliana]
    1517 12276 0 87 ref|NP_199691.1|protein binding/signal transducer [Arabidopsis CS
    thaliana]
    1518 12365 3.00E−66 100 ref|NP_181620.1|FL3-27; cysteine protease inhibitor CK
    [Arabidopsis thaliana]
    • Trait Enhancement Screens
  • DS-Enhancement of Drought Tolerance Identified by a Soil Drought Stress Tolerance Screen:
  • Drought or water deficit conditions impose mainly osmotic stress on plants. Plants are particularly vulnerable to drought during the flowering stage. The drought condition in the screening process disclosed in Example 1B started from the flowering time and was sustained to the end of harvesting. The present invention provides recombinant DNA that can improve the plant survival rate under such sustained drought condition. Exemplary recombinant DNA for conferring such drought tolerance are identified as such in Table 3. Such recombinant DNA may find particular use in generating transgenic plants that are tolerant to the drought condition imposed during flowering time and in other stages of the plant life cycle. As demonstrated from the model plant screen, in some embodiments of transgenic plants with trait-improving recombinant DNA grown under such sustained drought condition can also have increased total seed weight per plant in addition to the increased survival rate within a transgenic population, providing a higher yield potential as compared to control plants.
  • PEG-Enhancement of Drought Tolerance Identified by PEG Induced Osmotic Stress Tolerance Screen:
  • Various drought levels can be artificially induced by using various concentrations of polyethylene glycol (PEG) to produce different osmotic potentials (Pilon-Smits e.g., (1995) Plant Physiol. 107:125-130). Several physiological characteristics have been reported as being reliable indications for selection of plants possessing drought tolerance. These characteristics include the rate of seed germination and seedling growth. The traits can be assayed relatively easily by measuring the growth rate of seedling in PEG solution. Thus, a PEG-induced osmotic stress tolerance screen is a useful surrogate for drought tolerance screen. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in the PEG-induced osmotic stress tolerance screen can survive better drought conditions providing a higher yield potential as compared to control plants.
  • SS-Enhancement of Drought Tolerance Identified by High Salinity Stress Tolerance Screen:
  • Three different factors are responsible for salt damages: (1) osmotic effects, (2) disturbances in the mineralization process, and (3) toxic effects caused by the salt ions, e.g., inactivation of enzymes. While the first factor of salt stress results in the wilting of the plants that is similar to drought effect, the ionic aspect of salt stress is clearly distinct from drought. The present invention provides genes that help plants maintain biomass, root growth, and/or plant development in high salinity conditions, which are identified as such in Table 3. Since osmotic effect is one of the major components of salt stress, which is common to the drought stress, trait-improving recombinant DNA identified in a high salinity stress tolerance screen can also provide transgenic crops with enhanced drought tolerance. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a high salinity stress tolerance screen can survive better drought conditions and/or high salinity conditions providing a higher yield potential as compared to to control plants.
  • HS-Enhancement of Drought Tolerance Identified by Heat Stress Tolerance Screen:
  • Heat and drought stress often occur simultaneously, limiting plant growth. Heat stress can cause the reduction in photosynthesis rate, inhibition of leaf growth and osmotic potential in plants. Thus, genes identified by the present invention as heat stress tolerance conferring genes may also impart enhanced drought tolerance to plants. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a heat stress tolerance screen can survive better heat stress conditions and/or drought conditions providing a higher yield potential as compared to control plants.
  • CK and CS-Enhancement of Tolerance to Cold Stress:
  • Low temperature may immediately result in mechanical constraints, changes in activities of macromolecules, and reduced osmotic potential. In the present invention, two screening conditions, i.e., cold shock tolerance screen (CK) and cold germination tolerance screen (CS), were set up to look for transgenic plants that display visual growth advantage at lower temperature. In cold germination tolerance screen, the transgenic Arabidopsis plants were exposed to a constant temperature of 8° C. from planting until day 28 post plating. The trait-improving recombinant DNA identified by such screen are particular useful for the production of transgenic plant that can germinate more robustly in a cold temperature as compared to the wild type plants. In cold shock tolerance screen, the transgenic plants were first grown under the normal growth temperature of 22° C. until day 8 post plating, and subsequently were placed under 8° C. until day 28 post plating. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a cold shock stress tolerance screen and/or a cold germination stress tolerance screen can survive better cold conditions providing a higher yield potential as compared to control plants.
  • Enhancement of Tolerance to Multiple Stresses:
  • Different kinds of stresses often lead to identical or similar reaction in the plants. Genes that are activated or inactivated as a reaction to stress can either act directly in a way the genetic product reduces a specific stress, or they can act indirectly by activating other specific stress genes. By manipulating the activity of such regulatory genes, i.e., multiple stress tolerance genes, the plant can be enabled to react to different kinds of stresses. For examples, PEP SEQ ID NO: 892 can be used to enhance both salt stress tolerance and cold stress tolerance in plants. Of particular interest, plants transformed with PEP SEQ ID NO: 835 can resist heat stress, salt stress and cold stress. Plants transformed with PEP SEQ ID NO: 835 can also improve growth in early stage and under osmotic stress. In addition to these multiple stress tolerance genes, the stress tolerance conferring genes provided by the present invention may be used in combinations to generate transgenic plants that can resist multiple stress conditions.
  • PP-Enhancement of Early Plant Growth and Development:
  • It has been known in the art that to minimize the impact of disease on crop profitability, it is important to start the season with healthy and vigorous plants. This means avoiding seed and seedling diseases, leading to increased nutrient uptake and increased yield potential. Traditionally early planting and applying fertilizer are the methods used for promoting early seedling vigor. In early development stage, plant embryos establish only the basic root-shoot axis, a cotyledon storage organ(s), and stem cell populations, called the root and shoot apical meristems, that continuously generate new organs throughout post-embryonic development. “Early growth and development” used herein encompasses the stages of seed imbibition through the early vegetative phase. The present invention provides genes that are useful to produce transgenic plants that have advantages in one or more processes including, but not limited to, germination, seedling vigor, root growth and root morphology under non-stressed conditions. The transgenic plants starting from a more robust seedling are less susceptible to the fungal and bacterial pathogens that attach germinating seeds and seedling. Furthermore, seedlings with advantage in root growth are more resistant to drought stress due to extensive and deeper root architecture. Therefore, it can be recognized by those skilled in the art that genes conferring the growth advantage in early stages to plants may also be used to generate transgenic plants that are more resistant to various stress conditions due to enhanced early plant development. The present invention provides such exemplary, recombinant DNA that confer both the stress tolerance and growth advantages to plants, identified as such in Table 3, e.g. PEP SEQ ID NO: 799 which can improve the plant early growth and development, and impart heat and cold tolerance to plants. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in the early plant development screen can grow better under non-stress conditions and/or stress conditions providing a higher yield potential as compared to control plants.
  • SP-Enhancement of Late Plant Growth and Development:
  • “Late growth and development” used herein encompasses the stages of leaf development, flower production, and seed maturity. In certain embodiments, transgenic plants produced using genes that confer growth advantages to plants provided by the present invention, identified as such in Table 3, exhibit at least one phenotypic characteristics including, but not limited to, increased rosette radius, increased rosette dry weight, seed dry weight, silique dry weight, and silique length. On one hand, the rosette radius and rosette dry weight are used as the indexes of photosynthesis capacity, and thereby plant source strength and yield potential of a plant. On the other hand, the seed dry weight, silique dry weight and silique length are used as the indexes for plant sink strength, which are considered as the direct determinants of yield. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in the late development screen can grow better and/or have enhanced development during leaf development and seed maturation providing a higher yield potential as compared to control plants.
  • LL-Enhancement of Tolerance to Shade Stress Identified in a Low Light Screen:
  • The effects of light on plant development are especially prominent at the seedling stage. Under normal light conditions with unobstructed direct light, a plant seeding develops according to a characteristic photomorphogenic pattern, in which plants have open and expanded cotyledons and short hypocotyls. Then the plant's energy is devoted to cotyledon and leaf development while longitudinal extension growth is minimized. Under low light condition where light quality and intensity are reduced by shading, obstruction or high population density, a seedling displays a shade-avoidance pattern, in which the seedling displays a reduced cotyledon expansion, and hypocotyls extension is greatly increased. As the result, a plant under low light condition increases significantly its stem length at the expanse of leaf, seed or fruit and storage organ development, thereby adversely affecting of yield. The present invention provides recombinant DNA that enable plants to have an attenuated shade avoidance response so that the source of plant can be contributed to reproductive growth efficiently, resulting higher yield as compared to the wild type plants. As demonstrated from the model plant screen, embodiments of transgenic plants with trait-improving recombinant DNA identified in a shade stress tolerance screen can have attenuated shade response under shade conditions providing a higher yield potential as compared to control plants. The transgenic plants generated by the present invention may be suitable for a higher density planting, thereby resulting increased yield per unit area.
  • LN-Enhancement of Tolerance to Low Nitrogen Availability Stress
  • Nitrogen is a key factor in plant growth and crop yield. The metabolism, growth and development of plants are profoundly affected by their nitrogen supply. Restricted nitrogen supply alters shoot to root ratio, root development, activity of enzymes of primary metabolism and the rate of senescence (death) of older leaves. All field crops have a fundamental dependence on inorganic nitrogenous fertilizer. Since fertilizer is rapidly depleted from most soil types, it must be supplied to growing crops two or three times during the growing season. Enhanced nitrogen use efficiency by plants should enable crops cultivated under low nitrogen availability stress condition resulted from low fertilizer input or poor soil quality.
  • According to the present invention, transgenic plants generated using the recombinant nucleotides, which confer enhanced nitrogen use efficiency, identified as such in Table 3, exhibit one or more desirable traits including, but not limited to, increased seedling weight, greener leaves, increased number of rosette leaves, increased or decreased root length. One skilled in the art may recognize that the transgenic plants provided by the present invention with enhanced nitrogen use efficiency may also have altered amino acid or protein compositions, increased yield and/or better seed quality. The transgenic plants of the present invention may be productively cultivated under low nitrogen growth conditions, i.e., nitrogen-poor soils and low nitrogen fertilizer inputs, which would cause the growth of wild type plants to cease or to be so diminished as to make the wild type plants practically useless. The transgenic plants also may be advantageously used to achieve earlier maturing, faster growing, and/or higher yielding crops and/or produce more nutritious foods and animal feedstocks when cultivated using nitrogen non-limiting growth conditions.
  • Stacked Traits:
  • The present invention also encompasses transgenic plants with stacked engineered traits, e.g., a crop having an enhanced phenotype resulting from expression of a trait-improving recombinant DNA, in combination with herbicide and/or pest resistance traits. For example, genes of the current invention can be stacked with other traits of agronomic interest, such as a trait providing herbicide resistance, for example a RoundUp Ready® trait, or insect resistance, such as using a gene from Bacillus thuringensis to provide resistance against lepidopteran, coliopteran, homopteran, hemiopteran, and other insects. Herbicides for which resistance is useful in a plant include glyphosate herbicides, phosphinothricin herbicides, oxynil herbicides, imidazolinone herbicides, dinitroaniline herbicides, pyridine herbicides, sulfonylurea herbicides, bialaphos herbicides, sulfonamide herbicides and gluphosinate herbicides. To illustrate that the production of transgenic plants with herbicide resistance is a capability of those of ordinary skill in the art, reference is made to U.S. patent application publications 2003/0106096A1 and 2002/0112260A1 and U.S. Pat. Nos. 5,034,322; 5,776,760, 6,107,549 and 6,376,754, all of which are incorporated herein by reference. To illustrate that the production of transgenic plants with pest resistance is a capability of those of ordinary skill in the art reference is made to U.S. Pat. Nos. 5,250,515 and 5,880,275 which disclose plants expressing an endotoxin of Bacillus thuringiensis bacteria, to U.S. Pat. No. 6,506,599 which discloses control of invertebrates which feed on transgenic plants which express dsRNA for suppressing a target gene in the invertebrate, to U.S. Pat. No. 5,986,175 which discloses the control of viral pests by transgenic plants which express viral replicase, and to U.S. Patent Application Publication 2003/0150017 A1 which discloses control of pests by a transgenic plant which express a dsRNA targeted to suppressing a gene in the pest, all of which are incorporated herein by reference.
  • Once one recombinant DNA has been identified as conferring an enhanced trait of interest in transgenic Arabidopsis plants, several methods are available for using the sequence of that recombinant DNA and knowledge about the protein it encodes to identify homologs of that sequence from the same plant or different plant species or other organisms, e.g., bacteria and yeast. Thus, in one aspect, the invention provides methods for identifying a homologous gene with a DNA sequence homologous to any of SEQ ID NO: 1 through SEQ ID NO: 759, or a homologous protein with an amino acid sequence homologous to any of SEQ ID NO: 760 through SEQ ID NO: 1518. In another aspect, the present invention provides the protein sequences of identified homologs for a sequence listed; as SEQ ID NO: 1519 through SEQ ID NO: 67778. In yet another aspect, the present invention also includes linking or associating one or more desired traits, or gene function with a homolog sequence provided herein.
  • The trait-improving recombinant DNA and methods of using such trait-improving recombinant DNA for generating transgenic plants with enhanced traits provided by the present invention are not limited to any particular plant species. Indeed, the plants according to the present invention may be of any plant species, i.e., may be monocotyledonous or dicotyledonous. Preferably, they will be agricultural useful plants, i.e., plants cultivated by man for purposes of food production or technical, particularly industrial applications. Of particular interest in the present invention are corn and soybean plants. The recombinant DNA constructs optimized for soybean transformation and recombinant DNA constructs optimized for corn transformation are provided by the present invention. Other plants of interest in the present invention for production of transgenic plants having enhanced traits include, without limitation, cotton, canola, wheat, sunflower, sorghum, alfalfa, barley, millet, rice, tobacco, fruit and vegetable crops, and turfgrass.
  • In certain embodiments, the present invention contemplates to use an orthologous gene in generating the transgenic plants with similarly enhanced traits as the transgenic Arabidopsis counterpart. Enhanced physiological properties in transgenic plants of the present invention may be confirmed in responses to stress conditions, for example in assays using imposed stress conditions to detect enhanced responses to drought stress, nitrogen deficiency, cold growing conditions, or alternatively, under naturally present stress conditions, for example under field conditions. Biomass measures may be made on greenhouse or field grown plants and may include such measurements as plant height, stem diameter, root and shoot dry weights, and, for corn plants, ear length and diameter.
  • Trait data on morphological changes may be collected by visual observation during the process of plant regeneration as well as in regenerated plants transferred to soil. Such trait data includes characteristics such as normal plants, bushy plants, taller plants, thicker stalks, narrow leaves, striped leaves, knotted phenotype, chlorosis, albino, anthocyanin production, or altered tassels, ears or roots. Other enhanced traits may be identified by measurements taken under field conditions, such as days to pollen shed, days to silking, leaf extension rate, chlorophyll content, leaf temperature, stand, seedling vigor, internode length, plant height, leaf number, leaf area, tillering, brace roots, stay green, stalk lodging, root lodging, plant health, barreness/prolificacy, green snap, and pest resistance. In addition, trait characteristics of harvested grain may be confirmed, including number of kernels per row on the ear, number of rows of kernels on the ear, kernel abortion, kernel weight, kernel size, kernel density and physical grain quality.
  • To confirm hybrid yield in transgenic corn plants expressing genes of the present invention, it may be desirable to test hybrids over multiple years at multiple locations in a geographical location where maize is conventionally grown, e.g., in Iowa, Illinois or other locations in the midwestern United States, under “normal” field conditions as well as under stress conditions, e.g., under drought or population density stress.
  • Transgenic plants can be used to provide plant parts according to the invention for regeneration or tissue culture of cells or tissues containing the constructs described herein. Plant parts for these purposes can include leaves, stems, roots, flowers, tissues, epicotyl, meristems, hypocotyls, cotyledons, pollen, ovaries, cells and protoplasts, or any other portion of the plant which can be used to regenerate additional transgenic plants, cells, protoplasts or tissue culture. Seeds of transgenic plants are provided by this invention can be used to propagate more plants containing the trait-improving recombinant DNA constructs of this invention. These descendants are intended to be included in the scope of this invention if they contain a trait-improving recombinant DNA construct of this invention, whether or not these plants are selfed or crossed with different varieties of plants.
  • The various aspects of the invention are illustrated by means of the following examples which are in no way intended to limit the full breath and scope of claims.
    • EXAMPLES Example 1 Identification of Recombinant DNA that Confers Enhanced Trait(s) to Plants A. Plant Expression Constructs for Arabidopsis Transformation
  • Each gene of interest was amplified from a genomic or cDNA library using primers specific to sequences upstream and downstream of the coding region. Transformation vectors were prepared to constitutively transcribe DNA in either sense orientation (for enhanced protein expression) or anti-sense orientation (for endogenous gene suppression) under the control of an enhanced Cauliflower Mosaic Virus 35S promoter (U.S. Pat. No. 5,359,142) directly or indirectly (Moore, e.g., PNAS 95:376-381, 1998; Guyer, e.g., Genetics 149: 633-639, 1998; International patent application NO. PCT/EP98/07577). The transformation vectors also contain a bar gene as a selectable marker for resistance to glufosinate herbicide. The transformation of Arabidopsis plants was carried out using the vacuum infiltration method known in the art (Bethtold, e.g. Methods Mol. Biol. 82:259-66, 1998). Seeds harvested from the plants, named as T1 seeds, were subsequently grown in a glufosinate-containing selective medium to select for plants which were actually transformed and which produced T2 transgenic seed.
    • B. Soil Drought Tolerance Screen
  • This example describes a soil drought tolerance screen to identify Arabidopsis plants transformed with recombinant DNA that wilt less rapidly and/or produce higher seed yield when grown in soil under drought conditions
  • T2 seeds were sown in flats filled with Metro/Mix® 200 (The Scotts® Company, USA). Humidity domes were added to each flat and flats were assigned locations and placed in climate-controlled growth chambers. Plants were grown under a temperature regime of 22° C. at day and 20° C. at night, with a photoperiod of 16 hours and average light intensity of 170 μmol/m2/s. After the first true leaves appeared, humidity domes were removed. The plants were sprayed with glufosinate herbicide and put back in the growth chamber for 3 additional days. Flats were watered for 1 hour the week following the herbicide treatment. Watering was continued every seven days until the flower bud primordia became apparent, at which time plants were watered for the last time.
  • To identify drought tolerant plants, plants were evaluated for wilting response and seed yield. Beginning ten days after the last watering, plants were examined daily until 4 plants/line had wilted. In the next six days, plants were monitored for wilting response. Five drought scores were assigned according to the visual inspection of the phenotypes: 1 for healthy, 2 for dark green, 3 for wilting, 4 severe wilting, and 5 for dead. A score of 3 or higher was considered as wilted.
  • At the end of this assay, seed yield measured as seed weight per plant under the drought condition was characterized for the transgenic plants and their controls and analyzed as a quantitative response according to example 1M.
  • Two approaches were used for statistical analysis on the wilting response. First, the risk score was analyzed for wilting phenotype and treated as a qualitative response according to the example 1L. Alternatively, the survival analysis was carried out in which the proportions of wilted and non-wilted transgenic and control plants were compared over each of the six days under scoring and an overall log rank test was performed to compare the two survival curves using S-PLUS statistical software (S-PLUS 6, Guide to statistics, Insightful, Seattle, Wash., USA). A list of recombinant DNA constructs which improve drought tolerance in transgenic plants is illustrated in Table 4.
  • TABLE 4
    PEP Drought Time to
    SEQ score Seed yield wilting
    ID Construct Nomination Delta Delta Risk score
    NO ID ID Orientation mean P-value mean P-value mean P-value
    968 10359 CGPG430 ANTI-SENSE −0.103 0.104 0.134 0.469 −0.147 1.000
    863 10462 CGPG240 ANTI-SENSE 0.133 0.006 −0.101 0.331 0.306 1.000
    1115 11149 CGPG587 SENSE −0.021 0.741 0.277 0.158 −0.105 0.852
    769 12040 CGPG1092 SENSE 0.025 0.240 0.227 0.258 0.058 1.000
    771 12156 CGPG1136 ANTI-SENSE −0.009 0.068 0.512 0.045 0.154 0.857
    784 12733 CGPG1291 ANTI-SENSE 0.165 0.034 −0.368 0.009 0.209 1.000
    760 12792 CGPG1022 ANTI-SENSE 0.070 0.184 0.223 0.077 0.083 1.000
    786 13504 CGPG1311 SENSE −0.055 0.704 0.109 0.445 −0.042 1.000
    1150 13518 CGPG620 ANTI-SENSE 0.176 0.023 0.026 0.891 0.160 1.000
    807 14271 CGPG1575 ANTI-SENSE 0.163 0.014 −0.144 0.536 −0.186 1.000
    822 14827 CGPG1895 ANTI-SENSE 0.171 0.047 0.001 0.995 0.092 1.000
    845 16007 CGPG2142 ANTI-SENSE −0.234 0.127 0.992 0.006 −0.217 1.000
    827 16182 CGPG1922 SENSE 0.034 0.424 0.171 0.298 0.127 1.000
    854 17003 CGPG2304 SENSE 0.372 0.005 0.083 0.267 0.613 1.000
    923 18408 CGPG3612 SENSE −0.009 0.589 0.494 0.002 0.134 0.941
    900 18644 CGPG3236 SENSE 0.016 0.758 0.072 0.432 0.049 0.920
    832 19133 CGPG1973 SENSE 0.308 0.019 0.410 0.074 0.192 1.000
    885 19166 CGPG2914 SENSE 0.152 0.037 0.370 0.292 0.152 1.000
    896 19256 CGPG3137 SENSE −0.121 0.142 0.168 0.056 −0.087 0.939
    927 19328 CGPG3665 SENSE 0.161 0.027 −0.388 0.337 −0.011 1.000
    921 19623 CGPG3579 SENSE 0.039 0.689 0.232 0.084 0.051 1.000
    966 70632 CGPG4297 SENSE 0.116 0.004 −0.281 0.185 0.080 1.000
    918 71115 CGPG351 SENSE 0.240 0.005 −0.793 0.088 0.257 0.936
    1054 72067 CGPG5262 SENSE 0.194 0.021 −0.633 0.034 0.138 1.000
    1011 72650 CGPG4882 SENSE 0.187 0.032 −1.980 0.088 0.481 1.000
    1098 73088 CGPG5729 SENSE −0.134 0.488 0.027 0.792 0.066 1.000
    982 73214 CGPG4432 SENSE 1.524 0.033 / / 0.484 1.000
    1032 73314 CGPG5100 SENSE 0.117 0.018 −1.005 0.082 0.056 1.000
    1195 73567 CGPG6509 SENSE 0.216 0.159 0.581 0.020 0.067 0.961
    1027 73683 CGPG5062 SENSE 0.275 0.012 −0.547 0.085 0.109 0.946
    819 73986 CGPG1837 SENSE −0.280 0.122 0.214 0.010 −0.152 1.000
    1036 74218 CGPG5159 SENSE 0.241 0.006 −0.057 0.670 0.140 0.785
    800 74775 CGPG1492 SENSE 0.156 0.105 0.231 0.049 0.122 0.804
    1306 75365 CGPG7503 SENSE 0.830 0.001 −3.139 0.047 1.008 1.000
    1343 75716 CGPG7881 SENSE −0.079 0.018 0.040 0.135 0.010 0.852
    1243 75869 CGPG6974 SENSE −0.016 0.708 0.133 0.162 −0.136 0.893
    798 76013 CGPG1445 SENSE 0.414 0.021 −0.269 0.297 0.386 1.000
    806 76049 CGPG1568 SENSE 0.196 0.025 −0.991 0.033 0.221 1.000
    1123 76214 CGPG5930 SENSE −0.069 0.101 0.158 0.001 −0.157 1.000
    1155 76226 CGPG6211 SENSE 0.261 0.019 −1.212 0.007 0.298 1.000
    1160 76436 CGPG6233 SENSE 0.412 0.017 −0.566 0.040 0.316 0.837
    1173 76528 CGPG6336 SENSE 0.732 0.009 −0.069 0.624 0.898 0.833
    1481 76988 CGPG9106 SENSE 0.395 0.021 −0.841 0.026 0.270 1.000
    1500 77147 CGPG9201 SENSE 0.493 0.005 −1.475 0.015 0.997 0.909
    1355 77565 CGPG7996 SENSE 0.778 0.049 −0.185 0.190 0.170 1.000
    891 77909 CGPG3056 SENSE −0.140 0.118 0.093 0.458 −0.220 0.813
    1358 77920 CGPG8023 SENSE −0.221 0.070 0.232 0.313 −0.159 0.947
    1438 78060 CGPG8640 SENSE 0.550 0.008 −2.055 0.013 0.390 0.944
    1442 78177 CGPG8677 SENSE 0.029 0.548 0.496 0.007 0.020 1.000
    1337 78238 CGPG7813 SENSE 0.250 0.020 −0.915 0.029 0.110 1.000
    1514 78277 CGPG9327 SENSE 0.274 0.003 −0.267 0.456 0.064 1.000
    1172 78367 CGPG6334 SENSE 0.169 0.037 −0.691 0.039 0.305 0.941
    1069 78434 CGPG5473 SENSE 0.327 0.018 −2.055 0.112 0.196 1.000
    1396 78612 CGPG8320 SENSE 0.198 0.017 0.374 0.237 −0.020 0.953
    1414 78620 CGPG8471 SENSE 0.248 0.030 −0.127 0.108 0.016 1.000
    960 78665 CGPG4240 SENSE 0.605 0.035 −2.631 0.047 0.376 1.000
    If p < 0.05 and delta or risk score mean >0, the transgenic plants showed statistically significant trait enhancement as compared to the reference (p value, of the delta of a quantitative response or of the risk score of a qualitative response, is the probability that the observed difference between the transgenic plants and the reference occur by chance)
    If p < 0.2 and delta or risk score mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference.
    • C. Heat Stress Tolerance Screen
  • Under high temperatures, Arabidopsis seedlings become chlorotic and root growth is inhibited. This example sets forth the heat stress tolerance screen to identify Arabidopsis plants transformed with the gene of interest that are more resistant to heat stress based on primarily their seedling weight and root growth under high temperature. T2 seeds were plated on 1/2×MS salts, 1/% phytagel, with 10 μg/ml BASTA (7 per plate with 2 control seeds; 9 seeds total per plate). Plates were placed at 4° C. for 3 days to stratify seeds. Plates were then incubated at room temperature for 3 hours and then held vertically for 11 additional days at temperature of 34° C. at day and 20° C. at night. Photoperiod was 16 h. Average light intensity was ˜140 μmol/m2/s. After 14 days of growth, plants were scored for glufosinate resistance, root length, final growth stage, visual color, and seedling fresh weight. A photograph of the whole plate was taken on day 14.
  • The seedling weight and root length were analyzed as quantitative responses according to example 1M. The final grow stage at day 14 was scored as success if 50% of the plants had reached 3 rosette leaves and size of leaves are greater than 1 mm (Boyes, e.g. (2001) The Plant Cell 13, 1499-1510). The growth stage data was analyzed as a qualitative response according to example 1L. A list of recombinant DNA constructs that improve heat tolerance in transgenic plants illustrated in Table 5.
  • TABLE 5
    Root Growth Seedling
    PEP length stage weight
    SEQ at day 14 at day 14 at day 14
    ID Construct Nomination Delta Risk score Delta
    NO ID ID Orientation mean P-value mean P-value mean P-value
    763 10174 CGPG105 ANTI-SENSE 0.263 0.011 −0.010 0.930 1.029 0.003
    778 14803 CGPG1192 SENSE 0.202 0.011 1.151 0.391 0.828 0.015
    835 14909 CGPG2005 ANTI-SENSE 0.394 0.050 0.093 0.553 1.084 0.044
    847 17310 CGPG2190 SENSE 0.140 0.039 1.726 0.160 1.100 0.027
    920 19619 CGPG3575 SENSE 0.342 0.020 1.537 0.108 1.277 0.000
    1018 70822 CGPG499 SENSE 0.402 0.015 0.644 0.180 1.386 0.005
    1080 73173 CGPG5596 SENSE 0.686 0.003 1.254 0.054 1.482 0.002
    1180 73416 CGPG6388 SENSE 0.184 0.013 0.640 0.454 0.830 0.008
    1147 74658 CGPG6174 SENSE 0.298 0.036 1.390 0.166 0.933 0.008
    1278 74805 CGPG7327 SENSE 0.441 0.017 0.071 0.080 1.258 0.019
    839 75221 CGPG2065 SENSE 0.345 0.049 0.686 0.402 1.294 0.005
    1320 75465 CGPG7599 SENSE 0.160 0.030 0.000 0.998 1.010 0.007
    1318 75486 CGPG7577 SENSE 0.361 0.024 −0.046 0.172 1.009 0.008
    1336 75618 CGPG7801 SENSE 0.364 0.038 0.136 0.664 1.246 0.006
    1339 75633 CGPG7826 SENSE 0.325 0.010 0.100 0.609 0.948 0.024
    1245 75876 CGPG6996 SENSE 0.186 0.041 −0.162 0.005 0.834 0.032
    1393 75932 CGPG8269 SENSE 0.379 0.000 0.377 0.333 0.836 0.008
    1394 75956 CGPG8271 SENSE 0.265 0.047 0.751 0.248 1.071 0.011
    806 76049 CGPG1568 SENSE 0.422 0.035 0.795 0.179 1.058 0.088
    1125 76118 CGPG5958 SENSE 0.248 0.032 0.316 0.503 0.921 0.002
    1177 77725 CGPG6364 SENSE 0.181 0.029 0.469 0.266 1.059 0.005
    1003 78207 CGPG4713 SENSE 0.330 0.039 0.578 0.488 1.079 0.006
    1251 78377 CGPG7075 SENSE 0.519 0.004 0.051 0.442 0.908 0.004
    962 78970 CGPG4248 SENSE 0.251 0.017 1.680 0.056 1.044 0.007
    If p < 0.05 and delta or risk score mean >0, the transgenic plants showed statistically significant trait enhancement as compared to the reference.
    If p < 0.2 and delta or risk score mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference.
    • D. Salt Stress Tolerance Screen
  • This example sets forth the high salinity stress screen to identify Arabidopsis plants transformed with the gene of interest that are tolerant to high levels of salt based on their rate of development, root growth and chlorophyll accumulation under high salt conditions.
  • T2 seeds were plated on glufosinate selection plates containing 90 mM NaCl and grown under standard light and temperature conditions. All seedlings used in the experiment were grown at a temperature of 22° C. at day and 20° C. at night, a 16-hour photoperiod, an average light intensity of approximately 120 umol/m2. On day 11, plants were measured for primary root length. After 3 more days of growth (day 14), plants were scored for transgenic status, primary root length, growth stage, visual color, and the seedlings were pooled for fresh weight measurement. A photograph of the whole plate was also taken on day 14.
  • The seedling weight and root length were analyzed as quantitative responses according to example 1M. The final growth stage at day 14 was scored as success if 50% of the plants reached 3 rosette leaves and size of leaves are greater than 1 mm (Boyes, D. C., et al., (2001), The Plant Cell 13, 1499/1510). The growth stage data was analyzed as a qualitative response according to example 1L. A list of recombinant DNA constructs that improve high salinity tolerance in transgenic plants illustrated in Table 6.
  • TABLE 6
    Root Root Growth Seedling
    length length stage weight
    PEP at day 11 at day 14 at day 14 at day 14
    SEQ Construct Delta Delta Delta Delta
    ID ID mean P-value mean P-value mean P-value mean P-value
    799 10192 0.372 0.009 0.330 0.001 0.915 0.033 0.668 0.005
    772 11853 0.141 0.208 0.082 0.241 / / 0.319 0.025
    792 12766 0.317 0.048 0.253 0.112 / / 0.360 0.006
    1031 12772 0.150 0.111 0.178 0.014 / / 0.223 0.175
    761 13673 0.101 0.216 0.174 0.009 0.134 0.521 0.534 0.002
    813 14341 0.490 0.012 0.487 0.014 2.561 0.007 1.051 0.025
    835 14909 0.406 0.004 0.504 0.001 1.099 0.100 0.802 0.015
    849 15627 0.168 0.123 0.208 0.000 0.735 0.500 0.512 0.089
    796 15806 0.180 0.003 0.122 0.025 / / −0.023 0.780
    838 16553 0.229 0.004 0.243 0.016 0.399 0.157 0.552 0.104
    854 17003 0.214 0.002 0.174 0.006 0.672 0.060 0.383 0.021
    844 17014 0.080 0.200 0.182 0.080 0.912 0.283 0.468 0.022
    870 17813 0.385 0.044 0.428 0.038 2.319 0.112 1.246 0.006
    882 17930 0.330 0.021 0.224 0.102 0.860 0.133 0.414 0.009
    922 18381 0.209 0.200 0.191 0.041 0.521 0.192 0.496 0.301
    919 18406 0.272 0.077 0.351 0.022 1.292 0.106 0.783 0.046
    888 18418 0.203 0.070 0.186 0.014 0.031 0.823 0.086 0.365
    883 18442 0.186 0.152 0.205 0.038 0.341 0.307 0.417 0.072
    894 18874 0.238 0.058 0.182 0.278 0.854 0.044 0.462 0.026
    895 18875 0.299 0.003 0.316 0.009 0.332 0.102 0.569 0.022
    928 19312 0.309 0.066 0.293 0.008 0.549 0.025 0.475 0.024
    892 19656 0.093 0.126 0.198 0.008 0.054 0.698 0.453 0.031
    954 19927 0.454 0.033 0.401 0.018 0.887 0.023 0.499 0.013
    946 19966 0.184 0.210 0.345 0.052 0.088 0.490 0.514 0.038
    860 70123 0.175 0.019 0.119 0.026 0.367 0.171 0.335 0.026
    1138 70243 0.347 0.036 0.386 0.026 0.479 0.331 0.551 0.007
    937 70477 0.123 0.093 0.045 0.570 0.682 0.218 0.278 0.008
    929 70538 0.455 0.003 0.356 0.006 1.166 0.321 0.598 0.005
    963 71250 0.262 0.147 0.299 0.033 0.999 0.124 0.592 0.067
    1050 72037 0.336 0.054 0.356 0.004 0.046 0.770 0.564 0.016
    1071 72713 0.064 0.675 0.204 0.183 0.520 0.383 0.528 0.030
    1093 73009 0.383 0.028 0.323 0.030 2.526 0.076 0.749 0.013
    1102 73042 0.278 0.087 0.216 0.031 0.703 0.011 0.360 0.158
    1097 73158 0.210 0.259 0.251 0.101 0.655 0.229 0.482 0.009
    1086 73163 0.327 0.016 0.422 0.028 1.516 0.357 0.666 0.034
    789 73333 0.024 0.728 0.012 0.855 0.380 0.191 0.400 0.032
    1189 73436 0.340 0.106 0.315 0.016 3.045 0.086 0.697 0.055
    1178 73437 0.232 0.100 0.268 0.030 0.239 0.433 0.157 0.592
    1181 73452 −0.026 0.593 0.238 0.029 −0.028 / 0.345 0.274
    1183 73454 −0.072 0.456 0.020 0.863 −0.307 0.041 0.337 0.026
    1070 73932 0.191 0.068 0.254 0.058 2.253 0.125 0.524 0.006
    1081 73979 0.323 0.014 0.241 0.207 1.728 0.066 0.957 0.000
    1213 74172 0.235 0.015 0.261 0.024 0.476 0.513 0.276 0.567
    1214 74184 0.183 0.139 0.193 0.049 −0.143 0.317 0.308 0.305
    899 74233 / / / / / / 0.599 0.029
    1068 74238 0.129 0.171 0.147 0.030 1.234 0.173 0.492 0.047
    1063 74272 0.187 0.339 0.226 0.051 1.278 0.447 0.553 0.040
    1140 74373 0.058 0.684 0.102 0.644 1.245 0.465 0.734 0.049
    1220 74430 0.286 0.054 0.128 0.086 2.820 0.139 0.500 0.001
    1218 74461 0.324 0.001 0.197 0.025 −0.064 0.428 0.457 0.017
    1141 74615 0.245 0.042 0.223 0.045 2.483 0.082 0.600 0.035
    1149 74673 0.083 0.465 0.160 0.052 −0.241 0.465 0.422 0.012
    1175 74677 0.319 0.032 0.317 0.000 2.140 0.155 0.724 0.003
    1113 74738 −0.081 0.388 −0.050 0.733 0.471 0.274 0.310 0.018
    1275 74802 0.256 0.035 0.251 0.027 1.218 0.019 0.481 0.096
    1279 74842 0.091 0.269 0.196 0.001 0.858 0.085 0.410 0.055
    1281 74867 0.195 0.125 0.170 0.041 −0.518 0.560 −0.101 0.439
    1299 74944 / / / / / / 0.499 0.002
    967 75205 0.195 0.114 0.210 0.085 0.941 0.098 0.458 0.010
    1170 75292 −0.056 0.658 −0.086 0.593 1.203 0.180 0.380 0.026
    1305 75388 0.263 0.028 0.305 0.006 1.879 0.037 0.655 0.027
    1333 75617 0.352 0.044 0.366 0.025 0.878 0.179 0.854 0.010
    1330 75663 0.151 0.148 0.147 0.044 / / 0.251 0.102
    1335 75665 0.468 0.009 0.276 0.109 0.302 0.052 0.779 0.001
    1128 75810 0.238 0.058 0.230 0.002 1.794 0.286 0.599 0.006
    1385 75903 0.198 0.104 0.176 0.049 / / 0.171 0.401
    1387 75916 0.318 0.041 0.360 0.049 0.819 0.245 0.677 0.015
    1388 75917 0.391 0.012 0.428 0.006 0.269 0.200 0.861 0.013
    1234 76548 0.237 0.051 0.266 0.014 0.385 0.336 0.680 0.049
    1480 76975 0.216 0.114 0.198 0.001 −0.162 0.362 0.316 0.061
    1486 77151 0.181 0.001 0.235 0.017 0.641 0.099 0.365 0.034
    1505 77229 0.265 0.226 0.338 0.088 1.988 0.005 1.093 0.003
    1506 77241 0.039 0.795 0.038 0.632 0.903 0.388 0.350 0.038
    1374 77361 0.271 0.000 0.232 0.156 0.508 0.273 0.238 0.016
    1512 77428 0.355 0.005 0.429 0.012 1.455 0.381 0.800 0.042
    1255 77528 0.284 0.126 0.254 0.031 0.608 0.368 0.753 0.087
    1349 77545 0.469 0.004 0.324 0.072 0.283 0.300 0.652 0.022
    1352 77556 0.068 0.597 0.017 0.884 1.080 0.379 0.320 0.044
    1372 77590 0.342 0.026 0.250 0.145 2.393 0.019 0.549 0.039
    1399 77627 0.192 0.005 0.146 0.011 −0.147 0.734 0.275 0.025
    1467 77831 0.299 0.087 0.332 0.062 3.081 0.079 0.774 0.006
    1472 77838 0.301 0.041 0.296 0.005 0.121 0.423 1.151 0.258
    1502 77854 0.131 0.183 0.205 0.082 0.341 0.470 0.419 0.036
    1364 77926 0.232 0.030 0.219 0.049 2.642 0.061 0.321 0.089
    1433 78055 0.244 0.007 0.393 0.011 1.371 0.410 0.634 0.024
    1257 78106 0.276 0.017 0.327 0.003 2.062 0.024 0.900 0.001
    830 78355 0.295 0.044 0.309 0.005 1.146 0.284 0.549 0.028
    1067 78361 0.217 0.032 0.220 0.016 1.351 0.181 0.463 0.057
    1418 78540 0.116 0.039 0.166 0.021 1.290 0.473 0.170 0.191
    1436 78553 0.236 0.083 0.190 0.016 / / 0.219 0.253
    965 78677 0.126 0.074 0.217 0.005 / / 0.205 0.068
    1254 78984 0.206 0.183 0.283 0.044 / / 0.575 0.019
    If p < 0.05 and delta or risk score mean >0, the transgenic plants showed statistically significant trait enhancement as compared to the reference.
    If p < 0.2 and delta or risk score mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference.
    • E. Polyethylene Glycol (PEG) Induced Osmotic Stress Tolerance Screen
  • There are numerous factors, which can influence seed germination and subsequent seedling growth, one being the availability of water. Genes, which can directly affect the success rate of germination and early seedling growth, are potentially useful agronomic traits for improving the germination and growth of crop plants under drought stress. In this assay, PEG was used to induce osmotic stress on germinating transgenic lines of Arabidopsis thaliana seeds in order to screen for osmotically resistant seed lines.
  • T2 seeds were plated on BASTA selection plates containing 3% PEG and grown under standard light and temperature conditions. Seeds were plated on each plate containing 3% PEG, 1/2×MS salts, 1% phytagel, and 10 μg/ml glufosinate. Plates were placed at 4° C. for 3 days to stratify seeds. On day 11, plants were measured for primary root length. After 3 more days of growth, i.e., at day 14, plants were scored for transgenic status, primary root length, growth stage, visual color, and the seedlings were pooled for fresh weight measurement. A photograph of the whole plate was taken on day 14.
  • Seedling weight and root length were analyzed as quantitative responses according to example 1M. The final growth stage at day 14 was scored as success or failure based on whether the plants reached 3 rosette leaves and size of leaves are greater than 1 mm. The growth stage data was analyzed as a qualitative response according to example 1L. A list of recombinant DNA constructs that improve osmotic stress tolerance in transgenic plants illustrated in Table 7.
  • TABLE 7
    Root Root Growth Seedling
    length length stage at weight
    PEP at day 11 at day 14 day 14 at day 14
    SEQ Construct Delta Delta Delta Delta
    ID ID mean P-value mean P-value mean P-value mean P-value
    763 10174 0.193 0.202 0.148 0.120 0.926 0.610 0.228 0.043
    1040 12773 0.142 0.020 0.138 0.086 3.109 0.073 0.465 0.020
    835 14909 0.167 0.038 0.057 0.383 3.041 0.087 0.411 0.014
    850 15409 0.017 0.742 −0.042 0.706 1.533 0.369 0.299 0.014
    844 17014 0.164 0.005 0.116 0.074 4.000 0.000 0.287 0.002
    850 17201 0.305 0.041 0.290 0.023 2.929 0.112 0.122 0.441
    903 18830 0.038 0.553 −0.100 0.008 1.463 0.372 0.427 0.004
    826 70401 0.041 0.558 0.025 0.833 3.230 0.052 0.281 0.033
    840 70746 / / / / / / 0.462 0.003
    952 70902 0.268 0.064 0.276 0.021 4.000 0.000 0.510 0.013
    955 70976 0.198 0.199 0.159 0.200 / / 0.477 0.033
    971 71839 0.269 0.008 0.185 0.019 1.178 0.506 0.108 0.316
    1073 72678 0.373 0.087 0.404 0.027 2.998 0.096 0.188 0.527
    1077 72755 0.206 0.089 0.132 0.048 4.000 0.000 0.397 0.136
    1074 72765 0.169 0.040 −0.006 0.836 4.000 0.000 0.335 0.008
    1084 72960 0.111 0.065 0.197 0.050 3.068 0.081 0.243 0.110
    1085 73021 0.364 0.011 0.300 0.018 4.000 0.000 0.758 0.023
    1094 73109 0.261 0.045 0.202 0.004 4.000 0.000 0.344 0.027
    1095 73121 0.503 0.003 0.508 0.013 4.000 0.000 0.713 0.029
    1088 73188 0.298 0.109 0.539 0.048 3.140 0.067 0.860 0.029
    1198 73545 0.115 0.037 0.110 0.275 4.000 0.000 0.378 0.023
    1034 73676 0.169 0.005 0.130 0.118 4.000 0.000 0.405 0.008
    1033 73861 0.055 0.321 0.009 0.777 0.510 0.151 0.203 0.036
    1081 73979 0.274 0.063 0.249 0.202 4.000 0.000 0.325 0.017
    1200 74138 0.146 0.006 0.141 0.008 2.512 0.233 0.080 0.734
    1225 74495 0.091 0.636 0.294 0.028 2.352 0.290 −0.029 0.911
    1227 74514 0.181 0.342 0.219 0.232 4.000 0.000 0.441 0.036
    1229 74552 0.238 0.100 0.177 0.092 3.055 0.084 0.261 0.005
    1167 74674 0.196 0.073 0.289 0.008 2.780 0.150 0.261 0.138
    1279 74842 0.012 0.920 −0.027 0.757 4.000 0.000 0.281 0.021
    1288 74985 0.401 0.014 0.421 0.036 2.179 0.139 0.756 0.041
    1124 75238 0.176 0.226 0.123 0.362 4.000 0.000 0.364 0.040
    1310 75343 0.216 0.078 0.465 0.025 1.251 0.464 0.420 0.005
    1342 75750 0.161 0.266 0.216 0.094 4.000 0.000 0.281 0.004
    1340 75761 0.437 0.006 0.385 0.024 4.000 0.000 0.473 0.023
    1391 75943 0.316 0.001 0.390 0.025 1.263 0.454 −0.029 0.627
    793 76025 0.356 0.074 0.309 0.076 2.832 0.136 0.519 0.019
    1263 76166 0.179 0.190 0.003 0.894 0.470 0.590 0.397 0.038
    1460 76362 0.153 0.302 0.174 0.385 2.051 0.403 0.746 0.043
    1511 76402 0.224 0.153 0.215 0.192 4.000 0.000 0.448 0.006
    1269 76572 0.256 0.026 0.289 0.106 2.708 0.171 0.294 0.031
    1262 76755 0.245 0.141 0.153 0.143 1.174 0.493 0.299 0.043
    1490 77154 0.208 0.114 0.215 0.043 4.000 0.000 0.403 0.060
    1497 77192 0.075 0.400 −0.036 0.402 4.000 0.000 0.559 0.009
    1499 77193 0.256 0.116 0.207 0.141 3.235 0.052 0.498 0.041
    1509 77293 0.424 0.034 0.280 0.106 2.931 0.111 0.609 0.002
    1362 77337 0.182 0.077 0.109 0.098 4.000 0.000 0.571 0.032
    1268 77533 0.143 0.089 0.146 0.002 1.381 0.404 0.257 0.030
    1369 77586 0.227 0.020 0.160 0.138 3.298 0.042 0.723 0.014
    1373 77592 / / / / / / 0.397 0.014
    1474 77834 0.180 0.025 0.211 0.009 / / −0.019 0.787
    1375 77934 0.179 0.081 0.183 0.327 0.556 0.316 0.349 0.003
    1419 77993 0.074 0.395 0.131 0.147 1.394 0.406 0.380 0.004
    1424 78018 0.192 0.073 0.135 0.014 0.322 0.626 0.284 0.096
    1429 78032 0.142 0.010 0.099 0.050 4.000 0.000 0.266 0.049
    1438 78060 0.235 0.207 0.381 0.030 1.696 0.325 0.285 0.327
    1118 78113 0.122 0.032 −0.106 0.179 2.732 0.164 0.353 0.002
    1402 78141 0.119 0.497 0.152 0.349 2.567 0.215 0.202 0.033
    1448 78185 0.283 0.048 0.344 0.079 4.000 0.000 0.513 0.000
    1024 78341 0.148 0.031 0.270 0.010 −0.914 0.129 −0.182 0.172
    1417 78537 −0.001 0.988 0.191 0.014 1.801 0.499 −0.171 0.287
    974 78717 −0.022 0.692 0.106 0.037 1.170 0.497 0.284 0.042
    1164 78734 0.145 0.233 0.068 0.620 4.000 0.000 0.375 0.012
    If p < 0.05 and delta or risk score mean >0, the transgenic plants showed statistically significant trait enhancement as compared to the reference.
    If p < 0.2 and delta or risk score mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference.
    • F. Cold Shock Tolerance Screen
  • This example set forth a screen to identify Arabidopsis plants transformed with the genes of interest that are more tolerant to cold stress subjected during day 8 to day 28 after seed planting. During these crucial early stages, seedling growth and leaf area increase were measured to assess tolerance when Arabidopsis seedlings were exposed to low temperatures. Using this screen, genetic alterations can be found that enable plants to germinate and grow better than wild type plants under sudden exposure to low temperatures.
  • Eleven seedlings from T2 seeds of each transgenic line plus one control line were plated together on a plate containing 1/2× Gamborg Salts with 0.8 Phytagel™, 1% Phytagel, and 0.3% Sucrose. Plates were then oriented horizontally and stratified for three days at 4° C. At day three, plates were removed from stratification and exposed to standard conditions (16 hr photoperiod, 22° C. at day and 20° C. at night) until day 8. At day eight, plates were removed from standard conditions and exposed to cold shock conditions (24 hr photoperiod, 8° C. at both day and night) until the final day of the assay, i.e., day 28. Rosette areas were measured at day 8 and day 28, which were analyzed as quantitative responses according to example 1M. A list of recombinant nucleotides that improve cold shock stress tolerance in plants illustrated in Table 8.
  • TABLE 8
    Rosette area Rosette area Rosette area
    PEP at day 8 at day 28 difference
    SEQ Construct Delta P- Risk score Delta
    ID ID Orientation mean value mean P-value mean P-value
    943 10366 ANTI-SENSE 0.361 0.009 0.569 0.038 0.588 0.036
    1518 12365 SENSE −0.114 0.771 0.663 0.009 0.717 0.008
    939 12601 SENSE −0.240 0.390 0.612 0.034 1.531 0.003
    781 12714 ANTI-SENSE 0.818 0.064 0.896 0.025 0.901 0.016
    850 15409 ANTI-SENSE 0.637 0.157 0.426 0.220 0.615 0.050
    851 15903 ANTI-SENSE −0.276 0.592 0.287 0.041 0.247 0.102
    842 15966 ANTI-SENSE 0.140 0.650 0.282 0.015 0.297 0.003
    915 18403 SENSE 0.366 0.197 0.729 0.007 0.785 0.004
    888 18418 SENSE −0.236 0.125 0.379 0.023 0.366 0.026
    924 18720 SENSE 0.620 0.144 0.740 0.015 0.659 0.014
    948 19906 SENSE 0.788 0.005 0.635 0.030 0.560 0.039
    860 70123 SENSE 0.556 0.114 0.968 0.067 1.245 0.028
    908 70415 SENSE 0.334 0.147 0.763 0.009 0.977 0.023
    930 70440 SENSE −0.175 0.249 0.541 0.049 0.622 0.067
    817 70748 ANTI-SENSE 0.503 0.075 0.700 0.048 0.527 0.116
    1150 70824 SENSE −0.134 0.679 0.829 0.002 0.921 0.011
    989 71347 SENSE −0.346 0.381 0.401 0.003 0.412 0.014
    1053 72007 SENSE 0.161 0.573 1.180 0.026 1.302 0.042
    1056 72022 SENSE 0.976 0.025 1.051 0.001 1.124 0.002
    1059 72138 SENSE 0.486 0.009 0.817 0.005 0.669 0.000
    994 72469 SENSE 0.335 0.300 0.767 0.025 0.948 0.023
    1007 72526 SENSE 0.323 0.223 0.413 0.003 0.505 0.002
    1076 72707 SENSE 0.146 0.596 0.396 0.012 0.400 0.074
    1089 73153 SENSE 0.728 0.031 0.290 0.044 0.311 0.047
    1101 73171 SENSE 0.333 0.336 0.320 0.059 0.378 0.038
    1087 73187 SENSE 0.454 0.037 0.492 0.008 0.460 0.003
    1182 73453 SENSE 0.672 0.013 0.708 0.010 0.879 0.004
    1012 73686 SENSE 0.704 0.040 0.906 0.000 0.888 0.000
    1090 73983 SENSE −0.071 0.867 0.431 0.004 0.286 0.037
    1036 74218 SENSE 0.002 0.993 0.294 0.020 0.089 0.625
    1276 74851 SENSE 0.626 0.184 0.917 0.074 1.028 0.033
    1277 74864 SENSE 0.879 0.041 0.742 0.031 0.752 0.044
    1302 75374 SENSE 0.278 0.273 2.374 0.016 2.950 0.013
    1307 75377 SENSE −0.307 0.316 0.085 0.166 0.212 0.009
    1331 75616 SENSE 0.399 0.473 0.807 0.022 1.015 0.015
    1392 75967 SENSE 0.714 0.027 1.588 0.007 1.793 0.006
    1458 76314 SENSE 0.420 0.049 0.787 0.004 0.970 0.002
    1459 76326 SENSE 0.232 0.383 0.894 0.018 0.930 0.034
    1462 76377 SENSE 0.263 0.137 0.254 0.014 0.227 0.435
    1511 76402 SENSE −0.265 0.435 0.402 0.024 0.490 0.046
    1065 76709 SENSE −0.566 0.063 0.091 0.110 0.250 0.016
    1488 77105 SENSE 0.954 0.016 0.817 0.015 0.925 0.011
    1494 77144 SENSE 0.163 0.523 0.946 0.003 0.906 0.000
    1374 77361 SENSE 0.595 0.065 1.056 0.006 1.207 0.016
    1510 77473 SENSE −0.048 0.732 0.170 0.019 0.091 0.057
    1238 77522 SENSE 0.132 0.616 1.709 0.011 2.008 0.009
    1351 77552 SENSE 1.221 0.028 1.687 0.004 1.900 0.004
    1106 77723 SENSE −0.342 0.151 0.100 0.051 0.141 0.037
    1485 77852 SENSE 0.236 0.151 0.416 0.197 0.587 0.040
    891 77909 SENSE 0.722 0.034 1.330 0.003 1.285 0.010
    1363 77924 SENSE 0.547 0.057 0.480 0.017 0.576 0.016
    1354 77957 SENSE 0.417 0.256 0.930 0.026 0.827 0.013
    1411 77974 SENSE 0.512 0.030 1.175 0.013 1.036 0.013
    1425 78021 SENSE 0.391 0.250 0.460 0.005 0.532 0.009
    1434 78057 SENSE 0.086 0.766 0.534 0.007 0.588 0.013
    1344 78129 SENSE 1.189 0.001 0.613 0.030 0.599 0.111
    1426 78158 SENSE 1.261 0.005 0.732 0.001 1.040 0.016
    1002 78202 SENSE 0.842 0.004 0.835 0.000 0.865 0.000
    1326 78233 SENSE 0.162 0.477 0.771 0.013 0.822 0.007
    1172 78367 SENSE −0.153 0.668 0.522 0.047 0.514 0.068
    1408 78530 SENSE 2.039 0.005 2.026 0.002 2.244 0.002
    1381 78905 SENSE 0.615 0.181 0.863 0.007 0.925 0.007
    1447 78932 SENSE 0.472 0.046 0.626 0.027 0.715 0.030
    If p < 0.05 and delta or risk score mean >0, the transgenic plants showed statistically significant trait enhancement as compared to the reference (p value, of the delta of a quantitative response or of the risk score of a qualitative response, is the probability that the observed difference between the transgenic plants and the reference occur by chance)
    If p < 0.2 and delta or risk score mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference.
    • G. Cold Germination Tolerance Screen
  • This example sets forth a screen to identify Arabidopsis plants transformed with the genes of interests are resistant to cold stress based on their rate of development, root growth and chlorophyll accumulation under low temperature conditions.
  • T2 seeds were plated and all seedlings used in the experiment were grown at 8° C. Seeds were first surface disinfested using chlorine gas and then seeded on assay plates containing an aqueous solution of 1/2× Gamborg's B/5 Basal Salt Mixture (Sigma/Aldrich Corp., St. Louis, Mo., USA G/5788), 1% Phytagel™ (Sigma-Aldrich, P-8169), and 10 ug/ml glufosinate with the final pH adjusted to 5.8 using KOH. Test plates were held vertically for 28 days at a constant temperature of 8° C., a photoperiod of 16 hr, and average light intensity of approximately 100 umol/m2/s. At 28 days post plating, root length was measured, growth stage was observed, the visual color was assessed, and a whole plate photograph was taken.
  • The root length at day 28 was analyzed as a quantitative response according to example 1M. The growth stage at day 7 was analyzed as a qualitative response according to example 1L. A list of recombinant DNA constructs that improve cold stress tolerance in transgenic plants illustrated in Table 9.
  • TABLE 9
    Root length Growth stage
    PEP at day 28 at day 28
    SEQ Construct Nomination Delta- Delta
    ID ID ID Orientation mean P-value mean P-value
    799 10192 CGPG146 ANTI-SENSE 0.461 0.094 4.000 0.000
    1517 12276 CGPG967 ANTI-SENSE 0.203 0.217 4.000 0.000
    835 14909 CGPG2005 ANTI-SENSE 0.311 0.005 4.000 0.000
    828 15126 CGPG1929 SENSE 0.216 0.016 4.000 0.000
    829 15628 CGPG1938 ANTI-SENSE 0.132 0.205 4.000 0.000
    846 16208 CGPG2148 SENSE −0.068 0.734 4.000 0.000
    864 17402 CGPG2426 SENSE 0.105 0.581 4.000 0.000
    780 18011 CGPG126 SENSE −0.248 0.184 4.000 0.000
    812 18116 CGPG1656 ANTI-SENSE −0.231 0.358 4.000 0.000
    905 18226 CGPG3269 SENSE 0.196 0.313 4.000 0.000
    887 18415 CGPG3004 SENSE −0.024 0.845 4.000 0.000
    901 18827 CGPG3248 SENSE 0.023 0.845 4.000 0.000
    889 19532 CGPG3030 SENSE 0.332 0.044 4.000 0.000
    912 19608 CGPG3400 SENSE −0.053 0.705 4.000 0.000
    892 19656 CGPG3084 SENSE 0.037 0.746 4.000 0.000
    951 19746 CGPG4099 SENSE 0.328 0.209 4.000 0.000
    940 19747 CGPG3931 SENSE −0.008 0.938 4.000 0.000
    950 19802 CGPG4071 SENSE 0.150 0.602 4.000 0.000
    954 19927 CGPG4153 SENSE / / 4.000 0.000
    1168 70225 CGPG63 SENSE 0.291 0.006 4.000 0.000
    816 70240 CGPG177 SENSE 0.033 0.755 4.000 0.000
    932 70443 CGPG3724 SENSE −0.087 0.321 4.000 0.000
    831 70560 CGPG1964 SENSE 0.401 0.128 4.000 0.000
    818 70807 CGPG182 SENSE 0.200 0.055 4.000 0.000
    985 70834 CGPG445 SENSE −0.300 0.322 4.000 0.000
    871 70845 CGPG253 SENSE 0.094 0.290 4.000 0.000
    944 70935 CGPG3975 SENSE −0.087 0.236 4.000 0.000
    942 70965 CGPG3964 SENSE 0.318 0.030 4.000 0.000
    956 71440 CGPG4169 SENSE 0.046 0.154 4.000 0.000
    999 71638 CGPG4691 SENSE 0.362 0.225 4.000 0.000
    1049 72025 CGPG5223 SENSE / / 4.000 0.000
    1057 72096 CGPG5304 SENSE / / 4.000 0.000
    1005 72457 CGPG4747 SENSE −0.010 0.907 4.000 0.000
    1008 72531 CGPG4779 SENSE 0.062 0.704 4.000 0.000
    910 72606 CGPG3361 SENSE 0.133 0.315 4.000 0.000
    1075 72730 CGPG5546 SENSE 0.179 0.134 4.000 0.000
    1100 73005 CGPG5732 SENSE / / 4.000 0.000
    1085 73021 CGPG5642 SENSE 0.110 0.531 4.000 0.000
    1107 73048 CGPG5797 SENSE / / 4.000 0.000
    1103 73067 CGPG5771 SENSE −0.244 0.395 4.000 0.000
    1104 73148 CGPG5778 SENSE 0.211 0.260 4.000 0.000
    1096 73157 CGPG5715 SENSE 0.168 0.440 4.000 0.000
    1086 73163 CGPG5644 SENSE 0.327 0.003 4.000 0.000
    884 73207 CGPG2874 SENSE −0.185 0.626 4.000 0.000
    986 73215 CGPG4453 SENSE 0.433 0.010 4.000 0.000
    1016 73230 CGPG4949 SENSE 0.273 0.150 4.000 0.000
    1039 73251 CGPG5186 SENSE 0.061 0.636 4.000 0.000
    1041 73254 CGPG5190 SENSE 0.205 0.018 4.000 0.000
    1030 73313 CGPG5097 SENSE 0.638 0.006 3.090 0.077
    1187 73434 CGPG6437 SENSE 0.116 0.345 4.000 0.000
    1179 73450 CGPG6375 SENSE 0.174 0.250 4.000 0.000
    1186 73469 CGPG6432 SENSE / / 4.000 0.000
    1188 73471 CGPG6445 SENSE −0.101 0.604 4.000 0.000
    1184 73491 CGPG6418 SENSE 0.061 0.230 4.000 0.000
    1193 73519 CGPG6505 SENSE 0.118 0.064 4.000 0.000
    1194 73543 CGPG6507 SENSE 0.219 0.385 4.000 0.000
    1195 73567 CGPG6509 SENSE 0.371 0.101 4.000 0.000
    833 73602 CGPG1977 SENSE −0.037 0.762 4.000 0.000
    1006 73639 CGPG4755 SENSE 0.035 0.724 4.000 0.000
    865 73707 CGPG2433 SENSE 0.149 0.133 4.000 0.000
    1010 73722 CGPG4879 SENSE 0.022 0.763 4.000 0.000
    1038 73731 CGPG5161 SENSE 0.050 0.825 3.321 0.039
    808 73927 CGPG1619 SENSE 0.083 0.050 4.000 0.000
    811 73948 CGPG1651 SENSE 0.203 0.154 4.000 0.000
    995 73951 CGPG4660 SENSE 0.220 0.104 4.000 0.000
    1209 74170 CGPG6619 SENSE −0.054 0.750 4.000 0.000
    1207 74179 CGPG6596 SENSE 0.258 0.237 4.000 0.000
    1214 74184 CGPG6636 SENSE 0.415 0.000 4.000 0.000
    1201 74186 CGPG6557 SENSE −0.426 0.017 4.000 0.000
    916 74206 CGPG3465 SENSE 0.346 0.088 4.000 0.000
    1045 74231 CGPG5211 SENSE 0.191 0.235 4.000 0.000
    1061 74264 CGPG5355 SENSE / / 4.000 0.000
    1062 74271 CGPG5376 SENSE 0.390 0.096 4.000 0.000
    1140 74373 CGPG6082 SENSE / / 4.000 0.000
    1223 74434 CGPG6729 SENSE −0.073 0.551 4.000 0.000
    1228 74515 CGPG6768 SENSE 0.333 0.170 4.000 0.000
    1231 74519 CGPG6800 SENSE 0.245 0.075 4.000 0.000
    1230 74529 CGPG6785 SENSE 0.186 0.034 4.000 0.000
    876 74535 CGPG268 SENSE 0.085 0.201 4.000 0.000
    857 74567 CGPG2349 SENSE 0.223 0.189 4.000 0.000
    1215 74582 CGPG6641 SENSE / / 4.000 0.000
    1216 74584 CGPG6642 SENSE 0.065 0.795 4.000 0.000
    1146 74656 CGPG6172 SENSE 0.225 0.005 4.000 0.000
    1148 74659 CGPG6176 SENSE −0.112 0.271 4.000 0.000
    1015 74715 CGPG4937 SENSE 0.167 0.043 4.000 0.000
    1116 74739 CGPG5889 SENSE 0.154 0.356 4.000 0.000
    1285 74845 CGPG7362 SENSE 0.248 0.021 4.000 0.000
    1287 74859 CGPG7379 SENSE 0.331 0.115 4.000 0.000
    1294 74917 CGPG7424 SENSE 0.028 0.885 4.000 0.000
    1292 74928 CGPG7417 SENSE 0.227 0.263 4.000 0.000
    1298 74932 CGPG7449 SENSE 0.053 0.562 4.000 0.000
    1297 74955 CGPG7443 SENSE 0.232 0.010 4.000 0.000
    1290 74962 CGPG7404 SENSE 0.194 0.433 4.000 0.000
    1300 74968 CGPG7452 SENSE 0.184 0.204 4.000 0.000
    1295 74989 CGPG7430 SENSE 0.098 0.494 4.000 0.000
    1066 75002 CGPG539 SENSE 0.529 0.001 4.000 0.000
    1129 75094 CGPG5994 SENSE 0.087 0.017 4.000 0.000
    839 75221 CGPG2065 SENSE 0.447 0.028 4.000 0.000
    1114 75225 CGPG5868 SENSE −0.063 0.602 4.000 0.000
    1119 75233 CGPG5914 SENSE / / 4.000 0.000
    1126 75243 CGPG5977 SENSE 0.298 0.017 4.000 0.000
    1165 75274 CGPG6267 SENSE −0.038 0.744 4.000 0.000
    1169 75291 CGPG6311 SENSE −0.095 0.371 4.000 0.000
    1309 75331 CGPG7516 SENSE −0.336 0.022 4.000 0.000
    1316 75335 CGPG7548 SENSE −0.059 0.778 4.000 0.000
    1310 75343 CGPG7517 SENSE 0.098 0.652 4.000 0.000
    1303 75386 CGPG7481 SENSE 0.463 0.072 4.000 0.000
    1315 75393 CGPG7537 SENSE −0.122 0.605 4.000 0.000
    1322 75442 CGPG7605 SENSE 0.183 0.133 4.000 0.000
    1319 75452 CGPG7590 SENSE 0.554 0.054 4.000 0.000
    1317 75462 CGPG7575 SENSE 0.244 0.345 4.000 0.000
    1323 75466 CGPG7607 SENSE 0.028 0.042 4.000 0.000
    1325 75481 CGPG7632 SENSE 0.110 0.284 4.000 0.000
    1341 75785 CGPG7863 SENSE −0.038 0.826 4.000 0.000
    1162 75814 CGPG6243 SENSE 0.008 0.952 4.000 0.000
    1130 75818 CGPG5996 SENSE 0.050 0.550 4.000 0.000
    1236 75856 CGPG6920 SENSE 0.118 0.579 4.000 0.000
    1246 75878 CGPG7002 SENSE 0.182 0.165 4.000 0.000
    1252 75896 CGPG7080 SENSE / / 4.000 0.000
    1386 75904 CGPG8235 SENSE 0.089 0.730 4.000 0.000
    1393 75932 CGPG8269 SENSE 0.567 0.067 4.000 0.000
    788 75935 CGPG1335 SENSE 0.306 0.098 4.000 0.000
    862 75936 CGPG2397 SENSE 0.212 0.090 4.000 0.000
    1389 75942 CGPG8254 SENSE 0.038 0.373 4.000 0.000
    1391 75943 CGPG8262 SENSE 0.121 0.566 4.000 0.000
    1390 75954 CGPG8255 SENSE 0.215 0.436 4.000 0.000
    856 76041 CGPG2348 SENSE 0.362 0.096 4.000 0.000
    1241 76275 CGPG6946 SENSE −0.079 0.533 4.000 0.000
    1137 76610 CGPG6069 SENSE 0.521 0.112 4.000 0.000
    1475 76823 CGPG9060 SENSE 0.068 0.707 4.000 0.000
    1482 76953 CGPG9111 SENSE −0.271 0.139 4.000 0.000
    820 77005 CGPG1873 SENSE 0.235 0.102 4.000 0.000
    1121 77008 CGPG5925 SENSE 0.076 0.709 4.000 0.000
    1163 77016 CGPG6248 SENSE 0.121 0.325 4.000 0.000
    1492 77107 CGPG9166 SENSE 0.036 0.900 4.000 0.000
    1489 77129 CGPG9152 SENSE 0.198 0.069 4.000 0.000
    1495 77156 CGPG9178 SENSE 0.440 0.110 4.000 0.000
    1484 77161 CGPG9123 SENSE 0.265 0.223 4.000 0.000
    1505 77229 CGPG9248 SENSE −0.024 0.810 4.000 0.000
    1508 77233 CGPG9280 SENSE 0.451 0.020 4.000 0.000
    1503 77287 CGPG9237 SENSE 0.249 0.157 4.000 0.000
    1174 77319 CGPG6349 SENSE −0.144 0.485 4.000 0.000
    1122 77321 CGPG5926 SENSE −0.241 0.172 4.000 0.000
    1366 77346 CGPG8076 SENSE 0.001 0.993 4.000 0.000
    1367 77350 CGPG8084 SENSE −0.221 0.300 4.000 0.000
    1376 77367 CGPG8157 SENSE 0.130 0.228 4.000 0.000
    1378 77370 CGPG8165 SENSE −0.114 0.477 4.000 0.000
    1513 77429 CGPG9315 SENSE 0.336 0.042 4.000 0.000
    1239 77516 CGPG6934 SENSE 0.452 0.002 1.413 0.409
    1248 77525 CGPG7021 SENSE 0.450 0.038 4.000 0.000
    1253 77527 CGPG7094 SENSE 0.300 0.045 4.000 0.000
    1261 77530 CGPG7166 SENSE −0.031 0.790 4.000 0.000
    925 77537 CGPG3631 SENSE 0.167 0.539 4.000 0.000
    1353 77559 CGPG7967 SENSE −0.205 0.278 4.000 0.000
    945 77717 CGPG3983 SENSE 0.147 0.350 4.000 0.000
    1106 77723 CGPG5785 SENSE −0.078 0.573 4.000 0.000
    1358 77920 CGPG8023 SENSE / / 4.000 0.000
    1368 77929 CGPG8093 SENSE 0.445 0.031 4.000 0.000
    1371 77930 CGPG8097 SENSE 0.039 0.737 4.000 0.000
    1360 77961 CGPG8038 SENSE 0.218 0.019 4.000 0.000
    1365 77964 CGPG8073 SENSE 0.270 0.022 2.762 0.156
    1415 77975 CGPG8474 SENSE 0.116 0.035 1.333 0.423
    1422 78014 CGPG8544 SENSE 0.415 0.030 4.000 0.000
    1423 78015 CGPG8546 SENSE 0.157 0.597 4.000 0.000
    1428 78028 CGPG8573 SENSE 0.238 0.346 4.000 0.000
    1432 78047 CGPG8611 SENSE / / 4.000 0.000
    1435 78059 CGPG8634 SENSE −0.009 0.947 4.000 0.000
    1439 78062 CGPG8642 SENSE −0.034 0.909 4.000 0.000
    1440 78065 CGPG8646 SENSE 0.004 0.782 4.000 0.000
    1176 78109 CGPG6353 SENSE 0.198 0.277 4.000 0.000
    1274 78112 CGPG7291 SENSE −0.173 0.212 4.000 0.000
    1379 78117 CGPG8169 SENSE 0.319 0.051 4.000 0.000
    1398 78136 CGPG8344 SENSE 0.410 0.030 4.000 0.000
    1404 78153 CGPG8378 SENSE 0.102 0.238 4.000 0.000
    1446 78178 CGPG8716 SENSE −0.027 0.861 4.000 0.000
    1449 78186 CGPG8774 SENSE −0.002 0.993 4.000 0.000
    998 78203 CGPG4689 SENSE 0.001 0.995 4.000 0.000
    1003 78207 CGPG4713 SENSE 0.131 0.276 4.000 0.000
    1052 78213 CGPG5254 SENSE 0.260 0.001 4.000 0.000
    1326 78233 CGPG7673 SENSE 0.169 0.183 4.000 0.000
    1026 78349 CGPG5061 SENSE 0.096 0.479 4.000 0.000
    881 78362 CGPG2832 SENSE / / 4.000 0.000
    1416 78536 CGPG8475 SENSE −0.104 0.537 4.000 0.000
    1456 78589 CGPG8853 SENSE −0.154 0.060 4.000 0.000
    1265 78990 CGPG7192 SENSE / / 4.000 0.000
    If p < 0.05 and delta or risk score mean >0, the transgenic plants showed statistically significant trait enhancement as compared to the reference.
    If p < 0.2 and delta or risk score mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference.
    • H. Shade Tolerance Screen
  • Plants undergo a characteristic morphological response in shade that includes the elongation of the petiole, a change in the leaf angle, and a reduction in chlorophyll content. While these changes may confer a competitive advantage to individuals, in a monoculture the shade avoidance response is thought to reduce the overall biomass of the population. Thus, genetic alterations that prevent the shade avoidance response may be associated with higher yields. Genes that favor growth under low light conditions may also promote yield, as inadequate light levels frequently limit yield. This protocol describes a screen to look for Arabidopsis plants that show an attenuated shade avoidance response and/or grow better than control plants under low light intensity. Of particular interest, we were looking for plants that didn't extend their petiole length, had an increase in seedling weight relative to the reference and had leaves that were more close to parallel with the plate surface.
  • T2 seeds were plated on glufosinate selection plates with ½ MS medium. Seeds were sown on 1/2×MS salts, 1% Phytagel, 10 ug/ml BASTA. Plants were grown on vertical plates at a temperature of 22° C. at day, 20° C. at night and under low light (approximately 30 uE/m2/s, far/red ratio (655/665/725/735) ˜0.35 using PLAQ lights with GAM color filter #680). Twenty-three days after seedlings were sown, measurements were recorded including seedling status, number of rosette leaves, status of flower bud, petiole leaf angle, petiole length, and pooled fresh weights. A digital image of the whole plate was taken on the measurement day. Seedling weight and petiole length were analyzed as quantitative responses according to example 1M. The number of rosette leaves, flowering bud formation and leaf angel were analyzed as qualitative responses according to example 1L.
  • A list of recombinant DNA constructs that improve shade tolerance in plants illustrated in Table 10.
  • TABLE 10
    Seedling Petiole
    weight length
    PEP at day 23 at day 23
    SEQ Construct Nomination Delta Delta
    ID ID ID Orientation mean P-value mean P-value
    877 10204 CGPG274 ANTI-SENSE 0.763 0.001 0.617 0.141
    1136 11152 CGPG606 SENSE 0.658 0.006 0.784 0.002
    968 11408 CGPG430 SENSE −0.458 0.210 −0.311 0.065
    773 12224 CGPG1143 SENSE 0.010 0.974 −0.378 0.055
    823 19122 CGPG1899 SENSE −0.397 0.110 −0.291 0.043
    897 19537 CGPG3156 SENSE −0.299 0.107 −0.245 0.054
    934 70466 CGPG3781 SENSE −0.531 0.071 −0.342 0.031
    992 70680 CGPG4583 SENSE 0.051 0.591 −0.345 0.038
    991 70764 CGPG4553 SENSE −0.407 0.550 −0.991 0.012
    926 70833 CGPG365 SENSE −0.195 0.201 −0.247 0.084
    997 71613 CGPG4684 SENSE −0.464 0.031 −0.328 0.014
    1000 71631 CGPG4702 SENSE −0.806 0.032 −0.607 0.011
    834 71702 CGPG1996 SENSE 0.385 0.053 0.293 0.032
    990 71820 CGPG4506 SENSE −0.663 0.053 −0.921 0.094
    973 71952 CGPG4344 SENSE −1.336 0.011 −0.931 0.054
    1055 72008 CGPG5265 SENSE −0.515 0.042 −0.379 0.043
    867 72665 CGPG2452 SENSE −0.229 0.236 −0.314 0.052
    873 72675 CGPG2567 SENSE −1.355 0.051 −1.051 0.024
    874 72677 CGPG2571 SENSE −1.011 0.070 −1.259 0.017
    1092 73179 CGPG5686 SENSE 0.230 0.030 0.186 0.133
    1021 73309 CGPG5032 SENSE −0.347 0.026 −0.277 0.007
    1009 73336 CGPG4848 SENSE −1.640 0.045 −1.744 0.008
    1199 73511 CGPG6531 SENSE 0.103 0.505 −0.210 0.016
    1192 73551 CGPG6476 SENSE −0.881 0.070 −0.744 0.050
    1012 73686 CGPG4892 SENSE 0.080 0.905 −1.178 0.007
    1079 73953 CGPG5576 SENSE 0.381 0.054 0.325 0.098
    1210 74123 CGPG6623 SENSE −0.442 0.002 −0.424 0.048
    1035 74212 CGPG5155 SENSE −0.380 0.069 −0.262 0.026
    1023 74222 CGPG5045 SENSE −0.913 0.051 −1.766 0.051
    1060 74261 CGPG5350 SENSE −0.207 0.140 −0.532 0.022
    1112 74332 CGPG5837 SENSE −0.544 0.015 −0.630 0.019
    1219 74403 CGPG6671 SENSE −1.289 0.039 −1.057 0.038
    1221 74443 CGPG6706 SENSE −0.664 0.057 −0.968 0.015
    1222 74457 CGPG6723 SENSE −0.913 0.008 −0.993 0.066
    1226 74513 CGPG6752 SENSE −0.405 0.010 −0.356 0.042
    1228 74515 CGPG6768 SENSE −0.523 0.258 −0.227 0.070
    857 74567 CGPG2349 SENSE −0.424 0.132 −0.532 0.026
    1132 74605 CGPG6027 SENSE −0.353 0.268 −0.652 0.097
    1135 74611 CGPG6049 SENSE −0.732 0.015 −0.985 0.023
    1143 74626 CGPG6128 SENSE −0.638 0.084 −0.691 0.030
    1145 74636 CGPG6149 SENSE −0.259 0.527 −0.597 0.095
    1217 74687 CGPG6645 SENSE −0.882 0.027 −0.431 0.024
    1117 74748 CGPG5893 SENSE −0.731 0.175 −0.825 0.080
    1291 74939 CGPG7410 SENSE −0.867 0.020 −0.620 0.001
    1301 74957 CGPG7459 SENSE −1.058 0.008 −0.937 0.088
    1296 74990 CGPG7438 SENSE −1.717 0.007 −1.271 0.032
    975 75040 CGPG4349 SENSE −0.643 0.100 −0.406 0.000
    1131 75248 CGPG6021 SENSE −0.504 0.069 −0.247 0.051
    1133 75252 CGPG6035 SENSE −0.395 0.097 −0.290 0.072
    1151 75267 CGPG6201 SENSE −0.243 0.267 −0.193 0.080
    1314 75333 CGPG7532 SENSE −0.632 0.031 −0.362 0.089
    1308 75354 CGPG7510 SENSE −0.658 0.018 −1.165 0.019
    1306 75365 CGPG7503 SENSE −0.329 0.033 −0.526 0.061
    1324 75479 CGPG7616 SENSE −1.296 0.018 −1.485 0.027
    1327 75539 CGPG7683 SENSE −0.463 0.183 −1.074 0.052
    1338 75608 CGPG7816 SENSE −0.392 0.145 −0.101 0.046
    1332 75640 CGPG7787 SENSE −0.603 0.006 −0.539 0.041
    1047 75823 CGPG5213 SENSE −0.433 0.132 −0.505 0.076
    1240 75864 CGPG6945 SENSE 0.596 0.008 0.045 0.730
    1247 75881 CGPG7013 SENSE −1.632 0.014 −1.898 0.000
    1250 75895 CGPG7071 SENSE −0.808 0.006 −0.543 0.084
    1382 75913 CGPG8212 SENSE −0.866 0.072 −0.779 0.030
    815 75957 CGPG1740 SENSE −0.514 0.006 −0.383 0.032
    790 75993 CGPG1352 SENSE −0.606 0.040 −0.590 0.008
    856 76041 CGPG2348 SENSE 0.642 0.006 0.151 0.187
    1270 76186 CGPG7243 SENSE −0.603 0.016 −0.427 0.080
    1271 76190 CGPG7258 SENSE −0.032 0.887 −0.125 0.011
    1156 76222 CGPG6214 SENSE −0.653 0.011 −0.632 0.046
    1158 76228 CGPG6222 SENSE −0.259 0.179 −0.310 0.013
    1463 76319 CGPG8917 SENSE −0.354 0.147 −0.767 0.097
    1465 76320 CGPG8925 SENSE −0.655 0.087 −1.218 0.010
    980 76410 CGPG4405 SENSE −1.709 0.008 −2.126 0.042
    1159 76435 CGPG6229 SENSE −0.308 0.051 −0.453 0.078
    1249 76454 CGPG7056 SENSE −0.603 0.016 −0.821 0.052
    1173 76528 CGPG6336 SENSE −0.086 0.245 −0.337 0.069
    1157 76611 CGPG6215 SENSE −0.624 0.077 −0.668 0.008
    1237 76642 CGPG6921 SENSE −1.027 0.010 −0.738 0.041
    1256 76752 CGPG7118 SENSE −0.345 0.286 −0.600 0.066
    1470 76838 CGPG8990 SENSE −1.442 0.073 −1.521 0.049
    1478 76927 CGPG9093 SENSE −0.384 0.161 −0.261 0.039
    1500 77147 CGPG9201 SENSE −0.975 0.035 −0.888 0.099
    1498 77181 CGPG9188 SENSE −1.360 0.000 −1.347 0.016
    1491 77190 CGPG9165 SENSE 0.005 0.954 −0.239 0.021
    1503 77287 CGPG9237 SENSE −0.315 0.377 −0.602 0.097
    1348 77543 CGPG7911 SENSE −0.166 0.104 −0.676 0.072
    1311 77809 CGPG7523 SENSE −0.466 0.063 −0.144 0.035
    1471 77841 CGPG9001 SENSE −0.651 0.072 −0.316 0.022
    1361 77922 CGPG8053 SENSE −0.447 0.020 −0.270 0.050
    1401 77973 CGPG8370 SENSE −0.722 0.059 −1.092 0.036
    1421 78009 CGPG8533 SENSE −0.468 0.072 −0.268 0.034
    1427 78026 CGPG8569 SENSE −0.555 0.154 −0.467 0.085
    1431 78044 CGPG8607 SENSE −0.838 0.007 −0.803 0.013
    1440 78065 CGPG8646 SENSE −0.085 0.595 −0.517 0.096
    1377 78121 CGPG8158 SENSE 0.274 0.079 0.172 0.036
    1395 78135 CGPG8305 SENSE −1.246 0.024 −1.112 0.023
    1405 78156 CGPG8383 SENSE −0.343 0.243 −1.089 0.002
    1280 78231 CGPG7347 SENSE −0.441 0.022 −0.297 0.084
    1020 78339 CGPG5028 SENSE −0.295 0.147 −0.334 0.042
    1025 78342 CGPG5051 SENSE −1.534 0.023 −1.513 0.022
    1013 78353 CGPG4903 SENSE −1.018 0.043 −1.290 0.020
    970 78358 CGPG4307 SENSE −0.531 0.022 −0.430 0.066
    1111 78371 CGPG5822 SENSE −0.743 0.091 −1.382 0.002
    1430 78388 CGPG8597 SENSE −0.200 0.409 −0.417 0.055
    1064 78442 CGPG5382 SENSE −1.106 0.000 −1.187 0.012
    1356 78508 CGPG8006 SENSE −1.184 0.009 −0.784 0.071
    1418 78540 CGPG8490 SENSE 0.253 0.057 0.289 0.137
    1450 78572 CGPG8778 SENSE −0.586 0.088 −0.474 0.070
    1441 78590 CGPG8666 SENSE −0.854 0.073 −0.875 0.043
    1409 78618 CGPG8450 SENSE −0.953 0.037 −1.088 0.008
    1451 78631 CGPG8784 SENSE −1.128 0.250 −1.224 0.048
    1420 78924 CGPG8530 SENSE 0.213 0.001 0.305 0.058
    1443 78952 CGPG8688 SENSE −0.264 0.282 −0.721 0.023
    For “seeding weight”, if p < 0.05 and delta or risk score mean >0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p < 0.2 and delta or risk score mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference with p < 0.2.
    For “petiole length”, if p < 0.05 and delta <0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p < 0.2 and delta <0, the transgenic plants showed a trend of trait enhancement as compared to the reference.
    • I. Early Plant Growth and Development Screen
  • This example sets forth a plate based phenotypic analysis platform for the rapid detection of phenotypes that are evident during the first two weeks of growth. In this screen, we were looking for genes that confer advantages in the processes of germination, seedling vigor, root growth and root morphology under non-stressed growth conditions to plants. The transgenic plants with advantages in seedling growth and development were determined by the seedling weight and root length at day 14 after seed planting.
  • T2 seeds were plated on glufosinate selection plates and grown under standard conditions (˜100 uE/m2/s, 16 h photoperiod, 22° C. at day, 20° C. at night). Seeds were stratified for 3 days at 4° C. Seedlings were grown vertically (at a temperature of 22° C. at day 20° C. at night). Observations were taken on day 10 and day 14. Both seedling weight and root length at day 14 were analyzed as quantitative responses according to example 1M.
  • A list recombinant DNA constructs that improve early plant growth and development illustrated in Table 11.
  • TABLE 11
    Root Root Seedling
    length length weight
    PEP at day 10 at day 14 at day 14
    SEQ Construct Delta Delta Delta
    ID ID Orientation mean P-value mean P-value mean P-value
    799 10192 ANTI-SENSE 0.269 0.024 0.222 0.026 0.417 0.021
    877 10204 ANTI-SENSE 0.290 0.057 0.234 0.095 0.512 0.014
    1328 11919 ANTI-SENSE 0.207 0.249 0.115 0.330 0.537 0.035
    1083 12776 ANTI-SENSE 0.237 0.002 0.092 0.280 0.233 0.147
    835 14909 ANTI-SENSE 0.151 0.053 0.074 0.582 0.398 0.001
    858 15809 ANTI-SENSE 0.212 0.184 0.066 0.493 0.403 0.061
    938 19713 SENSE 0.139 0.141 0.008 0.954 0.177 0.090
    841 70403 SENSE 0.295 0.017 0.077 0.280 0.337 0.044
    1037 71218 SENSE 0.208 0.308 0.145 0.034 0.554 0.138
    983 71963 SENSE 0.151 0.099 −0.094 0.359 0.106 0.030
    933 72357 SENSE 0.164 0.073 −0.033 0.571 −0.168 0.023
    1077 72755 SENSE 0.339 0.014 0.218 0.047 0.307 0.281
    1074 72765 SENSE 0.295 0.075 0.158 0.196 0.419 0.094
    1072 72773 SENSE 0.185 0.051 0.111 0.183 0.239 0.057
    880 72906 SENSE 0.224 0.086 0.074 0.246 0.150 0.027
    1085 73021 SENSE 0.134 0.098 0.141 0.083 0.217 0.036
    1099 73135 SENSE 0.255 0.073 0.214 0.057 0.329 0.082
    1046 73266 SENSE 0.222 0.085 0.038 0.745 0.175 0.183
    1183 73454 SENSE 0.276 0.046 0.201 0.131 0.277 0.234
    1190 73525 SENSE 0.204 0.016 −0.109 0.216 0.245 0.265
    1196 73579 SENSE 0.166 0.028 0.257 0.011 0.379 0.024
    1211 74159 SENSE 0.413 0.025 0.218 0.012 0.548 0.010
    1202 74163 SENSE 0.188 0.140 0.126 0.244 0.408 0.096
    1214 74184 SENSE 0.153 0.068 0.042 0.555 −0.084 0.710
    875 74534 SENSE 0.143 0.026 0.055 0.136 0.066 0.416
    1285 74845 SENSE 0.190 0.183 0.035 0.622 0.383 0.044
    1283 74868 SENSE 0.111 0.017 0.081 0.014 0.257 0.041
    1297 74955 SENSE 0.345 0.006 0.256 0.002 0.464 0.011
    1066 75002 SENSE 0.126 0.027 0.110 0.013 0.144 0.081
    1313 75344 SENSE 0.100 0.079 0.015 0.296 0.083 0.541
    1321 75489 SENSE −0.047 0.839 0.037 0.763 0.405 0.091
    1162 75814 SENSE 0.246 0.021 0.144 0.041 0.233 0.107
    1384 75974 SENSE 0.133 0.034 0.103 0.037 0.214 0.109
    843 76076 SENSE 0.417 0.050 0.250 0.028 0.347 0.034
    1125 76118 SENSE 0.200 0.035 0.127 0.024 0.311 0.125
    1154 76221 SENSE 0.188 0.086 −0.010 0.913 0.353 0.039
    1233 76547 SENSE 0.198 0.038 0.080 0.307 0.105 0.183
    1244 76558 SENSE 0.279 0.036 0.239 0.005 0.290 0.026
    1476 76836 SENSE 0.263 0.012 0.200 0.003 0.292 0.089
    1488 77105 SENSE 0.325 0.114 0.235 0.056 0.224 0.170
    1493 77167 SENSE 0.186 0.004 −0.068 0.308 0.235 0.068
    1499 77193 SENSE 0.312 0.027 0.275 0.007 0.444 0.005
    1352 77556 SENSE / / / / 0.468 0.001
    1412 77630 SENSE 0.146 0.199 0.180 0.025 0.236 0.060
    1380 77950 SENSE 0.121 0.084 0.088 0.302 0.141 0.259
    1397 77969 SENSE 0.461 0.009 0.375 0.008 0.503 0.001
    1439 78062 SENSE 0.163 0.060 0.185 0.043 0.380 0.080
    1445 78169 SENSE 0.104 0.358 0.143 0.014 0.096 0.071
    1455 78584 SENSE 0.164 0.056 −0.020 0.749 −0.108 0.303
    1259 78740 SENSE / / / / 0.367 0.099
    1410 78919 SENSE 0.273 0.052 0.155 0.085 0.225 0.310
    1453 78938 SENSE 0.187 0.107 0.113 0.010 0.309 0.303
    If p < 0.05 and delta or risk score mean >0, the transgenic plants showed statistically significant trait enhancement as compared to the reference.
    If p < 0.2 and delta or risk score mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference.
    • J. Late Plant Growth and Development Screen
  • This example sets forth a soil based phenotypic platform to identify genes that confer advantages in the processes of leaf development, flowering production and seed maturity to plants.
  • Arabidopsis plants were grown on a commercial potting mixture (Metro Mix 360, Scotts Co., Marysville, Ohio) consisting of 30-40% medium grade horticultural vermiculite, 35-55% sphagnum peat moss, 10-20% processed bark ash, 1-15% pine bark and a starter nutrient charge. Soil was supplemented with Osmocote time-release fertilizer at a rate of 30 mg/ft3. T2 seeds were imbibed in 1% agarose solution for 3 days at 4° C. and then sown at a density of ˜5 per 2½″ pot. Thirty-two pots were ordered in a 4 by 8 grid in standard greenhouse flat. Plants were grown in environmentally controlled rooms under a 16 h day length with an average light intensity of ˜200 mmoles/m2/s. Day and night temperature set points were 22° C. and 20° C., respectively. Humidity was maintained at 65%. Plants were watered by sub-irrigation every two days on average until mid-flowering, at which point the plants were watered daily until flowering was complete.
  • Application of the herbicide glufosinate was performed to select T2 individuals containing the target transgene. A single application of glufosinate was applied when the first true leaves were visible. Each pot was thinned to leave a single glufosinate-resistant seedling ˜3 days after the selection was applied.
  • The rosette radius was measured at day 25. The silique length was measured at day 40. The plant parts were harvested at day 49 for dry weight measurements if flowering production was stopped. Otherwise, the dry weights of rosette and silique were carried out at day 53. The seeds were harvested at day 58. All measurements were analyzed as quantitative responses according to example 1M.
  • A list of recombinant DNA constructs that improve late plant growth and development illustrated in Table 12.
  • TABLE 12
    Rosette dry Rosette Seed net Silique Silique
    weight at radius dry weight dry weight length
    PEP day 53 at day 25 at day 62 at day 53 at day 40
    SEQ Construct Delta Delta Delta Delta Delta
    ID ID mean P-value mean P-value mean P-value mean P-value mean P-value
    1515 11935 0.099 0.072 −0.093 0.030 1.235 0.027 0.041 0.679 0.039 0.247
    762 12020 −0.040 0.812 −0.191 0.054 0.871 0.010 −0.060 0.746 −0.075 0.107
    787 12932 0.438 0.013 / / −0.701 0.057 0.618 0.012 −0.013 0.692
    810 14730 −0.045 0.534 0.325 0.001 0.817 0.003 0.236 0.140 0.017 0.123
    824 16446 −0.152 0.214 −0.097 0.367 0.701 0.032 0.055 0.450 −0.017 0.832
    902 18220 0.209 0.049 −0.182 0.052 0.295 0.259 −0.205 0.036 −0.134 0.072
    907 18239 0.482 0.004 0.071 0.077 −0.245 0.113 −0.024 0.818 −0.045 0.346
    953 19933 0.211 0.020 / / −0.755 0.005 0.257 0.154 0.045 0.214
    821 70410 −0.208 0.070 / / 0.505 0.028 −0.348 0.015 −0.081 0.421
    978 71846 −0.285 0.012 / / 0.511 0.017 0.277 0.185 −0.046 0.534
    983 71963 −0.146 0.231 −0.035 0.312 0.421 0.037 0.120 0.131 0.037 0.048
    1051 72049 0.351 0.153 −0.047 0.683 0.419 0.025 −0.108 0.180 0.024 0.493
    1001 72368 0.282 0.013 −0.407 0.051 −0.912 0.082 −0.244 0.208 −0.096 0.017
    993 72375 0.327 0.002 / / −0.261 0.014 0.022 0.324 0.042 0.076
    1185 73445 −0.042 0.704 −0.126 0.091 1.499 0.015 −0.037 0.330 0.009 0.633
    852 10332 0.108 0.156 0.101 0.449 0.799 0.038 / / −0.072 0.208
    810 13938 0.450 0.064 0.225 0.094 0.874 0.021 0.331 0.029 0.258 0.005
    814 13960 −0.042 0.697 0.191 0.010 0.387 0.033 0.657 0.005 0.098 0.005
    872 16607 0.246 0.041 0.170 0.076 −1.029 0.012 −0.675 0.018 0.197 0.029
    914 18347 −0.240 0.238 0.188 0.026 1.183 0.017 −0.019 0.873 0.071 0.236
    935 70241 −0.146 0.264 0.116 0.068 0.851 0.012 0.245 0.007 0.023 0.640
    947 70909 −0.163 0.084 −0.026 0.345 0.792 0.004 0.484 0.011 0.647 0.001
    949 70974 −0.111 0.119 −0.036 0.794 1.359 0.002 / / −0.027 0.476
    979 71314 −0.076 0.209 −0.007 0.793 0.426 0.027 / / 0.021 0.098
    987 71334 1.355 0.001 −0.002 0.971 −0.472 0.206 0.328 0.052 −0.134 0.322
    1109 72923 0.331 0.002 −0.108 0.335 1.545 0.005 0.345 0.297 0.630 0.002
    1042 73255 0.147 0.018 −0.001 0.972 0.581 0.005 0.829 0.002 0.080 0.016
    1028 73280 −0.377 0.134 −0.042 0.512 0.824 0.014 0.324 0.202 0.003 0.976
    1189 73436 0.563 0.014 0.072 0.106 0.766 0.052 0.335 0.120 −0.049 0.171
    1191 73514 −0.409 0.051 −0.027 0.588 0.384 0.006 0.103 0.575 −0.032 0.335
    1197 73556 0.282 0.275 0.049 0.055 0.975 0.011 0.203 0.273 −0.106 0.220
    1208 74110 0.745 0.014 0.177 0.116 −0.983 0.178 1.131 0.009 −0.104 0.214
    814 74391 0.299 0.002 0.036 0.095 −0.578 0.004 / / 0.076 0.044
    861 74702 −0.335 0.019 0.092 0.173 1.364 0.003 0.080 0.546 0.083 0.041
    1293 74905 0.143 0.537 −0.085 0.246 1.488 0.002 0.092 0.454 −0.004 0.910
    1292 74928 0.330 0.031 0.087 0.114 0.303 0.173 0.542 0.050 0.082 0.019
    1312 75332 −0.145 0.035 0.222 0.027 0.919 0.021 0.149 0.476 0.012 0.694
    1323 75466 0.137 0.237 0.264 0.009 0.479 0.039 0.539 0.010 0.062 0.171
    1387 75916 0.342 0.027 0.029 0.549 −0.137 0.634 0.257 0.042 0.027 0.655
    1383 75925 −0.207 0.072 0.038 0.662 1.374 0.001 −0.025 0.853 −0.009 0.727
    837 75945 0.550 0.001 −0.188 0.113 0.440 0.022 0.050 0.769 −0.236 0.045
    1154 76221 −0.042 0.742 0.090 0.132 0.863 0.002 0.295 0.139 0.029 0.469
    1166 76233 0.115 0.162 0.110 0.160 1.062 0.008 0.196 0.005 0.065 0.343
    1242 76276 0.295 0.029 0.058 0.333 0.732 0.022 0.258 0.110 −0.060 0.400
    1473 76865 −0.084 0.474 −0.155 0.034 0.719 0.039 0.267 0.104 −0.005 0.968
    1483 76965 0.107 0.469 −0.329 0.058 0.446 0.001 0.067 0.770 −0.174 0.320
    1272 77071 −0.354 0.006 0.108 0.020 0.854 0.002 −0.200 0.125 0.012 0.647
    1492 77107 0.077 0.748 −0.026 0.709 1.343 0.003 −0.451 0.256 −0.092 0.349
    1487 77116 −0.064 0.634 0.048 0.066 1.289 0.003 0.006 0.935 0.004 0.475
    1496 77168 −0.287 0.410 −0.105 0.148 0.389 0.018 −0.407 0.281 −0.069 0.161
    1261 77530 0.535 0.050 −0.055 0.706 −1.462 0.041 / / −0.240 0.224
    1345 77539 0.655 0.009 −0.079 0.264 0.618 0.022 / / 0.041 0.044
    1347 77542 0.161 0.003 0.035 0.273 0.708 0.010 −0.480 0.039 0.025 0.461
    1350 77550 0.606 0.015 −0.187 0.043 −0.907 0.002 / / −0.338 0.044
    1304 77807 −0.079 0.511 0.078 0.184 0.770 0.008 0.162 0.258 0.039 0.112
    1110 78501 0.073 0.568 −0.202 0.040 0.292 0.006 / / −0.009 0.796
    1185 73445
    If p < 0.05 and delta or risk score mean >0, the transgenic plants showed statistically significant trait enhancement as compared to the reference.
    If p < 0.2 and delta or risk score mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference.
    • K. Limited Nitrogen Tolerance Screen
  • Under low nitrogen conditions, Arabidopsis seedlings become chlorotic and have less biomass. This example sets forth the limited nitrogen tolerance screen to identify Arabidopsis plants transformed with the gene of interest that are altered in their ability to accumulate biomass and/or retain chlorophyll under low nitrogen condition.
  • T2 seeds were plated on glufosinate selection plates containing 0.5×N-Free Hoagland's T 0.1 mM NH4NO3 T 0.1% sucrose T 1% phytagel media and grown under standard light and temperature conditions. At 12 days of growth, plants were scored for seedling status (i.e., viable or non-viable) and root length. After 21 days of growth, plants were scored for BASTA resistance, visual color, seedling weight, number of green leaves, number of rosette leaves, root length and formation of flowering buds. A photograph of each plant was also taken at this time point.
  • The seedling weight and root length were analyzed as quantitative responses according to example 1M. The number green leaves, the number of rosette leaves and the flowerbud formation were analyzed as qualitative responses according to example 1L. The leaf color raw data were collected on each plant as the percentages of five color elements (Green, DarkGreen, LightGreen, RedPurple, YellowChlorotic) using a computer imaging system. A statistical logistic regression model was developed to predict an overall value based on five colors for each plant.
  • A list of recombinant DNA constructs that improve low nitrogen availability tolerance in plants illustrated in Table 13.
  • TABLE 13
    Root Leaf Rosette
    length color weight
    PEP at day 21 at day 21 at day 21
    SEQ Construct Delta Risk score Delta
    ID ID Orientation mean P-value mean P-value mean P-value
    779 10176 ANTI-SENSE −0.448 0.045 2.804 0.082 0.174 0.077
    893 10217 ANTI-SENSE −0.237 0.066 0.820 0.051 0.027 0.787
    911 10230 ANTI-SENSE / / 3.346 0.001 −0.006 0.844
    917 10234 ANTI-SENSE −0.415 0.068 7.023 0.002 0.028 0.772
    957 10413 ANTI-SENSE −0.401 0.084 3.636 0.046 −0.026 0.767
    879 10431 ANTI-SENSE −0.476 0.022 3.731 0.010 −0.037 0.731
    886 10469 SENSE −0.570 0.002 5.909 0.004 0.019 0.652
    878 10472 SENSE −0.337 0.013 3.669 0.035 −0.089 0.173
    782 10507 ANTI-SENSE −0.494 0.011 4.504 0.014 −0.134 0.200
    1078 10610 ANTI-SENSE −0.379 0.078 0.591 0.016 −0.039 0.413
    1108 10616 ANTI-SENSE −0.462 0.013 4.827 0.058 −0.122 0.054
    1134 10620 ANTI-SENSE −0.279 0.002 2.695 0.022 −0.057 0.244
    1144 10622 ANTI-SENSE −0.567 0.021 4.506 0.010 −0.160 0.252
    1212 10633 ANTI-SENSE −0.320 0.051 3.471 0.012 −0.165 0.055
    1232 10638 ANTI-SENSE −0.692 0.004 5.933 0.026 −0.089 0.346
    1058 10811 ANTI-SENSE −0.290 0.005 1.439 0.021 −0.002 0.952
    996 11003 ANTI-SENSE / / 3.118 0.019 −0.138 0.054
    1267 11022 ANTI-SENSE −0.273 0.033 4.514 0.044 0.000 0.987
    1044 11049 SENSE −0.173 0.177 0.986 0.059 0.086 0.406
    941 11117 ANTI-SENSE −0.707 0.027 5.220 0.004 −0.112 0.488
    958 11119 ANTI-SENSE / / 6.165 0.025 −0.012 0.899
    931 11319 ANTI-SENSE −0.334 0.293 1.469 0.062 −0.099 0.149
    1048 11353 SENSE −0.152 0.034 1.063 0.058 −0.072 0.044
    1091 11516 ANTI-SENSE −0.293 0.016 4.740 0.030 0.050 0.594
    1258 11720 ANTI-SENSE −0.553 0.007 4.801 0.007 −0.044 0.519
    1357 11748 ANTI-SENSE −0.181 0.032 1.491 0.022 0.034 0.679
    1406 11807 ANTI-SENSE −0.538 0.080 5.467 0.057 −0.001 0.985
    764 11827 ANTI-SENSE −0.510 0.005 6.450 0.001 0.080 0.391
    767 11836 ANTI-SENSE −0.154 0.001 0.513 0.099 −0.112 0.127
    774 11856 ANTI-SENSE −0.127 0.273 2.401 0.035 −0.023 0.788
    766 12015 SENSE −0.402 0.088 0.799 0.030 −0.104 0.162
    775 12065 SENSE 0.264 0.121 174.221 0.424 0.193 0.012
    768 12141 ANTI-SENSE −0.343 0.001 1.939 0.010 −0.059 0.278
    777 12208 SENSE 0.064 0.731 1.066 0.453 0.209 0.073
    776 12419 ANTI-SENSE −0.399 0.128 4.501 0.068 0.095 0.183
    1452 12425 ANTI-SENSE −0.894 0.160 4.996 0.056 −0.176 0.184
    765 12435 SENSE 0.101 0.355 −0.040 0.909 0.135 0.066
    770 12437 SENSE / / 1.828 0.051 −0.077 0.324
    785 13237 SENSE −0.287 0.009 4.272 0.017 0.169 0.174
    795 13305 ANTI-SENSE −0.221 0.051 0.981 0.076 −0.062 0.543
    943 13404 SENSE −0.372 0.121 3.277 0.059 0.089 0.096
    804 13650 ANTI-SENSE / / 3.220 0.055 0.302 0.004
    809 13657 ANTI-SENSE −0.500 0.018 5.368 0.037 −0.059 0.462
    794 13708 ANTI-SENSE −0.527 0.021 4.121 0.079 0.077 0.402
    1153 13805 SENSE / / 5.349 0.049 −0.085 0.433
    801 13841 ANTI-SENSE −0.460 0.009 5.012 0.009 0.162 0.031
    805 13855 ANTI-SENSE −0.141 0.024 1.477 0.072 0.056 0.426
    1477 14133 ANTI-SENSE −0.461 0.074 3.450 0.085 0.012 0.868
    803 14253 ANTI-SENSE / / 4.232 0.034 0.023 0.906
    1235 14703 SENSE −0.450 0.039 4.394 0.019 −0.001 0.990
    797 14712 SENSE −0.429 0.034 4.370 0.025 0.152 0.112
    836 14927 ANTI-SENSE −0.293 0.083 4.557 0.006 0.134 0.255
    783 15039 SENSE −0.491 0.102 4.688 0.003 −0.096 0.230
    825 15143 SENSE / / 5.445 0.010 −0.028 0.831
    848 15716 ANTI-SENSE −0.473 0.018 3.843 0.014 −0.087 0.024
    802 15805 SENSE −0.347 0.073 3.195 0.001 −0.003 0.931
    866 17129 ANTI-SENSE −0.356 0.185 2.082 0.099 −0.095 0.068
    869 17151 ANTI-SENSE / / 4.021 0.022 0.024 0.747
    868 18206 SENSE −0.160 0.337 1.069 0.052 0.643 0.014
    906 18227 SENSE −0.273 0.185 1.990 0.020 −0.045 0.201
    913 18271 SENSE −0.036 0.744 0.278 0.082 0.004 0.925
    909 18329 SENSE −0.220 0.418 5.264 0.067 0.118 0.119
    890 18423 SENSE −0.304 0.018 3.789 0.079 0.025 0.771
    904 19205 SENSE −0.313 0.084 0.702 0.004 −0.061 0.491
    791 19401 SENSE −0.032 0.850 0.086 0.874 0.161 0.096
    859 70110 SENSE −0.264 0.020 2.237 0.076 0.105 0.354
    930 70440 SENSE −0.347 0.017 1.576 0.032 0.115 0.251
    936 70476 SENSE −0.297 0.072 0.965 0.044 −0.141 0.095
    977 70666 SENSE −0.351 0.007 3.536 0.039 −0.085 0.127
    963 71250 SENSE −0.018 0.901 2.025 0.110 0.278 0.022
    981 71322 SENSE −0.046 0.431 1.676 0.080 0.026 0.628
    984 71326 SENSE −0.380 0.065 3.996 0.032 −0.047 0.399
    987 71334 SENSE −0.482 0.028 3.737 0.074 0.042 0.322
    988 71335 SENSE −0.264 0.060 3.812 0.035 0.133 0.220
    971 71839 SENSE 0.052 0.538 2.437 0.013 0.140 0.150
    976 71843 SENSE −0.316 0.045 1.660 0.219 0.232 0.038
    1127 72602 SENSE 0.021 0.833 0.410 0.025 0.043 0.751
    1017 72663 SENSE 0.002 0.989 −0.270 0.862 0.199 0.016
    873 72675 SENSE −0.173 0.135 1.435 0.055 −0.117 0.096
    1019 72827 SENSE −0.264 0.054 1.909 0.080 0.000 0.995
    1105 72933 SENSE −0.245 0.122 3.963 0.025 0.076 0.442
    1043 73257 SENSE / / 4.972 0.090 −0.045 0.609
    1029 73281 SENSE −0.305 0.097 4.638 0.040 −0.043 0.175
    1181 73452 SENSE 0.043 0.102 0.097 0.808 0.154 0.053
    969 73616 SENSE 0.307 0.023 1.292 0.012 −0.036 0.222
    1014 73726 SENSE −0.049 0.097 2.396 0.041 −0.024 0.788
    855 73847 SENSE −0.100 0.149 1.517 0.044 −0.075 0.036
    1082 73966 SENSE −0.273 0.001 2.969 0.035 −0.179 0.224
    853 73968 SENSE / / 4.339 0.056 −0.022 0.584
    1205 74141 SENSE −0.362 0.112 1.484 0.051 −0.224 0.015
    1203 74175 SENSE −0.305 0.069 3.974 0.023 −0.007 0.901
    1204 74176 SENSE 0.048 0.225 1.673 0.005 −0.042 0.558
    1206 74178 SENSE −0.546 0.051 3.934 0.038 −0.117 0.062
    898 74201 SENSE −0.223 0.046 1.264 0.077 −0.200 0.018
    1023 74222 SENSE / / 5.858 0.048 −0.076 0.268
    1139 74371 SENSE / / 4.728 0.007 −0.117 0.322
    1140 74373 SENSE −0.027 0.715 −0.646 0.465 0.106 0.051
    1224 74447 SENSE −0.867 0.064 3.200 0.055 −0.197 0.206
    1135 74611 SENSE −0.189 0.350 2.233 0.060 −0.118 0.205
    1142 74620 SENSE −0.736 0.094 5.605 0.047 0.004 0.979
    1113 74738 SENSE 0.036 0.145 −0.181 0.528 0.168 0.098
    1284 74809 SENSE −0.256 0.031 2.481 0.053 −0.021 0.606
    1282 74820 SENSE −0.173 0.032 1.129 0.036 −0.168 0.064
    1286 74870 SENSE −0.448 0.051 4.227 0.061 −0.103 0.154
    1289 74950 SENSE −0.115 0.085 1.801 0.070 −0.107 0.291
    1004 75209 SENSE −0.231 0.065 2.947 0.046 0.008 0.887
    1152 75283 SENSE −0.190 0.011 0.627 0.047 −0.038 0.323
    1306 75365 SENSE 0.125 0.219 1.830 0.047 −0.056 0.569
    1302 75374 SENSE −0.326 0.031 2.123 0.080 −0.193 0.015
    1321 75489 SENSE 0.208 0.053 −4.236 0.035 0.184 0.054
    1329 75603 SENSE 0.035 0.604 0.552 0.179 0.124 0.009
    1332 75640 SENSE −0.353 0.018 3.264 0.026 −0.152 0.231
    1334 75653 SENSE −0.256 0.151 3.269 0.076 −0.023 0.755
    1343 75716 SENSE −0.292 0.079 2.436 0.028 −0.066 0.580
    1386 75904 SENSE 0.254 0.052 −1.863 0.084 0.312 0.025
    1392 75967 SENSE / / 1.628 0.003 −0.038 0.729
    1260 76157 SENSE / / 2.689 0.064 0.155 0.058
    1273 76194 SENSE / / 7.881 0.009 −0.078 0.728
    1463 76319 SENSE / / 7.442 0.029 −0.388 0.417
    1468 76334 SENSE −0.338 0.068 1.019 0.036 −0.036 0.517
    1461 76340 SENSE −0.159 0.020 0.346 0.061 −0.026 0.682
    1464 76343 SENSE −0.042 0.710 0.257 0.390 0.111 0.081
    1466 76380 SENSE / / 2.459 0.019 −0.130 0.254
    1469 76382 SENSE −0.693 0.013 5.109 0.008 −0.304 0.007
    980 76410 SENSE −0.203 0.007 3.337 0.004 −0.107 0.294
    1264 76756 SENSE / / 3.459 0.034 −0.147 0.126
    1470 76838 SENSE / / 4.610 0.021 −0.067 0.168
    1479 76963 SENSE / / 1.779 0.046 −0.188 0.096
    1507 77265 SENSE / / 2.573 0.025 −0.097 0.265
    1504 77276 SENSE / / 3.580 0.010 −0.113 0.219
    1120 77311 SENSE / / 2.744 0.032 −0.035 0.696
    1346 77540 SENSE −0.322 0.016 3.433 0.004 −0.164 0.013
    1355 77565 SENSE / / 2.221 0.006 −0.026 0.272
    1359 77573 SENSE −0.404 0.005 5.266 0.007 0.092 0.178
    1501 77853 SENSE / / 4.686 0.004 −0.072 0.264
    1400 78142 SENSE / / 3.787 0.059 0.010 0.566
    1437 78163 SENSE / / 1.541 0.029 0.038 0.603
    1457 78252 SENSE / / 5.384 0.026 −0.043 0.728
    1516 78259 SENSE / / 3.387 0.036 0.004 0.928
    1024 78341 SENSE / / 4.261 0.040 −0.056 0.478
    1025 78342 SENSE −0.469 0.027 7.592 0.050 −0.272 0.023
    1013 78353 SENSE / / 7.028 0.040 0.013 0.930
    972 78417 SENSE 0.041 0.366 −0.590 0.551 0.282 0.076
    1266 78460 SENSE / / 2.353 0.087 −0.159 0.017
    1356 78508 SENSE / / 4.369 0.001 −0.241 0.000
    1370 78510 SENSE −0.216 0.041 3.626 0.043 −0.125 0.126
    1407 78528 SENSE / / 4.716 0.014 −0.241 0.075
    1444 78559 SENSE / / 4.385 0.022 −0.029 0.877
    1171 78607 SENSE / / 4.547 0.049 −0.162 0.319
    959 78659 SENSE / / 6.713 0.013 −0.060 0.637
    974 78717 SENSE / / 1.926 0.179 0.121 0.013
    1022 78725 SENSE −0.157 0.213 1.656 0.054 0.028 0.683
    1161 78743 SENSE / / 2.003 0.048 0.107 0.258
    1413 78921 SENSE / / 2.641 0.040 0.039 0.795
    1454 78961 SENSE −0.475 0.006 4.949 0.000 0.002 0.972
    1403 78963 SENSE / / 5.358 0.057 0.042 0.725
    961 78969 SENSE / / 2.921 0.097 0.196 0.127
    964 78972 SENSE / / 1.621 0.050 0.009 0.814
    For rosette weight, if p < 0.05 and delta or risk score mean >0, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p < 0.2 and delta or risk score mean >0, the transgenic plants showed a trend of trait enhancement as compared to the reference with p < 0.2.
    For root length, if p < 0.05, the transgenic plants showed statistically significant trait enhancement as compared to the reference. If p < 0.2, the transgenic plants showed a trend of trait enhancement as compared to the reference.
    • L. Statistic Analysis for Qualitative Responses
  • A list of responses that were analyzed as qualitative responses illustrated in Table 14.
  • TABLE 14
    categories
    response Screen (success vs. failure)
    Wilting response Soil drought tolerance non-wilted vs. wilted
    Risk Score screen
    growth stage at heat stress tolerance 50% of plants reach
    day 14 screen stage1.03 vs. not
    growth stage at salt stress tolerance 50% of plants reach
    day 14 screen stage1.03 vs. not
    growth stage at PEG induced osmotic 50% of plants reach
    day 14 stress tolerance screen stage1.03 vs. not
    growth stage at cold germination 50% of plants reach
    day 7 tolerance screen stage 0.5 vs. not
    number of rosette Shade tolerance screen 5 leaves appeared
    leaves at day 23 vs. not
    Flower bud forma- Shade tolerance screen flower buds appear
    tion at day 23 vs. not
    leaf angle at Shade tolerance screen >60 degree vs. <60
    day 23 degree
    number of green limited nitrogen tolerance 6 or 7 leaves appeared
    leaves at day 21 screen vs. not
    number of rosette limited nitrogen tolerance 6 or 7 leaves appeared
    leaves at day 21 screen vs. not
    Flower bud forma- limited nitrogen tolerance flower buds appear
    tion at day 21 screen vs. not
  • Plants were grouped into transgenic and reference groups and were scored as success or failure according to Table 14. First, the risk (R) was calculated, which is the proportion of plants that were scored as of failure plants within the group. Then the relative risk (RR) was calculated as the ratio of R (transgenic) to R (reference). Risk score (RS) was calculated as −log2 RR. Subsequently the risk scores from multiple events for each transgene of interest were evaluated for statistical significance by t-test using SAS statistical software (SAS 9, SAS/STAT User's Guide, SAS Institute Inc, Cary, N.C., USA). RS with a value greater than 0 indicates that the transgenic plants perform better than the reference. RS with a value less than 0 indicates that the transgenic plants perform worse than the reference. The RS with a value equal to 0 indicates that the performance of the transgenic plants and the reference don't show any difference.
    • M. Statistic Analysis for Quantitative Responses
  • A list of responses that were analyzed as quantitative responses illustrated in Table 15.
  • TABLE 15
    response screen
    seed yield Soil drought stress tolerance screen
    seedling weight at day 14 heat stress tolerance screen
    root length at day 14 heat stress tolerance screen
    seedling weight at day 14 salt stress tolerance screen
    root length at day 14 salt stress tolerance screen
    root length at day 11 salt stress tolerance screen
    seedling weight at day 14 PEG induced osmotic stress tolerance
    screen
    root length at day 11 PEG induced osmotic stress tolerance
    screen
    root length at day 14 PEG induced osmotic stress tolerance
    screen
    rosette area at day 8 cold shock tolerance screen
    rosette area at day 28 cold shock tolerance screen
    difference in rosette area cold shock tolerance screen
    from day 8 to day 28
    root length at day 28 cold germination tolerance screen
    seedling weight at day 23 Shade tolerance screen
    petiole length at day 23 Shade tolerance screen
    root length at day 14 Early plant growth and development
    screen
    Seedling weight at day 14 Early plant growth and development
    screen
    Rosette dry weight at day 53 Late plant growth and development
    screen
    rosette radius at day 25 Late plant growth and development
    screen
    seed dry weight at day 58 Late plant growth and development
    screen
    silique dry weight at day 53 Late plant growth and development
    screen
    silique length at day 40 Late plant growth and development
    screen
    Seedling weight at day 21 Limited nitrogen tolerance screen
    Root length at day 21 Limited nitrogen tolerance screen
  • The measurements (M) of each plant were transformed by log2 calculation. The Delta was calculated as log2 M(transgenic)−log2 M(reference). Subsequently the mean delta from multiple events of the transgene of interest was evaluated for statistical significance by t-test using SAS statistical software (SAS 9, SAS/STAT User's Guide, SAS Institute Inc, Cary, N.C., USA). The Delta with a value greater than 0 indicates that the transgenic plants perform better than the reference. The Delta with a value less than 0 indicates that the transgenic plants perform worse than the reference. The Delta with a value equal to 0 indicates that the performance of the transgenic plants and the reference don't show any difference.
    • Example 2 Identification of Homologs
  • A BLAST searchable “All Protein Database” is constructed of known protein sequences using a proprietary sequence database and the National Center for Biotechnology Information (NCBI) non-redundant amino acid database (nr.aa). For each organism from which a DNA sequence provided herein was obtained, an “Organism Protein Database” is constructed of known protein sequences of the organism; the Organism Protein Database is a subset of the All Protein Database based on the NCBI taxonomy ID for the organism.
  • The All Protein Database is queried using amino acid sequence of cognate protein for gene DNA used in trait-improving recombinant DNA, i.e., sequences of SEQ ID NO: 760 through SEQ ID NO: 1518 using “blastp” with E-value cutoff of 1e-8. Up to 1000 top hits were kept, and separated by organism names. For each organism other than that of the query sequence, a list is kept for hits from the query organism itself with a more significant E-value than the best hit of the organism. The list contains likely duplicated genes, and is referred to as the Core List. Another list was kept for all the hits from each organism, sorted by E-value, and referred to as the Hit List.
  • The Organism Protein Database is queried using amino acid sequences of SEQ ID NO: 760 through SEQ ID NO: 1518 using “blastp” with E-value cutoff of 1e-4. Up to 1000 top hits are kept. A BLAST searchable database is constructed based on these hits, and is referred to as “SubDB”. SubDB was queried with each sequence in the Hit List using “blastp” with E-value cutoff of 1e-8. The hit with the best E-value is compared with the Core List from the corresponding organism. The hit is deemed a likely ortholog if it belongs to the Core List, otherwise it is deemed not a likely ortholog and there is no further search of sequences in the Hit List for the same organism. Likely orthologs from a large number of distinct organisms were identified and are reported by amino acid sequences of SEQ ID NO: 1519 to SEQ ID NO: 67778. These orthologs are reported in Tables 16 as homologs to the proteins cognate to genes used in trait-improving recombinant DNA.
    • Example 3 Consensus Sequence Build
  • ClustalW program is selected for multiple sequence alignments of an amino acid sequence of SEQ ID NO: 760 and its homologs, through SEQ ID NO: 1518 and its homologs. Three major factors affecting the sequence alignments dramatically are (1) protein weight matrices; (2) gap open penalty; (3) gap extension penalty. Protein weight matrices available for ClustalW program include Blosum, Pam and Gonnet series. Those parameters with gap open penalty and gap extension penalty were extensively tested. On the basis of the test results, Blosum weight matrix, gap open penalty of 10 and gap extension penalty of 1 were chosen for multiple sequence alignment. The consensus sequence of SEQ ID NO: 768 and its 17 homologs were derived according to the procedure described above and is displayed in FIG. 4.
    • Example 4 Pfam Module Annoation
  • This example illustrates the identification of domain and domain module by Pfam analysis.
  • The amino acid sequence of the expressed proteins that were shown to be associated with an enhanced trait were analyzed for Pfam protein family against the current Pfam collection of multiple sequence alignments and hidden Markov models using the HMMER software. The Pfam domain modules and individual protein domain for the proteins of SEQ ID NO: 760 through 1518 are shown in Table 17 and Table 18 respectively. The Hidden Markov model databases for the identified patent families allow identification of other homologous proteins and their cognate encoding DNA to enable the full breadth of the invention for a person of ordinary skill in the art. Certain proteins are identified by a single Pfam domain and others by multiple Pfam domains. For instance, the protein with amino acids of SEQ ID NO: 766 is characterized by two Pfam domains, i.e. “FHA” and “PP2C”. See also the protein with amino acids of SEQ ID NO: 1515 which is characterized by seven copies of the Pfam domain “WD40”. In Table 18 “score” is the gathering score for the Hidden Markov Model of the domain which exceeds the gathering cutoff reported in Table 19.
  • TABLE 17
    PEP SEQ ID Construct ID Module Position
    760 CGPG1022.pep RRM_1 95-165
    761 CGPG1035.pep Peptidase_C54 82-373
    763 CGPG105.pep AP2 48-112
    764 CGPG1060.pep DUF788 1-169
    765 CGPG1069.pep NDUF_B7 2-81
    766 CGPG108.pep FHA::PP2C 208-284::309-570
    771 CGPG1136.pep RRM_1 22-87
    774 CGPG1145.pep NUDIX 24-160
    776 CGPG1173.pep adh_short 6-181
    777 CGPG1176.pep F-box 2-50
    779 CGPG122.pep PTR2 113-517
    780 CGPG126.pep Response_reg 34-158
    781 CGPG1262.pep Gar1 51-152
    782 CGPG128.pep Response_reg 25-149
    783 CGPG1280.pep DUF676 515-717
    784 CGPG1291.pep DUF862 2-156
    785 CGPG1295.pep TMEM14 7-104
    787 CGPG1315.pep Brix 60-255
    788 CGPG1335.pep LRR_1 424-447
    789 CGPG1344.pep Pkinase 496-767
    790 CGPG1352.pep Pkinase_Tyr 154-425
    791 CGPG1364.pep Pkinase 38-416
    793 CGPG1396.pep malic::Malic_M 106-295::297-550
    794 CGPG1398.pep Glycolytic 11-358
    795 CGPG1399.pep Metallophos 161-360
    796 CGPG1429.pep NTP_transferase::Hexapep::Hexapep 86-365::413-430::466-483
    797 CGPG1430.pep E1_dh 89-393
    798 CGPG1445.pep Pkinase 33-294
    799 CGPG146.pep p450 38-482
    800 CGPG1492.pep Aldedh 29-491
    801 CGPG1528.pep ATP_synt_H 1-70
    802 CGPG1530.pep ArfGap::C2 15-137::183-262
    803 CGPG1535.pep SPT2 230-329
    804 CGPG1546.pep CTP_transf_1 101-300
    805 CGPG1567.pep Ribosomal_L19 107-212
    806 CGPG1568.pep FAD_binding_4 82-221
    807 CGPG1575.pep DUF740 24-595
    808 CGPG1619.pep Pyr_redox_2::Pyr_redox_dim 27-343::373-483
    810 CGPG1641.pep Di19 11-219
    811 CGPG1651.pep DEAD::Helicase_C::DSHCT 69-220::378-462::800-988
    812 CGPG1656.pep Cyt-b5::FA_desaturase 9-82::145-399
    813 CGPG1668.pep DUF791::MFS_1 4-358::42-406
    815 CGPG1740.pep DUF860 25-364
    816 CGPG177.pep WD40::WD40 168-205::257-296
    817 CGPG1785.pep PB1::Pkinase_Tyr 179-266::863-1126
    818 CGPG182.pep LRR_1::LRR_1::LRR_1::LRR_1::LRR_1:: 46-67::69-90::115-136::161-183::208-
    LRR_1::LRR_1::LRR_1::LRR_1:: 229::231-252::276-297::382-403::405-
    LRR_1::LRR_1::LRR_1::LRR_1 427::429-451::477-498::500-521::523-544
    819 CGPG1837.pep TFIIS_M::SPOC 328-445::656-762
    820 CGPG1873.pep Pkinase::NAF 20-275::314-374
    823 CGPG1899.pep F-box::Kelch_1::Kelch_1 18-65::139-186::189-235
    824 CGPG1913.pep F-box::FBA_1 31-78::268-416
    825 CGPG1918.pep F-box 30-77
    826 CGPG1919.pep F-box 65-112
    827 CGPG1922.pep F-box::Kelch_1::Kelch_1 25-72::118-163::165-210
    828 CGPG1929.pep F-box 1-44
    829 CGPG1938.pep F-box::LRR_2 8-55::159-185
    830 CGPG1956.pep Pre-SET::SET 409-558::560-702
    831 CGPG1964.pep zf-C3HC4::YDG_SRA 109-147::228-345
    832 CGPG1973.pep zf-UBR 40-109
    833 CGPG1977.pep TFIIF_alpha 18-542
    834 CGPG1996.pep Pkinase 3-286
    835 CGPG2005.pep NADPH_Ox::Ferric_reduct::FAD_binding_8:: 130-229::352-511::552-671::677-850
    NAD_binding_6
    837 CGPG2044.pep PTR2 99-507
    838 CGPG2059.pep Nuc_sug_transp 104-340
    839 CGPG2065.pep PEARLI-4 342-611
    841 CGPG2072.pep DUF1639 264-300
    842 CGPG2074.pep HMA::HMA 75-138::173-235
    843 CGPG2116.pep NOI 1-67
    845 CGPG2142.pep MATH::MATH 101-233::258-375
    847 CGPG2190.pep DJ-1_PfpI::DJ-1_PfpI 34-174::240-378
    849 CGPG221.pep DnaJ::DnaJ_CXXCXGXG::DnaJ_C 35-96::160-243::256-378
    850 CGPG2213.pep RNA_pol_I_A49 83-441
    851 CGPG2247.pep DUF23 256-497
    852 CGPG228.pep p450 67-511
    853 CGPG2301.pep PC_rep::PC_rep::PC_rep:: 414-447::448-484::485-519::523-
    PC_rep::PC_rep::PC_rep 557::671-705::706-740
    854 CGPG2304.pep Phi_1 32-309
    856 CGPG2348.pep Gal-bind_lectin::Galactosyl_T 165-343::385-580
    857 CGPG2349.pep IQ::IQ 120-140::142-162
    858 CGPG2354.pep ABC1 183-306
    859 CGPG2369.pep DAGK_cat 228-368
    860 CGPG2382.pep WD40::WD40::WD40::WD40 65-103::106-144::197-235::240-278
    861 CGPG2392.pep UBX 311-392
    862 CGPG2397.pep AA_permease 64-510
    863 CGPG240.pep Hydrolase 22-210
    865 CGPG2433.pep DUF23 289-544
    868 CGPG2464.pep Glyco_transf_8 83-345
    869 CGPG2472.pep Band_7 35-227
    870 CGPG2480.pep Prefoldin 53-175
    871 CGPG253.pep HEAT::HEAT::HEAT::HEAT:: 82-117::158-194::197-233::236-
    HEAT::HEAT::HEAT::HEAT:: 272::275-311::314-350::353-389::392-
    HEAT::HEAT::HEAT::HEAT 428::431-467::470-506::509-545:548-584
    872 CGPG2538.pep PfkB 7-297
    873 CGPG2567.pep zf-C3HC4 372-412
    874 CGPG2571.pep zf-C3HC4 146-187
    875 CGPG258.pep Cyclin_N::Cyclin_C 185-310::312-433
    876 CGPG268.pep PTR2 97-514
    877 CGPG274.pep WD40::WD40::WD40 259-298::303-342::350-389
    878 CGPG275.pep PP2C 32-271
    879 CGPG277.pep IGPD 103-247
    880 CGPG2785.pep SIR2 52-216
    881 CGPG2832.pep Myb_DNA-binding 195-243
    883 CGPG2865.pep SRF-TF 17-67
    884 CGPG2874.pep polyprenyl_synt 123-383
    885 CGPG2914.pep AP2 84-142
    886 CGPG295.pep Pro_isomerase 96-256
    888 CGPG3009.pep Arf 4-184
    889 CGPG3030.pep Pkinase 4-301
    890 CGPG3048.pep adh_short 18-186
    891 CGPG3056.pep PP2C 76-341
    893 CGPG309.pep Cyclin_N 4-143
    894 CGPG3094.pep C2 6-87
    895 CGPG3095.pep F-box::LRR_2::FBD 5-52::163-188::374-426
    896 CGPG3137.pep Spermine_synth 54-313
    897 CGPG3156.pep DEAD::Helicase_C 33-212::279-355
    898 CGPG3157.pep DEAD::Helicase_C 175-355::427-503
    899 CGPG3205.pep F-box::Kelch_1::Kelch_1 130-177::220-269::347-389
    900 CGPG3236.pep Thioredoxin 4-108
    901 CGPG3248.pep Copine 102-250
    902 CGPG3255.pep NTP_transferase::Hexapep::Hexapep:: 10-246::294-311:312-329::335-
    Hexapep::Hexapep 352::379-396
    903 CGPG3258.pep UDPGT 23-484
    904 CGPG3261.pep Pkinase 79-334
    907 CGPG3283.pep Mo25 1-339
    908 CGPG3302.pep SRF-TF::K-box 9-59::76-174
    909 CGPG3334.pep GRP 1-113
    910 CGPG3361.pep DUF1644 38-255
    911 CGPG337.pep Glyco_transf_8 19-264
    912 CGPG3400.pep IQ 304-324
    914 CGPG3424.pep TFlIS_C 79-117
    915 CGPG3428.pep DUF914 136-435
    916 CGPG3465.pep zf-MYND::UCH 57-94::326-630
    917 CGPG347.pep DREPP 1-225
    919 CGPG3567.pep DUF581 63-121
    920 CGPG3575.pep Mago-bind 22-48
    921 CGPG3579.pep SNARE 141-203
    926 CGPG365.pep MATH::BTB 53-182::206-328
    927 CGPG3665.pep BNR::BNR::BNR 138-149::189-200::239-250
    928 CGPG3684.pep Pro_dh 113-464
    929 CGPG3690.pep MtN3_slv::MtN3_slv 10-97::131-217
    930 CGPG3717.pep OTU 219-331
    931 CGPG372.pep SET 83-212
    934 CGPG3781.pep SRF-TF 11-65
    935 CGPG380.pep Histone 25-94
    936 CGPG3821.pep F-box::FBA_3 5-52::205-281
    937 CGPG3824.pep WRKY 107-169
    938 CGPG3901.pep 2OG-FeII_Oxy 166-271
    939 CGPG391.pep Histone 58-132
    941 CGPG394.pep DUF6::TPT 11-152::170-319
    942 CGPG3964.pep Pyr_redox 174-248
    943 CGPG397.pep SOR_SNZ::ThiG 24-229::123-290
    945 CGPG3983.pep DUF6::DUF6 31-164::213-342
    946 CGPG3986.pep WD40::WD40 160-197::249-288
    947 CGPG3991.pep SNARE_assoc 111-232
    948 CGPG4050.pep PP2C 49-327
    949 CGPG4070.pep Not3::NOT2_3_5 2-246::693-881
    950 CGPG4071.pep Pkinase_Tyr 135-389
    951 CGPG4099.pep 14-3-3 6-243
    952 CGPG4138.pep adh_short 44-217
    953 CGPG4152.pep RRM_1 11-78
    954 CGPG4153.pep HMG-CoA_red 190-583
    955 CGPG4164.pep PP2C 22-322
    956 CGPG4169.pep WD40::WD40::WD40::WD40 253-291::298-336::340-378::510-549
    957 CGPG421.pep Pkinase::efhand::efhand::efhand::efhand 22-280::327-355::363-391::399-427::433-461
    958 CGPG422.pep Pkinase 73-331
    959 CGPG4223.pep SRF-TF 23-76
    960 CGPG4240.pep F-box 8-56
    961 CGPG4242.pep PP2C 58-341
    962 CGPG4248.pep efhand::efhand::efhand 10-38::89-117::127-155
    963 CGPG425.pep Pkinase_Tyr 8-260
    964 CGPG4265.pep Cys_Met_Meta_PP 42-432
    965 CGPG4283.pep Dehydrin 36-183
    966 CGPG4297.pep Globin 10-149
    967 CGPG43.pep Aa_trans 46-481
    968 CGPG430.pep Pkinase 8-264
    969 CGPG4305.pep Rib_5-P_isom_A 85-273
    970 CGPG4307.pep Orn_Arg_deC_N::Orn_DAP_Arg_deC 98-348::351-459
    971 CGPG4315.pep PPR::PPR::PPR::PPR::PPR::PPR 139-173::209-243::286-320::321-
    355::356-390::391-425
    972 CGPG4320.pep DUF6::DUF6 20-153::190-319
    973 CGPG4344.pep Mito_carr::Mito_carr::Mito_carr 13-98::104-199::203-297
    975 CGPG4349.pep Aha1_N::AHSA1 29-165::233-291
    976 CGPG4365.pep CCT 220-258
    978 CGPG4389.pep Aminotran_1_2 23-376
    979 CGPG4404.pep p450 37-514
    980 CGPG4405.pep p450 69-504
    981 CGPG4419.pep p450 33-477
    982 CGPG4432.pep p450 70-528
    984 CGPG4443.pep p450 32-551
    985 CGPG445.pep PLAT::Lipoxygenase 54-159::171-843
    986 CGPG4453.pep p450 40-500
    987 CGPG4481.pep Glyco_hydro_17 34-352
    988 CGPG4490.pep AMP-binding 42-473
    989 CGPG4498.pep Glyco_hydro_1 40-516
    990 CGPG4506.pep RRM_1 18-89
    991 CGPG4553.pep DUF313 158-265
    992 CGPG4583.pep HIT 43-142
    993 CGPG4643.pep Pkinase 400-656
    994 CGPG4650.pep Pkinase 141-425
    996 CGPG468.pep Fer4::Fer4 116-139::155-178
    997 CGPG4684.pep MIP 11-232
    998 CGPG4689.pep LRRNT_2::LRR_1::LRR_1::Pkinase 29-70::120-142::144-165::261-532
    999 CGPG4691.pep PCI 281-385
    1000 CGPG4702.pep DUF6::TPT 106-231::240-385
    1001 CGPG4703.pep TPT 205-349
    1002 CGPG4710.pep CPSase_L_chain::CPSase_L_D2:: 97-217::219-455::515-638::648-775::
    CPSase_L_D3::CPSase_L_chain:: 777-989::1061-1148
    CPSase_L_D2::MGS
    1003 CGPG4713.pep DUF231 241-420
    1004 CGPG4730.pep DHquinase_I::Shikimate_dh_N::Shikimate_DH 96-313::328-408::440-558
    1005 CGPG4747.pep UQ_con 8-145
    1006 CGPG4755.pep Cpn60_TCP1 30-520
    1008 CGPG4779.pep Peptidase_M22 27-305
    1009 CGPG4848.pep PGAM 77-246
    1010 CGPG4879.pep SIS::CBS 64-197::229-350
    1011 CGPG4882.pep TFlIS 121-206
    1012 CGPG4892.pep DUF260 5-105
    1013 CGPG4903.pep DUF260 7-108
    1014 CGPG4925.pep WD40::WD40::WD40::WD40 74-112::116-153::207-245::249-287
    1015 CGPG4937.pep NLE::WD40::WD40::WD40::WD40 11-79::140-182::195-233::262-299::348-387
    1016 CGPG4949.pep Pkinase 208-470
    1017 CGPG4971.pep SKI 11-177
    1018 CGPG499.pep Voltage_CLC::CBS 138-560::593-759
    1019 CGPG5004.pep Adh_short 53-224
    1020 CGPG5028.pep Adh_short 42-200
    1021 CGPG5032.pep Adh_short 48-216
    1022 CGPG5038.pep DUF26::DUF26::Pkinase 74-134::200-254::345-620
    1023 CGPG5045.pep LRRNT_2::LRR_1::LRR_1::LRR_1:: 24-67::97-119::122-144::146-168::170-
    LRR_1::Pkinase 192::306-576
    1024 CGPG5048.pep LRRNT_2::LRR_1::LRR_1::LRR_1:: 22-59::89-111::113-135::137-159::161-
    LRR_1::LRR_1::Pkinase 182::183-205::307-578
    1025 CGPG5051.pep AOX 45-323
    1026 CGPG5061.pep Fibrillarin 1-99
    1027 CGPG5062.pep Skp1_POZ::Skp1 6-66::86-163
    1028 CGPG5069.pep Skp1_POZ::Skp1 4-64::89-167
    1029 CGPG5070.pep Skp1_POZ::Skp1 4-64::72-150
    1030 CGPG5097.pep Pkinase 295-579
    1031 CGPG510.pep Rho_GDI 20-223
    1032 CGPG5100.pep Pkinase 353-615
    1033 CGPG5117.pep efhand_like::PI-PLC-X::PI-PLC-Y::C2 25-105::107-251::294-412::430-523
    1034 CGPG5151.pep p450 1-282
    1035 CGPG5155.pep p450 27-493
    1036 CGPG5159.pep p450 26-520
    1037 CGPG516.pep HD::RelA_SpoT 233-337::427-537
    1038 CGPG5161.pep p450 31-503
    1039 CGPG5186.pep Thioredoxin 70-172
    1040 CGPG519.pep Abhydrolase_1 59-279
    1041 CGPG5190.pep Ribosomal_L37 15-125
    1042 CGPG5191.pep TPR_2 166-199
    1044 CGPG521.pep Abhydrolase_1 65-282
    1045 CGPG5211.pep DUF827 16-271
    1047 CGPG5213.pep DUF623 143-203
    1048 CGPG522.pep FA_desaturase 62-277
    1049 CGPG5223.pep PGM_PMM_I::PGM_PMM_II:: 79-222::251-360::362-486::507-612
    PGM_PMM_III::PGM_PMM_IV
    1050 CGPG5224.pep LRR_1::LRR_1::LRR_1::LRR_1:: 231-252::254-275::277-298::300-321::
    LRR_1::LRR_1::LRR_1::LRR_1 323-344::369-390::392-413::440-461
    1051 CGPG5225.pep p450 37-452
    1052 CGPG5254.pep 2OG-FeII_Oxy 162-279
    1053 CGPG5257.pep SpolIE 130-374
    1054 CGPG5262.pep SH3_1 303-359
    1056 CGPG5282.pep F-box::Sel1::Sel1::zf-MYND 17-69::129-167::168-203::273-317
    1058 CGPG532.pep Transket_pyr::Transketolase_C 30-207::222-342
    1059 CGPG5336.pep adh_short 19-188
    1060 CGPG5350.pep Aminotran_4 107-395
    1061 CGPG5355.pep GRAM 95-173
    1062 CGPG5376.pep DUF21::CBS 14-191::210-326
    1063 CGPG5377.pep CBS 81-226
    1064 CGPG5382.pep B56 93-416
    1065 CGPG5385.pep Pyridoxal_deC 146-452
    1066 CGPG539.pep Citrate_synt 78-455
    1067 CGPG5437.pep IQ 115-135
    1068 CGPG5450.pep DHDPS 64-341
    1069 CGPG5473.pep Xan_ur_permease 31-438
    1070 CGPG55.pep Sugar_tr 6-719
    1071 CGPG5505.pep AlaDh_PNT_N::AlaDh_PNT_C:: 18-154::194-400::477-583::589-1060
    Saccharop_dh_N::Saccharop_dh
    1073 CGPG5514.pep Cyclin_N::Cyclin_C 165-294::296-422
    1074 CGPG5541.pep Pkinase 316-590
    1075 CGPG5546.pep Cyclin 108-264
    1076 CGPG5552.pep Cornichon 2-125
    1077 CGPG5556.pep SAC3_GANP 20-211
    1078 CGPG557.pep Chitin_bind_1::Barwin 21-62::73-191
    1079 CGPG5576.pep zf-PARP::zf- 11-88::117-195::290-343::394-
    PARP::PADR1::BRCT::WGR:: 471::517-605::633-765::767-979
    PARP_reg::PARP
    1080 CGPG5596.pep Response_reg 9-143
    1081 CGPG5605.pep DEAD::Helicase_C 52-221::290-366
    1082 CGPG5606.pep LRRNT_2::LRR_1::LRR_1::LRR_1:: 21-62::90-113::115-137::140-162::164-
    LRR_1::LRR_1::LRR_1::LRR_1:: 186::188-211::213-235::237-259::261-
    LRR_1::LRR_1::LRR_1::LRR_1:: 283::308-330::332-354::356-375::380-
    LRR_1::LRR_1::LRR_1::LRR_1:: 402::404-426::428-450::452-474::500-
    LRR_1::LRR_1::LRR_1::LRR_1:: 522::524-546::548-570::571-592::683-
    Pkinase 964
    1083 CGPG561.pep XG_FTase 54-532
    1084 CGPG5618.pep Lectin_legB::Pkinase 20-247::376-651
    1085 CGPG5642.pep Aldedh 18-477
    1086 CGPG5644.pep ELFV_dehydrog_N::ELFV_dehydrog 51-181::197-428
    1087 CGPG5647.pep Aldedh 46-511
    1088 CGPG5655.pep Glutaminase 23-309
    1089 CGPG5660.pep Glutaminase 24-308
    1090 CGPG5662.pep Aminotran_3 47-381
    1091 CGPG568.pep FTHFS 14-634
    1092 CGPG5686.pep Aminotran_3 31-387
    1093 CGPG5702.pep Gln-synt_N::Gln-synt_C 28-109::116-397
    1094 CGPG5712.pep Pribosyltran 22-158
    1095 CGPG5713.pep Rib_5-P_isom_A 55-229
    1096 CGPG5715.pep Pribosyltran 27-163
    1097 CGPG5723.pep NDK 4-138
    1098 CGPG5729.pep Cyclin_N::Cyclin_C 210-336::338-457
    1099 CGPG5730.pep Lung_7-TM_R 151-444
    1101 CGPG5741.pep NIF 165-344
    1102 CGPG5752.pep CAF1 161-404
    1103 CGPG5771.pep Acyltransferase 84-277
    1104 CGPG5778.pep Aa_trans 51-498
    1105 CGPG5782.pep Sugar_tr 65-525
    1106 CGPG5785.pep Sugar_tr 69-530
    1107 CGPG5797.pep AA_permease 94-562
    1108 CGPG580.pep MGDG_synth::Glyco_tran_28_C 155-323::349-512
    1109 CGPG5805.pep AA_permease 57-511
    1110 CGPG5810.pep Ank::Ank::Pkinase_Tyr 74-106::107-139::200-468
    1111 CGPG5822.pep Pkinase 131-418
    1112 CGPG5837.pep Pkinase 14-275
    1113 CGPG5855.pep Pkinase 81-363
    1114 CGPG5868.pep Pkinase_Tyr 45-312
    1115 CGPG587.pep FKBP_C 104-208
    1117 CGPG5893.pep Pkinase 52-314
    1118 CGPG5909.pep ADH_zinc_N 163-310
    1119 CGPG5914.pep ADH_N::ADH_zinc_N 54-188::219-362
    1123 CGPG5930.pep Mov34 328-437
    1124 CGPG5945.pep Pyr_redox_2 8-305
    1125 CGPG5958.pep Pyr_redox_2 8-304
    1126 CGPG5977.pep Ank::Ank::Ank::Pkinase 48-80::81-113::114-146::166-424
    1127 CGPG598.pep Nramp 66-429
    1128 CGPG5986.pep Pkinase 43-329
    1129 CGPG5994.pep F-box::LRR_2 62-108::314-340
    1130 CGPG5996.pep Tetraspannin 4-230
    1131 CGPG6021.pep RRM_1::RRM_1 8-77::108-178
    1132 CGPG6027.pep RRM_1 42-113
    1133 CGPG6035.pep Pyr_redox_2::efhand 51-370::376-404
    1134 CGPG604.pep PSI_PsaH 6-145
    1136 CGPG606.pep Phytochelatin::DUF1984 46-178::179-259
    1137 CGPG6069.pep RNA_pol_A_bac 124-268
    1138 CGPG608.pep TB2_DP1_HVA22 11-108
    1139 CGPG6080.pep Str_synth 144-232
    1140 CGPG6082.pep Ras 8-179
    1141 CGPG6089.pep NicO 153-372
    1143 CGPG6128.pep Reticulon 22-197
    1144 CGPG614.pep cobW 74-246
    1145 CGPG6149.pep Glutaredoxin 84-148
    1146 CGPG6172.pep Ras 11-173
    1147 CGPG6174.pep Ras 19-180
    1148 CGPG6176.pep Ras 15-177
    1149 CGPG6197.pep Phi_1 55-334
    1150 CGPG620.pep tRNA-synt_1g 71-430
    1152 CGPG6204.pep mTERF 75-357
    1153 CGPG621.pep RRM_1 19-90
    1154 CGPG6210.pep Sugar_tr 29-459
    1155 CGPG6211.pep Sugar_tr 24-479
    1156 CGPG6214.pep Sugar_tr 26-487
    1157 CGPG6215.pep PTR2 93-486
    1158 CGPG6222.pep Sugar_tr 27-490
    1159 CGPG6229.pep Sugar_tr 28-490
    1160 CGPG6233.pep MFS_1 37-473
    1161 CGPG6237.pep Sugar_tr 25-483
    1162 CGPG6243.pep Pkinase 25-333
    1163 CGPG6248.pep Pkinase::NAF 22-276::306-366
    1164 CGPG6252.pep Pkinase::NAF 12-266::298-358
    1165 CGPG6267.pep Pkinase 68-306
    1166 CGPG6272.pep Pkinase 74-349
    1167 CGPG6294.pep Pkinase 75-352
    1168 CGPG63.pep p450 44-511
    1170 CGPG6317.pep PTR2 101-488
    1171 CGPG6328.pep Trehalose_PPase 121-354
    1172 CGPG6334.pep Sterol_desat 34-245
    1173 CGPG6336.pep Sterol_desat 38-247
    1174 CGPG6349.pep LRR_1::LRR_1::LRR_1::LRR_1:: 42-62::64-84::108-128::130-
    LRR_1::LRR_1::LRR_1 151::153-174::176-197::199-219
    1175 CGPG6352.pep zf-CCHC 81-98
    1177 CGPG6364.pep Gp_dh_N::Gp_dh_C 3-152::157-313
    1178 CGPG6366.pep Gp_dh_N::Gp_dh_C 3-153::158-314
    1179 CGPG6375.pep Aminotran_1_2 36-390
    1180 CGPG6388.pep NTP_transferase 15-285
    1181 CGPG6391.pep ADH_N::ADH_zinc_N 32-143::172-312
    1182 CGPG6399.pep ADH_N::ADH_zinc_N 27-155::186-332
    1183 CGPG6407.pep Glucokinase 5-341
    1184 CGPG6418.pep ADH_N::ADH_zinc_N 28-156::187-333
    1185 CGPG6430.pep Iso_dh 6-355
    1186 CGPG6432.pep ADH_N::ADH_zinc_N 25-135::166-305
    1187 CGPG6437.pep TPT 205-388
    1188 CGPG6445.pep Aldedh 45-511
    1189 CGPG6450.pep Aldedh 26-491
    1190 CGPG6458.pep Aldedh 22-480
    1191 CGPG6465.pep PfkB 10-314
    1192 CGPG6476.pep PFK 3-278
    1193 CGPG6505.pep Aminotran_3 123-449
    1194 CGPG6507.pep Gln-synt_N::Gln-synt_C 105-187::193-446
    1195 CGPG6509.pep Glutaminase 112-396
    1196 CGPG6510.pep Aldedh 17-476
    1197 CGPG6515.pep Aldedh 19-476
    1198 CGPG6520.pep Aldedh 29-491
    1199 CGPG6531.pep Enolase_N::Enolase_C 3-133::138-425
    1200 CGPG6553.pep Aldedh 103-563
    1201 CGPG6557.pep ELFV_dehydrog_N::ELFV_dehydrog 145-275::290-533
    1202 CGPG6563.pep Aminotran_1_2 120-472
    1203 CGPG6564.pep iPGM_N::Metalloenzyme 90-451::461-576
    1204 CGPG6572.pep Gp_dh_N::Gp_dh_C 91-241::246-402
    1205 CGPG6577.pep iPGM_N::Metalloenzyme 92-451::461-577
    1206 CGPG6588.pep Pyr_redox_2::Pyr_redox_dim 92-409::437-546
    1207 CGPG6596.pep Biotin_lipoyl::E3_binding::2-oxoacid_dh 91-164::228-264::296-521
    1209 CGPG6619.pep Transketolase_N::Transket_pyr::Transketolase_C 101-435::450-627::639-754
    1210 CGPG6623.pep PGAM 96-330
    1211 CGPG6626.pep OstA 109-219
    1212 CGPG663.pep Pro_CA 155-325
    1213 CGPG6635.pep Cytochrom_C 126-204
    1215 CGPG6641.pep AstE_AspA 93-372
    1216 CGPG6642.pep Transket_pyr::Transketolase_C 125-303::319-443
    1217 CGPG6645.pep TIM 95-336
    1218 CGPG6660.pep CBS 97-214
    1219 CGPG6671.pep NTP_transferase 102-374
    1220 CGPG6697.pep Transaldolase 100-400
    1221 CGPG6706.pep iPGM_N::Metalloenzyme 90-451:461-576
    1222 CGPG6723.pep Aminotran_1_2 124-478
    1223 CGPG6729.pep Gln-synt_N::Gln-synt_C 100-182::189-470
    1224 CGPG6738.pep Aminotran_1_2 123-473
    1225 CGPG6742.pep Aldedh 105-563
    1226 CGPG6752.pep TIM 92-334
    1227 CGPG6760.pep GATase_2::Asn_synthase 2-164::241-531
    1228 CGPG6768.pep PGI 55-545
    1229 CGPG6779.pep Isoamylase_N::Alpha-amylase 105-182::219-613
    1230 CGPG6785.pep Molybdop_Fe4S4::Molybdopterin:: 44-105::108-660::892-1011
    Molydop_binding
    1231 CGPG6800.pep PGI 52-541
    1232 CGPG686.pep RRM_1::zf-CCHC 9-80::118-135
    1233 CGPG6898.pep Hin1 28-163
    1234 CGPG6900.pep Pkinase 97-365
    1236 CGPG6920.pep Dehydrin 14-128
    1237 CGPG6921.pep CorA 48-440
    1240 CGPG6945.pep SNARE 37-99
    1241 CGPG6946.pep MATH 13-133
    1242 CGPG6948.pep PAP2 100-233
    1243 CGPG6974.pep DUF538 7-146
    1244 CGPG6976.pep DUF926 293-406
    1245 CGPG6996.pep CPDase 1-179
    1246 CGPG7002.pep zf-C3HC4 123-157
    1247 CGPG7013.pep zf-C3HC4 115-156
    1248 CGPG7021.pep Invertase_neut 98-564
    1251 CGPG7075.pep DUF1749 77-349
    1252 CGPG7080.pep Glutaredoxin 44-106
    1253 CGPG7094.pep DUF300 6-281
    1254 CGPG7095.pep Abhydrolase_3 107-321
    1255 CGPG7104.pep Saccharop_dh 13-445
    1256 CGPG7118.pep F-box 25-73
    1257 CGPG7122.pep Pkinase 20-280
    1258 CGPG713.pep Cyclin_N 5-135
    1259 CGPG7130.pep CS 145-220
    1260 CGPG7145.pep Transthyretin 191-310
    1261 CGPG7166.pep DnaJ 79-141
    1262 CGPG7179.pep Bystin 127-423
    1263 CGPG7184.pep PBD 27-127
    1264 CGPG7185.pep GAF::HisKA 190-346::382-445
    1265 CGPG7192.pep 2OG-FeII_Oxy 201-301
    1266 CGPG7199.pep RWD 3-122
    1267 CGPG72.pep Amino_oxidase 66-528
    1268 CGPG7231.pep B3_4::B5 118-280::305-378
    1269 CGPG7241.pep Peptidase_C26 58-281
    1272 CGPG7265.pep ARM_1 12-296
    1273 CGPG7274.pep DUF640 36-168
    1274 CGPG7291.pep eIF-1a 20-91
    1275 CGPG7303.pep Aldedh 20-484
    1276 CGPG7315.pep Y_phosphatase2 116-280
    1278 CGPG7327.pep Actin 2-470
    1280 CGPG7347.pep Tcp11 648-1133
    1281 CGPG7348.pep CorA 90-467
    1283 CGPG7356.pep Metallophos 2-120
    1284 CGPG7359.pep Methyltransf_12 38-133
    1286 CGPG7372.pep zf-C3HC4 119-160
    1287 CGPG7379.pep zf-C3HC4 36-76
    1288 CGPG7398.pep DUF212 22-167
    1289 CGPG7403.pep TLD 203-341
    1290 CGPG7404.pep PBP 25-170
    1291 CGPG7410.pep HLH 36-83
    1292 CGPG7417.pep MMR_HSR1 131-252
    1293 CGPG7423.pep Gln-synt_N::Gln-synt_C 102-183::190-471
    1294 CGPG7424.pep FBPase 92-424
    1297 CGPG7443.pep DUF1001 92-274
    1298 CGPG7449.pep ScpA_ScpB 104-347
    1301 CGPG7459.pep DUF1350 90-360
    1303 CGPG7481.pep Abhydrolase_1 113-361
    1304 CGPG7483.pep GTP_EFTU::GTP_EFTU_D2::EFG_C 62-260::281-355::461-551
    1306 CGPG7503.pep PBP 19-170
    1307 CGPG7504.pep MSF1 15-187
    1309 CGPG7516.pep DUF783 25-229
    1312 CGPG7524.pep lsy1 1-292
    1313 CGPG7525.pep UFD1 10-184
    1315 CGPG7537.pep KTI12 1-291
    1317 CGPG7575.pep Efhand 95-123
    1318 CGPG7577.pep TP_methylase 1-213
    1319 CGPG7590.pep Ribonuc_L-PSP 61-179
    1321 CGPG7601.pep CCT 237-275
    1322 CGPG7605.pep RRM_1 88-158
    1323 CGPG7607.pep Amidohydro_2 10-289
    1325 CGPG7632.pep zf-Tim10_DDP 12-77
    1326 CGPG7673.pep zf-MYND::UCH 76-113::468-774
    1327 CGPG7683.pep zf-LSD1::zf-LSD1::zf-LSD1 28-52::67-91::105-129
    1328 CGPG773.pep H_PPase 64-798
    1329 CGPG7776.pep DUF525 311-445
    1330 CGPG7781.pep SapB_1::SapB_2::SapB_1::SapB_2 45-83::86-119::131-169::172-206
    1331 CGPG7785.pep LRRNT_2::LRR_1::LRR_1::LRR_1:: 24-65::93-115::117-139::141-163::165-
    LRR_1::LRR_1::LRR_1::Pkinase 187::189-211::213-235::415-682
    1332 CGPG7787.pep Aldose_epim 26-301
    1334 CGPG7796.pep WD40::WD40::WD40::WD40::WD40:: 50-88::92-130::134-174::182-220::391-
    WD40::WD40::WD40::WD40::WD40:: 432::436-475::489-527::531-569::573-
    Utp13 611::615-653::674-809
    1335 CGPG7797.pep GILT 35-144
    1336 CGPG7801.pep LRR_1::LRR_1::LRR_1::LRR_1::LRR_1:: 106-129::132-154::156-178::180-199::201-
    LRR_1::LRR_1::LRR_1::Pkinase 223::225-246::249-272::273-294::456-716
    1337 CGPG7813.pep WD40::WD40::WD40::WD40::PWP2 379-417::421-459::507-545::549-
    587::785-900
    1341 CGPG7863.pep zf-CW::MBD 100-153::162-237
    1342 CGPG7868.pep BCNT 165-244
    1343 CGPG7881.pep Aldedh 99-558
    1344 CGPG7887.pep HEAT::Arm::HEAT::Arm 191-222::262-302::389-424::423-463
    1345 CGPG7899.pep RRM_1 225-295
    1346 CGPG7901.pep IQ::IQ 107-127::129-149
    1347 CGPG7909.pep DUF383::DUF384 92-271::272-330
    1348 CGPG7911.pep AAA 245-447
    1349 CGPG7919.pep Cullin 30-191
    1350 CGPG7935.pep IQ::IQ 93-113::115-135
    1351 CGPG7940.pep RRM_1 96-161
    1352 CGPG7959.pep Cyclin_N::Cyclin_C 180-306::308-428
    1353 CGPG7967.pep IQ::IQ 106-126::128-148
    1354 CGPG7975.pep Arm::Arm 28-68::70-110
    1355 CGPG7996.pep efhand 136-164
    1356 CGPG8006.pep AAA 241-440
    1357 CGPG801.pep Cyt-b5 74-171
    1358 CGPG8023.pep RRM_1 11-82
    1359 CGPG8025.pep IQ::IQ 93-113::115-135
    1360 CGPG8038.pep MFS_1 36-433
    1361 CGPG8053.pep DUF246 182-525
    1364 CGPG8070.pep GILT 32-136
    1365 CGPG8073.pep Dirigent 17-183
    1366 CGPG8076.pep Tryp_alpha_amyl 32-107
    1369 CGPG8095.pep IPK 16-279
    1370 CGPG8096.pep 60KD_IMP 151-348
    1374 CGPG8129.pep Ank::Ank::Ank 49-81::82-114::115-147
    1378 CGPG8165.pep Glutaredoxin 44-106
    1379 CGPG8169.pep Nol1_Nop2_Fmu 226-505
    1380 CGPG8203.pep Uricase::Uricase 11-140::147-300
    1381 CGPG8205.pep DZC 113-148
    1383 CGPG8213.pep Phosphoesterase 27-388
    1384 CGPG8225.pep FBPase 25-348
    1385 CGPG8227.pep NIR_SIR_ferr::NIR_SIR:: 44-111::119-275::331-399::405-553
    NIR_SIR_ferr::NIR_SIR
    1386 CGPG8235.pep Aldedh 12-471
    1387 CGPG8236.pep Molybdop_Fe4S4::Molybdopterin:: 9-63::66-495::593-703::852-903
    Molydop_binding::Fer2_BFD
    1388 CGPG8244.pep PAS_2::GAF::Phytochrome::HisKA:: 15-125::152-320::331-513::528-
    HATPase_c 596::637-747
    1389 CGPG8254.pep NIR_SIR_ferr::NIR_SIR:: 66-133::166-347::362-434::443-591
    NIR_SIR_ferr::NIR_SIR
    1390 CGPG8255.pep PPDK_N::PEP-utilizers::PEP-utilizers_C 16-384::439-531::559-914
    1391 CGPG8262.pep ELFV_dehydrog_N::ELFV_dehydrog 33-163::179-420
    1392 CGPG8264.pep Aldedh 17-480
    1393 CGPG8269.pep PGK 1-396
    1394 CGPG8271.pep Gln-synt_N::Gln-synt_C 16-97::104-386
    1395 CGPG8305.pep Sulfotransfer_1 70-336
    1396 CGPG8320.pep DUF1005 282-487
    1397 CGPG8326.pep Senescence 35-369
    1398 CGPG8344.pep PPR::PPR::PPR::PPR::PPR::PPR::PPR 173-207::208-242::243-277::279-
    312::314-348::349-383::384-418
    1399 CGPG8347.pep Ribosomal_S8 5-130
    1400 CGPG8359.pep Tryp_alpha_amyl 85-167
    1401 CGPG8370.pep Tim17 40-156
    1402 CGPG8371.pep PseudoU_synth_1::PseudoU_synth_1 62-167::324-431
    1404 CGPG8378.pep LysM 78-121
    1406 CGPG841.pep ArfGap 4-120
    1408 CGPG8438.pep DUF239 174-368
    1409 CGPG8450.pep DUF793 1-390
    1410 CGPG8451.pep IQ::IQ 105-125::127-147
    1411 CGPG8459.pep ubiquitin::UBA::XPC-binding::UBA 6-78::145-187::242-298::322-361
    1412 CGPG8461.pep Ribosomal_S8 5-130
    1413 CGPG8463.pep PI3_PI4_kinase 163-421
    1414 CGPG8471.pep F-box::FBA_1 1-46::211-383
    1415 CGPG8474.pep Metallothio_PEC 12-85
    1416 CGPG8475.pep DAO 10-372
    1417 CGPG8476.pep IQ::IQ 84-104::106-126
    1418 CGPG8490.pep ACT::ACT 21-85::110-174
    1419 CGPG8510.pep DUF538 9-149
    1420 CGPG8530.pep Radical_SAM 119-283
    1421 CGPG8533.pep DUF212 27-172
    1425 CGPG8555.pep NUDIX 59-196
    1426 CGPG8561.pep zf-C3HC4 154-191
    1427 CGPG8569.pep 2OG-FeII_Oxy 159-282
    1428 CGPG8573.pep DUF617 83-242
    1431 CGPG8607.pep DUF862 69-219
    1432 CGPG8611.pep Stig1 13-154
    1434 CGPG8632.pep Sina 86-273
    1435 CGPG8634.pep FA_desaturase 55-278
    1436 CGPG8635.pep DUF59 36-117
    1438 CGPG8640.pep DUF581 119-176
    1439 CGPG8642.pep CRAL_TRIO_N::CRAL_TRIO 5-80::93-266
    1441 CGPG8666.pep PetM 69-120
    1443 CGPG8688.pep Polyketide_cyc 60-191
    1444 CGPG8689.pep DUF506 74-282
    1445 CGPG8704.pep GHMP_kinases_N::GHMP_kinases_C 24-93::166-249
    1448 CGPG8769.pep Self-incomp_S1 35-144
    1449 CGPG8774.pep Maf 1-207
    1450 CGPG8778.pep PPR::PPR::PPR::PPR::PPR::PPR 13-47::115-149::249-283::284-
    318::320-354::386-420
    1451 CGPG8784.pep Snf7 16-189
    1452 CGPG879.pep ABC_tran::ABC2_membrane::PDR_assoc:: 195-418::520-733::738-812::887-
    ABC_tran::ABC2_membrane 1077::1174-1388
    1453 CGPG8797.pep AMP-binding 67-488
    1454 CGPG8810.pep DUF1645 80-252
    1455 CGPG8827.pep DUF623 199-263
    1456 CGPG8853.pep DUF1635 1-218
    1457 CGPG8873.pep p450 72-518
    1458 CGPG8877.pep Exo_endo_phos 33-310
    1459 CGPG8878.pep Pkinase::efhand::efhand 79-337::400-428::434-462
    1460 CGPG8881.pep DUF1677 3-107
    1461 CGPG8895.pep RNA_poll_A14 1-137
    1462 CGPG8906.pep MCM 272-635
    1463 CGPG8917.pep Pkinase 363-697
    1464 CGPG8919.pep Usp::Pkinase 11-141::405-676
    1465 CGPG8925.pep DUF617 82-260
    1466 CGPG8930.pep Lectin_legB::Pkinase 26-261::347-617
    1467 CGPG8937.pep LRR_1::LRR_1::LRR_1::Pkinase 440-461::463-485::487-510::602-873
    1468 CGPG8942.pep RRM_1 23-94
    1469 CGPG8946.pep Pkinase 516-786
    1470 CGPG8990.pep V-SNARE 71-221
    1472 CGPG9008.pep TPK_catalytic::TPK_B1_binding 40-180::191-259
    1473 CGPG9016.pep ETC_C1_NDUFA4 54-156
    1474 CGPG9036.pep MSP 93-329
    1475 CGPG9060.pep LSM 22-101
    1477 CGPG908.pep PPR::PPR::PPR::PPR::PPR::PPR:: 62-96::125-158::187-221::250-284::351-
    PPR::PPR 385::386-419::422-456::488-522
    1478 CGPG9093.pep AWPM-19 15-156
    1479 CGPG9096.pep OTU 11-121
    1482 CGPG9111.pep TB2_DP1_HVA22 4-101
    1483 CGPG9112.pep DUF778 10-177
    1484 CGPG9123.pep DUF833 1-264
    1485 CGPG9124.pep Exo_endo_phos 20-427
    1486 CGPG9138.pep ThiC 165-588
    1488 CGPG9150.pep Pkinase 56-326
    1489 CGPG9152.pep eIF2A 217-410
    1490 CGPG9162.pep AAA 211-398
    1491 CGPG9165.pep GATase::GMP_synt_C 11-201::432-524
    1492 CGPG9166.pep GATase::GMP_synt_C 28-210::447-539
    1493 CGPG9171.pep Zip 5-266
    1494 CGPG9177.pep Complex1_30 kDa::Complex1_49 kDa 113-181::329-600
    1495 CGPG9178.pep PRA-CH::PRA-PH 54-129::142-230
    1496 CGPG9179.pep Pkinase 4-283
    1497 CGPG9181.pep P21-Arc 17-187
    1499 CGPG9189.pep SAC3_GANP 19-164
    1500 CGPG9201.pep TPT 201-350
    1501 CGPG9222.pep YjeF_N::Carb_kinase 34-199::257-496
    1502 CGPG9234.pep DUF393 65-183
    1503 CGPG9237.pep Tim17 18-146
    1504 CGPG9244.pep TOM20_plant 9-200
    1506 CGPG9249.pep Pkinase 46-330
    1507 CGPG9251.pep Cyclin_N::Cyclin_C 54-186::188-314
    1508 CGPG9280.pep DUF1000 53-168
    1510 CGPG9302.pep Diphthamide_syn 30-398
    1511 CGPG931.pep Pkinase 114-398
    1512 CGPG9313.pep CN_hydrolase::NAD_synthase 5-200::338-652
    1514 CGPG9327.pep OPT 74-729
    1515 CGPG933.pep WD40:WD40::WD40::WD40:: 46-84::134-173::177-215::222-
    WD40::WD40::WD40 260::314-353::524-562::568-605
    1516 CGPG9334.pep Sugar_tr 7-720
    1517 CGPG967.pep BTB::NPH3 38-135::218-460
    1518 CGPG988.pep Cystatin 36-124
  • TABLE 18
    PEP SEQ Pfam domain
    ID Construct ID name begin start score E-value
    760 CGPG1022 RRM_1 95 165 58.4 2.40E−14 
    761 CGPG1035 Peptidase_C54 82 373 558.5 6.50E−165
    763 CGPG105 AP2 48 112 146.2 8.50E−41 
    764 CGPG1060 DUF788 1 169 339.1 7.70E−99 
    765 CGPG1069 NDUF_B7 2 81 20.4 9.50E−08 
    766 CGPG108 FHA 208 284 59.7 9.90E−15 
    766 CGPG108 PP2C 309 570 282.3 9.50E−82 
    771 CGPG1136 RRM_1 22 87 32.4 1.60E−06 
    774 CGPG1145 NUDIX 24 160 79.2 1.30E−20 
    776 CGPG1173 adh_short 6 181 −32 0.00071
    777 CGPG1176 F-box 2 50 21.6 0.0027
    779 CGPG122 PTR2 113 517 661.3 7.40E−196
    780 CGPG126 Response_reg 34 158 86 1.10E−22 
    781 CGPG1262 Gar1 51 152 251.2 2.10E−72 
    782 CGPG128 Response_reg 25 149 84.9 2.50E−22 
    783 CGPG1280 DUF676 515 717 301.1 2.10E−87 
    784 CGPG1291 DUF862 2 156 209.3 8.70E−60 
    785 CGPG1295 TMEM14 7 104 166.9 5.20E−47 
    787 CGPG1315 Brix 60 255 139.3 1.00E−38 
    788 CGPG1335 LRR_1 424 447 10.1 3.6
    789 CGPG1344 Pkinase 496 767 132.9 8.60E−37 
    789 CGPG1344 Pkinase_Tyr 497 767 81.2 3.30E−21 
    790 CGPG1352 Pkinase 154 425 140.3 5.20E−39 
    790 CGPG1352 Pkinase_Tyr 154 425 142.1 1.50E−39 
    791 CGPG1364 Pkinase 38 416 177.6 3.00E−50 
    793 CGPG1396 malic 106 295 422.9 4.50E−124
    793 CGPG1396 Malic_M 297 550 466.9 2.50E−137
    794 CGPG1398 Glycolytic 11 358 877.1 8.10E−261
    795 CGPG1399 Metallophos 161 360 87.4 4.50E−23 
    796 CGPG1429 NTP_transferase 86 365 444 2.00E−130
    796 CGPG1429 Hexapep 413 430 3.5 55
    796 CGPG1429 Hexapep 466 483 19.6 0.011
    797 CGPG1430 E1_dh 89 393 468.9 6.30E−138
    798 CGPG1445 Pkinase 33 294 257.4 2.90E−74 
    798 CGPG1445 Pkinase_Tyr 33 294 99.8 8.00E−27 
    799 CGPG146 p450 38 482 75.2 2.00E−19 
    800 CGPG1492 Aldedh 29 491 535.5 5.80E−158
    801 CGPG1528 ATP_synt_H 1 70 128.2 2.30E−35 
    802 CGPG1530 ArfGap 15 137 169.4 9.00E−48 
    802 CGPG1530 C2 183 262 103 8.90E−28 
    803 CGPG1535 SPT2 230 329 31.1 9.80E−07 
    804 CGPG1546 CTP_transf_1 101 300 20 2.00E−07 
    805 CGPG1567 Ribosomal_L19 107 212 72.7 1.20E−18 
    806 CGPG1568 FAD_binding_4 82 221 53.1 9.10E−13 
    807 CGPG1575 DUF740 24 595 626.7 1.90E−185
    808 CGPG1619 Pyr_redox_2 27 343 213.2 5.80E−61 
    808 CGPG1619 Pyr_redox 205 297 93.6 6.00E−25 
    808 CGPG1619 Pyr_redox_dim 373 483 158.2 2.10E−44 
    810 CGPG1641 Di19 11 219 487.1 2.10E−143
    811 CGPG1651 DEAD 69 220 110.3 5.50E−30 
    811 CGPG1651 Helicase_C 378 462 45.3 2.00E−10 
    811 CGPG1651 DSHCT 800 988 358.6 1.00E−104
    812 CGPG1656 Cyt-b5 9 82 94.5 3.30E−25 
    812 CGPG1656 FA_desaturase 145 399 256.9 4.10E−74 
    813 CGPG1668 DUF791 4 358 877.2 7.80E−261
    813 CGPG1668 MFS_1 42 406 33.6 6.70E−07 
    815 CGPG1740 DUF860 25 364 615 6.40E−182
    816 CGPG177 WD40 168 205 23.2 0.00096
    816 CGPG177 WD40 257 296 36 1.30E−07 
    817 CGPG1785 PB1 179 266 108.9 1.40E−29 
    817 CGPG1785 Pkinase 863 1126 202.7 8.80E−58 
    817 CGPG1785 Pkinase_Tyr 863 1126 253 6.30E−73 
    818 CGPG182 LRR_1 46 67 11.1 2.3
    818 CGPG182 LRR_1 69 90 12.4 1.4
    818 CGPG182 LRR_1 115 136 11.8 1.8
    818 CGPG182 LRR_1 161 183 8.6 7
    818 CGPG182 LRR_1 208 229 12.9 1.1
    818 CGPG182 LRR_1 231 252 9.4 4.9
    818 CGPG182 LRR_1 276 297 18.4 0.026
    818 CGPG182 LRR_1 382 403 8.8 6.5
    818 CGPG182 LRR_1 405 427 10.2 3.5
    818 CGPG182 LRR_1 429 451 8.8 6.5
    818 CGPG182 LRR_1 477 498 9.9 3.9
    818 CGPG182 LRR_1 500 521 17 0.069
    818 CGPG182 LRR_1 523 544 20.7 0.0052
    819 CGPG1837 TFIIS_M 328 445 155 1.90E−43 
    819 CGPG1837 SPOC 656 762 92.5 1.30E−24 
    820 CGPG1873 Pkinase 20 275 323.7 3.20E−94 
    820 CGPG1873 NAF 314 374 112 1.70E−30 
    823 CGPG1899 F-box 18 65 34.8 3.00E−07 
    823 CGPG1899 Kelch_1 139 186 33.7 6.30E−07 
    823 CGPG1899 Kelch_2 188 235 16.7 0.082
    823 CGPG1899 Kelch_1 189 235 51.4 3.00E−12 
    824 CGPG1913 F-box 31 78 39.4 1.20E−08 
    824 CGPG1913 FBA_1 268 416 −16.6 6.10E−05 
    825 CGPG1918 F-box 30 77 36 1.30E−07 
    826 CGPG1919 F-box 65 112 43.1 9.70E−10 
    827 CGPG1922 F-box 25 72 46.6 8.30E−11 
    827 CGPG1922 Kelch_2 118 163 24.4 0.0004
    827 CGPG1922 Kelch_1 118 163 39.1 1.50E−08 
    827 CGPG1922 Kelch_2 165 208 26.7 8.10E−05 
    827 CGPG1922 Kelch_1 165 210 49.6 1.00E−11 
    828 CGPG1929 F-box 1 44 14.8 0.31
    829 CGPG1938 F-box 8 55 35.4 2.00E−07 
    829 CGPG1938 LRR_2 159 185 29.1 1.60E−05 
    830 CGPG1956 Pre-SET 409 558 20.9 5.60E−06 
    830 CGPG1956 SET 560 702 157.5 3.40E−44 
    831 CGPG1964 zf-C3HC4 109 147 35.2 2.30E−07 
    831 CGPG1964 YDG_SRA 228 345 212.8 8.10E−61 
    832 CGPG1973 zf-UBR 40 109 73.4 7.10E−19 
    833 CGPG1977 TFIIF_alpha 18 542 984.3 4.60E−293
    834 CGPG1996 Pkinase 3 286 373.9 2.50E−109
    835 CGPG2005 NADPH_Ox 130 229 245.7 9.80E−71 
    835 CGPG2005 Ferric_reduct 352 511 177.6 3.00E−50 
    835 CGPG2005 FAD_binding_8 552 671 227.3 3.40E−65 
    835 CGPG2005 NAD_binding_6 677 850 271.5 1.60E−78 
    837 CGPG2044 PTR2 99 507 587.7 1.10E−173
    838 CGPG2059 Nuc_sug_transp 104 340 26.5 4.50E−15 
    839 CGPG2065 PEARLI-4 342 611 652.6 3.30E−193
    841 CGPG2072 DUF1639 264 300 60.4 5.90E−15 
    842 CGPG2074 HMA 75 138 46.4 9.40E−11 
    842 CGPG2074 HMA 173 235 50.6 5.40E−12 
    843 CGPG2116 NOI 1 67 147.8 2.80E−41 
    845 CGPG2142 MATH 101 233 5.3 0.028
    845 CGPG2142 MATH 258 375 33 1.00E−06 
    847 CGPG2190 DJ-1_PfpI 34 174 110.4 5.10E−30 
    847 CGPG2190 DJ-1_PfpI 240 378 129.9 6.90E−36 
    849 CGPG221 DnaJ 35 96 137.6 3.30E−38 
    849 CGPG221 DnaJ_CXXCXGXG 160 243 101 3.60E−27 
    849 CGPG221 DnaJ_C 256 378 210.4 4.00E−60 
    850 CGPG2213 RNA_pol_I_A49 83 441 629.1 3.80E−186
    851 CGPG2247 DUF23 256 497 99.8 8.20E−27 
    852 CGPG228 p450 67 511 252.1 1.10E−72 
    853 CGPG2301 PC_rep 414 447 28.8 1.90E−05 
    853 CGPG2301 PC_rep 448 484 28 3.20E−05 
    853 CGPG2301 PC_rep 485 519 33.7 6.30E−07 
    853 CGPG2301 PC_rep 523 557 10.4 0.45
    853 CGPG2301 PC_rep 671 705 11.9 0.28
    853 CGPG2301 PC_rep 706 740 32.7 1.30E−06 
    854 CGPG2304 Phi_1 32 309 680.3 1.40E−201
    856 CGPG2348 Gal-bind_lectin 165 343 143.9 4.40E−40 
    856 CGPG2348 Galactosyl_T 385 580 105.4 1.60E−28 
    857 CGPG2349 IQ 120 140 33.4 7.70E−07 
    857 CGPG2349 IQ 142 162 13.6 0.74
    858 CGPG2354 ABC1 183 306 132.6 1.00E−36 
    859 CGPG2369 DAGK_cat 228 368 129.9 7.20E−36 
    860 CGPG2382 WD40 65 103 48.6 2.20E−11 
    860 CGPG2382 WD40 106 144 32.1 2.00E−06 
    860 CGPG2382 WD40 197 235 34.5 3.70E−07 
    860 CGPG2382 WD40 240 278 47.3 5.30E−11 
    861 CGPG2392 UBX 311 392 104 4.40E−28 
    862 CGPG2397 AA_perrnease 64 510 34.5 3.70E−07 
    863 CGPG240 Hydrolase 22 210 118.1 2.50E−32 
    865 CGPG2433 DUF23 289 544 209.9 6.00E−60 
    868 CGPG2464 Glyco_transf_8 83 345 341.2 1.70E−99 
    869 CGPG2472 Band_7 35 227 90.6 4.80E−24 
    870 CGPG2480 Prefoldin 53 175 140.5 4.40E−39 
    871 CGPG253 HEAT 82 117 18.6 0.022
    871 CGPG253 HEAT 158 194 22.9 0.0012
    871 CGPG253 HEAT 197 233 15.3 0.22
    871 CGPG253 HEAT 236 272 31.1 3.80E−06 
    871 CGPG253 HEAT 275 311 27.5 4.80E−05 
    871 CGPG253 HEAT 314 350 26.6 8.60E−05 
    871 CGPG253 HEAT 353 389 27.9 3.60E−05 
    871 CGPG253 HEAT 392 428 24.6 0.00035
    871 CGPG253 HEAT 431 467 24.2 0.00045
    871 CGPG253 HEAT 470 506 21.3 0.0036
    871 CGPG253 HEAT 509 545 18.9 0.019
    871 CGPG253 HEAT 548 584 17.9 0.036
    872 CGPG2538 PfkB 7 297 115.6 1.40E−31 
    873 CGPG2567 zf-C3HC4 372 412 42.6 1.40E−09 
    874 CGPG2571 zf-C3HC4 146 187 39.3 1.30E−08 
    875 CGPG258 Cyclin_N 185 310 240.4 3.70E−69 
    875 CGPG258 Cyclin_C 312 433 188.8 1.30E−53 
    876 CGPG268 PTR2 97 514 458.7 7.20E−135
    877 CGPG274 WD40 259 298 36.8 7.40E−08 
    877 CGPG274 WD40 303 342 26.9 7.30E−05 
    877 CGPG274 WD40 350 389 26.6 9.10E−05 
    878 CGPG275 PP2C 32 271 205.2 1.50E−58 
    879 CGPG277 IGPD 103 247 372.6 6.20E−109
    880 CGPG2785 SIR2 52 216 107.2 4.70E−29 
    881 CGPG2832 Myb_DNA-binding 195 243 33.6 6.80E−07 
    883 CGPG2865 SRF-TF 17 67 94.4 3.50E−25 
    884 CGPG2874 polyprenyl_synt 123 383 275.6 9.70E−80 
    885 CGPG2914 AP2 84 142 18 5.20E−06 
    886 CGPG295 Pro_isomerase 96 256 405.8 6.30E−119
    888 CGPG3009 Arf 4 184 165.1 1.80E−46 
    889 CGPG3030 Pkinase 4 301 322.2 9.20E−94 
    890 CGPG3048 adh_short 18 186 135.3 1.60E−37 
    890 CGPG3048 KR 18 188 −35.3 2.60E−05 
    891 CGPG3056 PP2C 76 341 261.8 1.40E−75 
    893 CGPG309 Cyclin_N 4 143 8.9 2.50E−05 
    894 CGPG3094 C2 6 87 73.4 7.30E−19 
    895 CGPG3095 F-box 5 52 34.8 2.90E−07 
    895 CGPG3095 LRR_2 163 188 34.7 3.30E−07 
    895 CGPG3095 FBD 374 426 83.7 5.60E−22 
    896 CGPG3137 Spermine_synth 54 313 429.1 6.20E−126
    897 CGPG3156 DEAD 33 212 223 6.80E−64 
    897 CGPG3156 Helicase_C 279 355 131.8 1.90E−36 
    898 CGPG3157 DEAD 175 355 231.2 2.30E−66 
    898 CGPG3157 Helicase_C 427 503 130.3 5.40E−36 
    899 CGPG3205 F-box 130 177 35.8 1.50E−07 
    899 CGPG3205 Kelch_1 220 269 34.4 4.00E−07 
    899 CGPG3205 Kelch_2 220 269 16.3 0.11
    899 CGPG3205 Kelch_1 347 389 11.8 0.18
    900 CGPG3236 Thioredoxin 4 108 67.2 5.20E−17 
    901 CGPG3248 Copine 102 250 294.3 2.20E−85 
    902 CGPG3255 NTP_transferase 10 246 50.6 2.10E−13 
    902 CGPG3255 Hexapep 294 311 4.4 42
    902 CGPG3255 Hexapep 312 329 16.7 0.083
    902 CGPG3255 Hexapep 335 352 10.7 5.2
    902 CGPG3255 Hexapep 379 396 1.8 85
    903 CGPG3258 UDPGT 23 484 −66 2.70E−07 
    904 CGPG3261 Pkinase 79 334 261.2 2.00E−75 
    907 CGPG3283 Mo25 1 339 584.5 1.00E−172
    908 CGPG3302 SRF-TF 9 59 118.3 2.20E−32 
    908 CGPG3302 K-box 76 174 130.2 5.60E−36 
    909 CGPG3334 GRP 1 113 129.8 7.40E−36 
    910 CGPG3361 DUF1644 38 255 215.2 1.50E−61 
    911 CGPG337 Glyco_transf_8 19 264 298.7 1.10E−86 
    912 CGPG3400 IQ 304 324 14.7 0.33
    914 CGPG3424 TFIIS_C 79 117 31.8 2.40E−06 
    915 CGPG3428 DUF914 136 435 −191.9 0.0045
    916 CGPG3465 zf-MYND 57 94 50.2 6.80E−12 
    916 CGPG3465 UCH 326 630 175.9 1.00E−49 
    917 CGPG347 DREPP 1 225 483.5 2.50E−142
    917 CGPG347 PPAK 172 197 0.5 17
    919 CGPG3567 DUF581 63 121 135.5 1.40E−37 
    920 CGPG3575 Mago-bind 22 48 58.7 2.00E−14 
    921 CGPG3579 SNARE 141 203 59.8 8.90E−15 
    926 CGPG365 MATH 53 182 59.9 8.30E−15 
    926 CGPG365 BTB 206 328 86.5 7.90E−23 
    927 CGPG3665 BNR 138 149 10.5 5.1
    927 CGPG3665 BNR 189 200 8.4 9.7
    927 CGPG3665 BNR 239 250 10.7 4.8
    928 CGPG3684 Pro_dh 113 464 472.8 4.30E−139
    929 CGPG3690 MtN3_slv 10 97 116 1.10E−31 
    929 CGPG3690 MtN3_slv 131 217 119 1.30E−32 
    930 CGPG3717 OTU 219 331 154.2 3.50E−43 
    931 CGPG372 SET 83 212 181.8 1.70E−51 
    934 CGPG3781 SRF-TF 11 65 30.5 6.00E−06 
    935 CGPG380 Histone 25 94 67.1 5.70E−17 
    936 CGPG3821 F-box 5 52 36.5 9.50E−08 
    936 CGPG3821 FBA_3 205 281 −0.8 0.00013
    937 CGPG3824 WRKY 107 169 89.8 8.20E−24 
    938 CGPG3901 20G-FeII_Oxy 166 271 67.5 4.30E−17 
    939 CGPG391 Histone 58 132 144.1 3.60E−40 
    941 CGPG394 DUF6 11 152 22.3 0.0018
    941 CGPG394 TPT 170 319 165.1 1.80E−46 
    942 CGPG3964 Pyr_redox 174 248 7.9 0.0034
    943 CGPG397 SOR_SNZ 24 229 449.4 4.60E−132
    943 CGPG397 ThiG 123 290 −178.1 0.0011
    945 CGPG3983 DUF6 31 164 50.3 6.60E−12 
    945 CGPG3983 DUF6 213 342 60.5 5.40E−15 
    946 CGPG3986 WD40 160 197 27.3 5.50E−05 
    946 CGPG3986 WD40 249 288 33.1 9.60E−07 
    947 CGPG3991 SNARE_assoc 111 232 91.5 2.60E−24 
    948 CGPG4050 PP2C 49 327 107 5.40E−29 
    949 CGPG4070 Not3 2 246 527.4 1.50E−155
    949 CGPG4070 NOT2_3_5 693 881 217 4.30E−62 
    950 CGPG4071 Pkinase_Tyr 135 389 256.4 5.90E−74 
    950 CGPG4071 Pkinase 135 389 221.3 2.20E−63 
    951 CGPG4099 14-3-3 6 243 509.5 3.80E−150
    952 CGPG4138 adh_short 44 217 55.7 1.60E−13 
    953 CGPG4152 RRM_1 11 78 44.3 4.00E−10 
    954 CGPG4153 HMG-CoA_red 190 583 1044.7 0
    955 CGPG4164 PP2C 22 322 276.7 4.60E−80 
    956 CGPG4169 WD40 253 291 38.4 2.40E−08 
    956 CGPG4169 WD40 298 336 30.8 4.80E−06 
    956 CGPG4169 WD40 340 378 24.8 0.00031
    956 CGPG4169 WD40 510 549 55.3 2.00E−13 
    957 CGPG421 Pkinase 22 280 354.8 1.40E−103
    957 CGPG421 efhand 327 355 39.1 1.50E−08 
    957 CGPG421 efhand 363 391 26.9 7.30E−05 
    957 CGPG421 efhand 399 427 30.3 6.70E−06 
    957 CGPG421 efhand 433 461 37.9 3.50E−08 
    958 CGPG422 Pkinase 73 331 363.9 2.50E−106
    959 CGPG4223 SRF-TF 23 76 25.8 0.00015
    960 CGPG4240 F-box 8 56 30.1 7.90E−06 
    961 CGPG4242 PP2C 58 341 195.8 1.00E−55 
    962 CGPG4248 efhand 10 38 30.5 6.00E−06 
    962 CGPG4248 efhand 89 117 37 6.70E−08 
    962 CGPG4248 efhand 127 155 27.1 6.10E−05 
    963 CGPG425 Pkinase_Tyr 8 260 238.9 1.10E−68 
    963 CGPG425 Pkinase 8 260 224.7 2.00E−64 
    964 CGPG4265 Cys_Met_Meta_PP 42 432 263.8 3.50E−76 
    965 CGPG4283 Dehydrin 36 183 171.1 2.70E−48 
    966 CGPG4297 Globin 10 149 102.6 1.10E−27 
    967 CGPG43 Aa_trans 46 481 587.5 1.30E−173
    968 CGPG430 Pkinase_Tyr 8 264 127.5 3.70E−35 
    968 CGPG430 Pkinase 8 264 297.5 2.50E−86 
    969 CGPG4305 Rib_5-P_isom_A 85 273 −27.7 1.60E−07 
    970 CGPG4307 Orn_Arg_deC_N 98 348 174.8 2.20E−49 
    970 CGPG4307 Orn_DAP_Arg_deC 351 459 125.2 1.80E−34 
    971 CGPG4315 PPR 139 173 7.5 0.97
    971 CGPG4315 PPR 209 243 26.1 0.00013
    971 CGPG4315 PPR 286 320 36.6 8.60E−08 
    971 CGPG4315 PPR 321 355 11.6 0.32
    971 CGPG4315 PPR 356 390 3.1 3.2
    971 CGPG4315 PPR 391 425 11.4 0.33
    972 CGPG4320 DUF6 20 153 52.8 1.20E−12 
    972 CGPG4320 DUF6 190 319 40.8 4.70E−09 
    973 CGPG4344 Mito_carr 13 98 65.1 2.30E−16 
    973 CGPG4344 Mito_carr 104 199 103.1 8.20E−28 
    973 CGPG4344 Mito_carr 203 297 83.2 8.20E−22 
    975 CGPG4349 Aha1_N 29 165 185 1.80E−52 
    975 CGPG4349 AHSA1 233 291 17.7 0.0027
    976 CGPG4365 CCT 220 258 75.3 2.00E−19 
    978 CGPG4389 Aminotran_1_2 23 376 250.1 4.70E−72 
    979 CGPG4404 p450 37 514 135.5 1.40E−37 
    980 CGPG4405 p450 69 504 265.7 9.60E−77 
    981 CGPG4419 p450 33 477 342.6 6.60E−100
    982 CGPG4432 p450 70 528 261.7 1.50E−75 
    984 CGPG4443 p450 32 551 268.9 1.00E−77 
    985 CGPG445 PLAT 54 159 137.1 4.70E−38 
    985 CGPG445 Lipoxygenase 171 843 1610.6 0
    986 CGPG4453 p450 40 500 373.2 4.20E−109
    987 CGPG4481 Glyco_hydro_17 34 352 365.3 .9.40E−107
    988 CGPG4490 AMP-binding 42 473 358 1.50E−104
    989 CGPG4498 Glyco_hydro_1 40 516 757.2 1.10E−224
    990 CGPG4506 RRM_1 18 89 95.5 1.60E−25 
    991 CGPG4553 DUF313 158 265 219 1.10E−62 
    992 CGPG4583 HIT 43 142 152.5 1.10E−42 
    993 CGPG4643 Pkinase 400 656 303.4 4.20E−88 
    993 CGPG4643 Pkinase_Tyr 400 656 149.3 1.00E−41 
    994 CGPG4650 Pkinase 141 425 320.1 4.00E−93 
    996 CGPG468 Fer4 116 139 30.6 5.60E−06 
    996 CGPG468 Fer4 155 178 38.5 2.30E−08 
    997 CGPG4684 MIP 11 232 407.1 2.60E−119
    998 CGPG4689 LRRNT_2 29 70 63.6 6.40E−16 
    998 CGPG4689 LRR_1 120 142 10.7 2.8
    998 CGPG4689 LRR_1 144 165 8.2 8.5
    998 CGPG4689 Pkinase 261 532 154.6 2.70E−43 
    998 CGPG4689 Pkinase_Tyr 261 532 77.7 3.80E−20 
    999 CGPG4691 PCI 281 385 116.6 6.90E−32 
    1000 CGPG4702 UAA 92 388 −129.1 0.00058
    1000 CGPG4702 DUF6 106 231 27.4 5.10E−05 
    1000 CGPG4702 TPT 240 385 193.4 5.60E−55 
    1001 CGPG4703 UAA 55 355 −71.5 7.60E−07 
    1001 CGPG4703 TPT 205 349 160.4 4.80E−45 
    1002 CGPG4710 CPSase_L_chain 97 217 196.1 8.20E−56 
    1002 CGPG4710 CPSase_L_D2 219 455 449.7 3.80E−132
    1002 CGPG4710 CPSase_L_D3 515 638 255.2 1.30E−73 
    1002 CGPG4710 CPSase_L_chain 648 775 68.2 2.60E−17 
    1002 CGPG4710 CPSase_L_D2 777 989 118.2 2.40E−32 
    1002 CGPG4710 MGS 1061 1148 105.9 1.20E−28 
    1003 CGPG4713 DUF231 241 420 229.6 6.60E−66 
    1004 CGPG4730 DHquinase_I 96 313 281.4 1.80E−81 
    1004 CGPG4730 Shikimate_dh_N 328 408 148.1 2.40E−41 
    1004 CGPG4730 Shikimate_DH 440 558 118.7 1.60E−32 
    1005 CGPG4747 UQ_con 8 145 267.3 3.00E−77 
    1006 CGPG4755 Cpn60_TCP1 30 520 556.6 2.60E−164
    1008 CGPG4779 Peptidase_M22 27 305 238.7 1.20E−68 
    1009 CGPG4848 PGAM 77 246 22.5 4.10E−05 
    1010 CGPG4879 SIS 64 197 71.5 2.60E−18 
    1010 CGPG4879 CBS 229 350 83.4 6.80E−22 
    1011 CGPG4882 TFIIS 121 206 127 5.10E−35 
    1012 CGPG4892 DUF260 5 105 193.4 5.60E−55 
    1013 CGPG4903 DUF260 7 108 237 4.20E−68 
    1014 CGPG4925 WD40 74 112 34.3 4.30E−07 
    1014 CGPG4925 WD40 116 153 27.5 4.60E−05 
    1014 CGPG4925 WD40 207 245 42.3 1.60E−09 
    1014 CGPG4925 WD40 249 287 47.1 6.10E−11 
    1015 CGPG4937 NLE 11 79 115.3 1.70E−31 
    1015 CGPG4937 WD40 140 182 33.3 8.30E−07 
    1015 CGPG4937 WD40 195 233 31.2 3.50E−06 
    1015 CGPG4937 WD40 262 299 29.4 1.20E−05 
    1015 CGPG4937 WD40 348 387 34.5 3.70E−07 
    1016 CGPG4949 Pkinase 208 470 −29.3 8.10E−07 
    1017 CGPG4971 SKI 11 177 104 4.30E−28 
    1018 CGPG499 Voltage_CLC 138 560 690.2 1.50E−204
    1018 CGPG499 CBS 593 759 42.9 1.10E−09 
    1019 CGPG5004 adh_short 53 224 50.1 7.30E−12 
    1020 CGPG5028 adh_short 42 200 −2.3 7.90E−06 
    1021 CGPG5032 adh_short 48 216 81.4 2.80E−21 
    1022 CGPG5038 DUF26 74 134 74.3 3.90E−19 
    1022 CGPG5038 DUF26 200 254 94 4.40E−25 
    1022 CGPG5038 Pkinase 345 620 172.1 1.40E−48 
    1022 CGPG5038 Pkinase_Tyr 345 620 130.8 3.70E−36 
    1023 CGPG5045 LRRNT_2 24 67 38.3 2.70E−08 
    1023 CGPG5045 LRR_1 97 119 16.6 0.092
    1023 CGPG5045 LRR_1 122 144 10.9 2.6
    1023 CGPG5045 LRR_1 146 168 12.9 1.1
    1023 CGPG5045 LRR_1 170 192 14.8 0.31
    1023 CGPG5045 Pkinase 306 576 6.1 6.30E−09 
    1024 CGPG5048 LRRNT_2 22 59 39.5 1.20E−08 
    1024 CGPG5048 LRR_1 89 111 16.8 0.08
    1024 CGPG5048 LRR_1 113 135 13.6 0.72
    1024 CGPG5048 LRR_1 137 159 20.2 0.0076
    1024 CGPG5048 LRR_1 161 182 14.5 0.4
    1024 CGPG5048 LRR_1 183 205 14.1 0.49
    1024 CGPG5048 Pkinase 307 578 47.4 2.20E−11 
    1025 CGPG5051 AOX 45 323 739.1 3.00E−219
    1026 CGPG5061 Fibrillarin 1 99 56.9 6.50E−14 
    1027 CGPG5062 Skp1_POZ 6 66 115.7 1.30E−31 
    1027 CGPG5062 Skp1 86 163 168.3 2.00E−47 
    1028 CGPG5069 Skp1_POZ 4 64 108.8 1.60E−29 
    1028 CGPG5069 Skp1 89 167 169.2 1.10E−47 
    1029 CGPG5070 Skp1_POZ 4 64 93.5 6.40E−25 
    1029 CGPG5070 Skp1 72 150 113.9 4.50E−31 
    1030 CGPG5097 Pkinase 295 579 140.1 5.90E−39 
    1030 CGPG5097 Pkinase_Tyr 295 579 68.2 2.60E−17 
    1031 CGPG510 Rho_GDI 20 223 44 6.20E−12 
    1032 CGPG5100 Pkinase 353 615 −2.8 2.10E−08 
    1033 CGPG5117 efhand_like 25 105 66.7 7.50E−17 
    1033 CGPG5117 PI-PLC-X 107 251 133 8.30E−37 
    1033 CGPG5117 PI-PLC-Y 294 412 87.5 4.20E−23 
    1033 CGPG5117 C2 430 523 64.2 4.10E−16 
    1034 CGPG5151 p450 1 282 11.9 1.60E−11 
    1035 CGPG5155 p450 27 493 112.9 9.10E−31 
    1036 CGPG5159 p450 26 520 145.4 1.50E−40 
    1037 CGPG516 HD 233 337 53.7 6.00E−13 
    1037 CGPG516 RelA_SpoT 427 537 165 1.90E−46 
    1037 CGPG516 p450 31 503 89.9 8.00E−24 
    1039 CGPG5186 Thioredoxin 70 172 137.3 4.20E−38 
    1040 CGPG519 Abhydrolase_1 59 279 29.7 1.10E−05 
    1041 CGPG5190 Ribosomal_L37 15 125 143.9 4.40E−40 
    1042 CGPG5191 TPR_2 166 199 22 0.0022
    1044 CGPG521 Abhydrolase_1 65 282 21 0.00018
    1044 CGPG521 DUF827 16 271 333.9 2.80E−97 
    1047 CGPG5213 DUF623 143 203 116.7 6.40E−32 
    1048 CGPG522 FA_desaturase 62 277 200.7 3.50E−57 
    1049 CGPG5223 PGM_PMM_I 79 222 166.1 8.80E−47 
    1049 CGPG5223 PGM_PMM_II 251 360 96.4 8.30E−26 
    1049 CGPG5223 PGM_PMM_III 362 486 138.1 2.50E−38 
    1049 CGPG5223 PGM_PMM_IV 507 612 75.4 1.80E−19 
    1050 CGPG5224 LRR_1 231 252 9.5 4.7
    1050 CGPG5224 LRR_1 254 275 15.2 0.24
    1050 CGPG5224 LRR_1 277 298 18.3 0.027
    1050 CGPG5224 LRR_1 300 321 17.8 0.039
    1050 CGPG5224 LRR_1 323 344 12.7 1.2
    1050 CGPG5224 LRR_1 369 390 7.8 10
    1050 CGPG5224 LRR_1 392 413 13.5 0.75
    1050 CGPG5224 LRR_1 440 461 17.7 0.041
    1051 CGPG5225 p450 37 452 209.6 7.00E−60 
    1052 CGPG5254 2OG-FeII_Oxy 162 279 65.3 1.90E−16 
    1053 CGPG5257 SpoIIE 130 374 52.9 1.00E−12 
    1054 CGPG5262 SH3_1 303 359 75.4 1.80E−19 
    1054 CGPG5262 SH3_2 304 359 35.8 1.50E−07 
    1056 CGPG5282 F-box 17 69 14.5 0.39
    1056 CGPG5282 Sel1 129 167 19.9 0.0091
    1056 CGPG5282 Sel1 168 203 12.2 0.47
    1056 CGPG5282 zf-MYND 273 317 38.2 2.80E−08 
    1058 CGPG532 Transket_pyr 30 207 261.4 1.90E−75 
    1058 CGPG532 Transketolase_C 222 342 175.3 1.50E−49 
    1059 CGPG5336 adh_short 19 188 81.3 3.10E−21 
    1059 CGPG5336 KR 19 205 −66.7 0.0017
    1060 CGPG5350 Aminotran_4 107 395 353.2 4.30E−103
    1061 CGPG5355 GRAM 95 173 41.4 3.20E−09 
    1062 CGPG5376 DUF21 14 191 162.9 8.00E−46 
    1062 CGPG5376 CBS 210 326 27 6.60E−05 
    1063 CGPG5377 CBS 81 226 138.6 1.70E−38 
    1064 CGPG5382 B56 93 416 759.8 1.80E−225
    1065 CGPG5385 Pyridoxal_deC 146 452 −54.5 1.00E−10 
    1065 CGPG5385 Aminotran_5 150 491 −148.7 7.00E−05 
    1066 CGPG539 Citrate_synt 78 455 764.2 8.10E−227
    1067 CGPG5437 IQ 115 135 31.3 3.40E−06 
    1068 CGPG5450 DHDPS 64 341 486.2 4.00E−143
    1069 CGPG5473 Xan_ur_permease 31 438 164.5 2.70E−46 
    1070 CGPG55 Sugar_tr 6 719 208.1 2.10E−59 
    1070 CGPG55 MFS_1 11 678 137.1 4.70E−38 
    1071 CGPG5505 AlaDh_PNT_N 18 154 81.4 2.80E−21 
    1071 CGPG5505 AlaDh_PNT_C 194 400 134 4.10E−37 
    1071 CGPG5505 Saccharop_dh_N 477 583 228.5 1.50E−65 
    1071 CGPG5505 ThiF 585 714 −36.3 0.0039
    1071 CGPG5505 Saccharop_dh 589 1060 377.2 2.50E−110
    1073 CGPG5514 Cyclin_N 165 294 211.1 2.60E−60 
    1073 CGPG5514 Cyclin_C 296 422 111.3 2.70E−30 
    1074 CGPG5541 Pkinase 316 590 319.8 4.80E−93 
    1075 CGPG5546 Cyclin 108 264 289.2 7.70E−84 
    1076 CGPG5552 Cornichon 2 125 268.7 1.20E−77 
    1077 CGPG5556 SAC3_GANP 20 211 214.5 2.30E−61 
    1078 CGPG557 Chitin_bind_1 21 62 72.3 1.50E−18 
    1078 CGPG557 Barwin 73 191 311.7 1.30E−90 
    1079 CGPG5576 zf-PARP 11 88 88.5 2.10E−23 
    1079 CGPG5576 zf-PARP 117 195 65.3 2.00E−16 
    1079 CGPG5576 PADR1 290 343 120.6 4.40E−33 
    1079 CGPG5576 BRCT 394 471 47.4 4.80E−11 
    1079 CGPG5576 WGR 517 605 153 7.90E−43 
    1079 CGPG5576 PARP_reg 633 765 87.7 3.60E−23 
    1079 CGPG5576 PARP 767 979 434.2 1.80E−127
    1080 CGPG5596 Response_reg 9 143 77.4 4.60E−20 
    1081 CGPG5605 DEAD 52 221 246.1 7.20E−71 
    1081 CGPG5605 Helicase_C 290 366 89.9 7.50E−24 
    1082 CGPG5606 LRRNT_2 21 62 49.4 1.20E−11 
    1082 CGPG5606 LRR_1 90 113 14.1 0.52
    1082 CGPG5606 LRR_1 115 137 14.7 0.35
    1082 CGPG5606 LRR_1 140 162 19.3 0.014
    1082 CGPG5606 LRR_1 164 186 17.2 0.059
    1082 CGPG5606 LRR_1 188 211 11.7 1.9
    1082 CGPG5606 LRR_1 213 235 14.2 0.47
    1082 CGPG5606 LRR_1 237 259 16.1 0.13
    1082 CGPG5606 LRR_1 261 283 8.9 6.3
    1082 CGPG5606 LRR_1 308 330 12 1.6
    1082 CGPG5606 LRR_1 332 354 11.1 2.4
    1082 CGPG5606 LRR_1 356 375 9.3 5.1
    1082 CGPG5606 LRR_1 380 402 10.8 2.7
    1082 CGPG5606 LRR_1 404 426 17.1 0.065
    1082 CGPG5606 LRR_1 428 450 12 1.6
    1082 CGPG5606 LRR_1 452 474 14.6 0.36
    1082 CGPG5606 LRR_1 500 522 14.3 0.44
    1082 CGPG5606 LRR_1 524 546 14.9 0.28
    1082 CGPG5606 LRR_1 548 570 15.1 0.25
    1082 CGPG5606 LRR_1 571 592 15.6 0.18
    1082 CGPG5606 Pkinase 683 964 125.6 1.40E−34 
    1082 CGPG5606 Pkinase_Tyr 683 964 85 2.30E−22 
    1083 CGPG561 XG_FTase 54 532 1264.7 0
    1084 CGPG5618 Lectin_legB 20 247 260.2 4.30E−75 
    1084 CGPG5618 Pkinase 376 651 185.1 1.70E−52 
    1084 CGPG5618 Pkinase_Tyr 376 651 141.6 2.10E−39 
    1085 CGPG5642 Aldedh 18 477 674.3 9.50E−200
    1086 CGPG5644 ELFV_dehydrog_N 51 181 278.1 1.80E−80 
    1086 CGPG5644 ELFV_dehydrog 197 428 394.9 1.20E−115
    1087 CGPG5647 Aldedh 46 511 669.6 2.50E−198
    1088 CGPG5655 Glutaminase 23 309 642.2 4.30E−190
    1089 CGPG5660 Glutaminase 24 308 599 4.30E−177
    1090 CGPG5662 Aminotran_3 47 381 473.1 3.30E−139
    1091 CGPG568 FTHFS 14 634 1422.6 0
    1092 CGPG5686 Aminotran_3 31 387 365.8 7.00E−107
    1093 CGPG5702 Gln-synt_N 28 109 171.5 2.10E−48 
    1093 CGPG5702 Gln-synt_C 116 397 581.1 1.10E−171
    1094 CGPG5712 Pribosyltran 22 158 167.1 4.50E−47 
    1095 CGPG5713 Rib_5-P_isom_A 55 229 353.2 4.30E−103
    1096 CGPG5715 Pribosyltran 27 163 131.6 2.20E−36 
    1097 CGPG5723 NDK 4 138 304.7 1.80E−88 
    1098 CGPG5729 Cyclin_N 210 336 218.9 1.20E−62 
    1098 CGPG5729 Cyclin_C 338 457 133.1 7.50E−37 
    1099 CGPG5730 Lung_7-TM_R 151 444 474.5 1.30E−139
    1101 CGPG5741 NIF 165 344 184.2 3.20E−52 
    1102 CGPG5752 CAF1 161 404 356.1 5.80E−104
    1103 CGPG5771 Acyltransferase 84 277 123.8 4.90E−34 
    1104 CGPG5778 Aa_trans 51 498 498.7 6.60E−147
    1105 CGPG5782 Sugar_tr 65 525 819.5 1.80E−243
    1105 CGPG5782 MFS_1 69 485 103.5 6.40E−28 
    1106 CGPG5785 Sugar_tr 69 530 791.6 4.50E−235
    1106 CGPG5785 MFS_1 73 490 88.2 2.50E−23 
    1107 CGPG5797 AA_permease 94 562 588.2 7.60E−174
    1108 CGPG580 MGDG_synth 155 323 316.4 5.00E−92 
    1108 CGPG580 Glyco_tran_28_C 349 512 5.9 0.0004
    1109 CGPG5805 AA_permease 57 511 619.8 2.40E−183
    1110 CGPG5810 Ank 74 106 1.8 17
    1110 CGPG5810 Ank 107 139 51.9 2.10E−12 
    1110 CGPG5810 Pkinase 197 468 93.7 5.40E−25 
    1110 CGPG5810 Pkinase_Tyr 200 468 100.3 5.80E−27 
    1111 CGPG5822 Pkinase 131 418 302.6 7.40E−88 
    1112 CGPG5837 Pkinase 14 275 128.1 2.50E−35 
    1113 CGPG5855 Pkinase_Tyr 81 363 133.4 6.10E−37 
    1113 CGPG5855 Pkinase 81 363 158.3 2.00E−44 
    1114 CGPG5868 Pkinase_Tyr 45 312 154.4 3.00E−43 
    1114 CGPG5868 Pkinase 45 312 150.1 6.00E−42 
    1115 CGPG587 FKBP_C 104 208 138.8 1.50E−38 
    1117 CGPG5893 Pkinase 52 314 −49.3 1.30E−05 
    1118 CGPG5909 ADH_zinc_N 163 310 104.4 3.40E−28 
    1119 CGPG5914 ADH_N 54 188 144.5 2.80E−40 
    1119 CGPG5914 ADH_zinc_N 219 362 157.2 4.30E−44 
    1123 CGPG5930 Mov34 328 437 81.7 2.30E−21 
    1124 CGPG5945 Pyr_redox_2 8 305 125.3 1.70E−34 
    1124 CGPG5945 Pyr_redox 167 262 104.5 3.00E−28 
    1125 CGPG5958 Pyr_redox_2 8 304 126.4 8.20E−35 
    1125 CGPG5958 Pyr_redox 166 261 115.1 2.00E−31 
    1126 CGPG5977 Ank 48 80 1.7 18
    1126 CGPG5977 Ank 81 113 39.4 1.30E−08 
    1126 CGPG5977 Ank 114 146 18.6 0.023
    1126 CGPG5977 Pkinase 166 424 186.4 6.90E−53 
    1126 CGPG5977 Pkinase_Tyr 166 424 172.3 1.20E−48 
    1127 CGPG598 Nramp 66 429 644.5 8.90E−191
    1128 CGPG5986 Pkinase 43 329 323.5 3.60E−94 
    1129 CGPG5994 F-box 62 108 15.1 0.26
    1129 CGPG5994 LRR_2 314 340 17.1 0.063
    1130 CGPG5996 Tetraspannin 4 230 244.3 2.60E−70 
    1131 CGPG6021 RRM_1 8 77 73.1 8.60E−19 
    1131 CGPG6021 RRM_1 108 178 81.2 3.20E−21 
    1132 CGPG6027 RRM_1 42 113 104.5 3.10E−28 
    1133 CGPG6035 Pyr_redox_2 51 370 86.5 8.30E−23 
    1133 CGPG6035 Pyr_redox 216 323 55.5 1.80E−13 
    1133 CGPG6035 efhand 376 404 23.3 0.00087
    1134 CGPG604 PSI_PsaH 6 145 342.9 5.50E−100
    1136 CGPG606 Phytochelatin 46 178 381.8 1.10E−111
    1136 CGPG606 DUF1984 179 259 206.3 7.10E−59 
    1137 CGPG6069 RNA_pol_L 90 382 75.5 1.60E−19 
    1137 CGPG6069 RNA_pol_A_bac 124 268 113 8.80E−31 
    1138 CGPG608 TB2_DP1_HVA22 11 108 188.4 1.70E−53 
    1139 CGPG6080 Str_synth 144 232 164.7 2.40E−46 
    1140 CGPG6082 Miro 8 121 62.7 1.20E−15 
    1140 CGPG6082 Ras 8 179 254 3.00E−73 
    1141 CGPG6089 NicO 153 372 147.1 4.70E−41 
    1143 CGPG6128 Reticulon 22 197 303.7 3.40E−88 
    1144 CGPG614 cobW 74 246 232.9 6.80E−67 
    1145 CGPG6149 Glutaredoxin 84 148 115.9 1.10E−31 
    1146 CGPG6172 Miro 11 126 74.1 4.60E−19 
    1146 CGPG6172 Ras 11 173 288.8 1.00E−83 
    1147 CGPG6174 Miro 19 133 75.8 1.30E−19 
    1147 CGPG6174 Ras 19 180 326.5 4.80E−95 
    1148 CGPG6176 Miro 15 130 63.8 5.50E−16 
    1148 CGPG6176 Ras 15 177 285.5 1.00E−82 
    1149 CGPG6197 Phi_1 55 334 656.6 2.00E−194
    1150 CGPG620 tRNA-synt_1g 71 430 627.4 1.20E−185
    1152 CGPG6204 mTERF 75 357 69.9 8.00E−18 
    1153 CGPG621 RRM_1 19 90 20.7 0.0017
    1154 CGPG6210 MFS_1 26 419 55.8 1.40E−13 
    1154 CGPG6210 Sugar_tr 29 459 239.3 8.30E−69 
    1155 CGPG6211 Sugar_tr 24 479 469.9 3.00E−138
    1155 CGPG6211 MFS_1 30 443 98.8 1.60E−26 
    1156 CGPG6214 Sugar_tr 26 487 541.1 1.20E−159
    1156 CGPG6214 MFS_1 32 448 89.3 1.20E−23 
    1157 CGPG6215 MFS_1 34 498 52.2 1.80E−12 
    1157 CGPG6215 PTR2 93 486 181.3 2.40E−51 
    1158 CGPG6222 Sugar_tr 27 490 523.9 1.70E−154
    1158 CGPG6222 MFS_1 31 447 92.4 1.40E−24 
    1159 CGPG6229 MFS_1 23 447 97.4 4.40E−26 
    1159 CGPG6229 Sugar_tr 28 490 565.7 4.40E−167
    1160 CGPG6233 Sugar_tr 22 512 23.1 1.30E−07 
    1160 CGPG6233 MFS_1 37 473 69.1 1.40E−17 
    1161 CGPG6237 Sugar_tr 25 483 398.5 1.00E−116
    1161 CGPG6237 MFS_1 29 442 110 6.80E−30 
    1162 CGPG6243 Pkinase 25 333 289.3 7.40E−84 
    1163 CGPG6248 Pkinase 22 276 338.1 1.50E−98 
    1163 CGPG6248 NAF 306 366 64.3 3.90E−16 
    1164 CGPG6252 Pkinase 12 266 340.3 3.20E−99 
    1164 CGPG6252 NAF 298 358 110.9 3.70E−30 
    1165 CGPG6267 Pkinase 68 306 −7.3 4.00E−08 
    1166 CGPG6272 Pkinase 74 349 167.4 3.70E−47 
    1166 CGPG6272 Pkinase_Tyr 74 349 134.3 3.20E−37 
    1167 CGPG6294 Pkinase 75 352 −1.8 1.90E−08 
    1168 CGPG63 p450 44 511 425.2 8.90E−125
    1170 CGPG6317 MFS_1 39 504 44.5 3.50E−10 
    1170 CGPG6317 PTR2 101 488 297.8 2.00E−86 
    1171 CGPG6328 Trehalose_PPase 121 354 380.5 2.60E−111
    1172 CGPG6334 Sterol_desat 34 245 281.2 2.00E−81 
    1173 CGPG6336 Sterol_desat 38 247 261.6 1.60E−75 
    1174 CGPG6349 LRR_1 42 62 15.7 0.17
    1174 CGPG6349 LRR_1 64 84 7.9 9.3
    1174 CGPG6349 LRR_1 108 128 11.6 1.9
    1174 CGPG6349 LRR_1 130 151 12.5 1.3
    1174 CGPG6349 LRR_1 153 174 10.7 2.9
    1174 CGPG6349 LRR_1 176 197 11.9 1.7
    1174 CGPG6349 LRR_1 199 219 7.9 9.6
    1175 CGPG6352 zf-CCHC 81 98 18.4 0.00091
    1177 CGPG6364 Gp_dh_N 3 152 341.6 1.30E−99 
    1177 CGPG6364 Gp_dh_C 157 313 381.4 1.40E−111
    1178 CGPG6366 Gp_dh_N 3 153 301.7 1.40E−87 
    1178 CGPG6366 Gp_dh_C 158 314 334 2.60E−97 
    1179 CGPG6375 Aminotran_1_2 36 390 217 4.30E−62 
    1180 CGPG6388 NTP_transferase 15 285 397.9 1.50E−116
    1181 CGPG6391 ADH_N 32 143 172.7 9.30E−49 
    1181 CGPG6391 ADH_zinc_N 172 312 193.2 6.00E−55 
    1182 CGPG6399 ADH_N 27 155 135.6 1.30E−37 
    1182 CGPG6399 ADH_zinc_N 186 332 115.4 1.70E−31 
    1183 CGPG6407 Glucokinase 5 341 569.2 4.00E−168
    1184 CGPG6418 ADH_N 28 156 128.2 2.40E−35 
    1184 CGPG6418 ADH_zinc_N 187 333 135.1 2.00E−37 
    1185 CGPG6430 Iso_dh 6 355 346.2 5.40E−101
    1186 CGPG6432 ADH_N 25 135 157.5 3.40E−44 
    1186 CGPG6432 ADH_zinc_N 166 305 114.8 2.40E−31 
    1187 CGPG6437 TPT 205 388 167.3 4.00E−47 
    1188 CGPG6445 Aldedh 45 511 720.6 1.10E−213
    1189 CGPG6450 Aldedh 26 491 797.6 7.00E−237
    1190 CGPG6458 Aldedh 22 480 796.6 1.40E−236
    1191 CGPG6465 PfkB 10 314 274.5 2.10E−79 
    1192 CGPG6476 PFK 3 278 659.8 2.20E−195
    1193 CGPG6505 Aminotran_3 123 449 321.7 1.30E−93 
    1194 CGPG6507 Gln-synt_N 105 187 85.7 1.50E−22 
    1194 CGPG6507 Gln-synt_C 193 446 528.1 9.40E−156
    1195 CGPG6509 Glutaminase 112 396 599 4.30E−177
    1196 CGPG6510 Aldedh 17 476 689.2 3.10E−204
    1197 CGPG6515 Aldedh 19 476 789.7 1.70E−234
    1198 CGPG6520 Aldedh 29 491 790.7 8.30E−235
    1199 CGPG6531 Enolase_N 3 133 215.5 1.20E−61 
    1199 CGPG6531 Enolase_C 138 425 571.7 7.20E−169
    1200 CGPG6553 Aldedh 103 563 768.4 4.40E−228
    1201 CGPG6557 ELFV_dehydrog_N 145 275 294.9 1.50E−85 
    1201 CGPG6557 ELFV_dehydrog 290 533 486.7 2.80E−143
    1202 CGPG6563 Aminotran_1_2 120 472 403.3 3.50E−118
    1203 CGPG6564 iPGM_N 90 451 876.8 1.00E−260
    1203 CGPG6564 Metalloenzyme 461 576 173.3 5.90E−49 
    1204 CGPG6572 Gp_dh_N 91 241 301.7 1.40E−87 
    1204 CGPG6572 Gp_dh_C 246 402 334 2.60E−97 
    1205 CGPG6577 iPGM_N 92 451 863.6 9.30E−257
    1205 CGPG6577 Metalloenzyme 461 577 195.7 1.10E−55 
    1206 CGPG6588 DAO 92 493 −24.3 0.00021
    1206 CGPG6588 FAD_binding_2 92 421 −110.2 0.0013
    1206 CGPG6588 GIDA 92 418 −223.3 0.0021
    1206 CGPG6588 Pyr_redox_2 92 409 252.3 9.90E−73 
    1206 CGPG6588 Pyr_redox 265 362 125.3 1.70E−34 
    1206 CGPG6588 Pyr_redox_dim 437 546 222.4 9.80E−64 
    1207 CGPG6596 Biotin_lipoyl 91 164 76 1.20E−19 
    1207 CGPG6596 E3_binding 228 264 68.1 2.70E−17 
    1207 CGPG6596 2-oxoacid_dh 296 521 326.6 4.20E−95 
    1209 CGPG6619 Transketolase_N 101 435 777.9 5.90E−231
    1209 CGPG6619 Transket_pyr 450 627 245.4 1.20E−70 
    1209 CGPG6619 Transketolase_C 639 754 36.1 1.30E−07 
    1210 CGPG6623 PGAM 96 330 130.8 3.80E−36 
    1211 CGPG6626 OstA 109 219 106.8 6.20E−29 
    1212 CGPG663 Pro_CA 155 325 357.7 1.90E−104
    1213 CGPG6635 Cytochrom_C 126 204 55.4 1.90E−13 
    1215 CGPG6641 AstE_AspA 93 372 312.6 7.00E−91 
    1216 CGPG6642 Transket_pyr 125 303 234.2 2.70E−67 
    1216 CGPG6642 Transketolase_C 319 443 196.1 8.20E−56 
    1217 CGPG6645 TIM 95 336 398.9 7.60E−117
    1218 CGPG6660 CBS 97 214 118.4 2.00E−32 
    1219 CGPG6671 NTP_transferase 102 374 277.3 2.90E−80 
    1220 CGPG6697 Transaldolase 100 400 657.9 7.90E−195
    1221 CGPG6706 iPGM_N 90 451 870.1 1.00E−258
    1221 CGPG6706 Metalloenzyme 461 576 191.4 2.10E−54 
    1222 CGPG6723 Aminotran_1_2 124 478 217 4.30E−62 
    1223 CGPG6729 Gln-synt_N 100 182 148.3 2.00E−41 
    1223 CGPG6729 Gln-synt_C 189 470 568.5 6.70E−168
    1224 CGPG6738 Aminotran_1_2 123 473 205.6 1.10E−58 
    1225 CGPG6742 Aldedh 105 563 730.5 1.10E−216
    1226 CGPG6752 TIM 92 334 465.9 5.00E−137
    1227 CGPG6760 GATase_2 2 164 −6.7 1.70E−10 
    1227 CGPG6760 Asn_synthase 241 531 383.2 3.80E−112
    1228 CGPG6768 PGI 55 545 770.6 9.60E−229
    1229 CGPG6779 Isoamylase_N 105 182 91.3 2.90E−24 
    1229 CGPG6779 Alpha-amylase 219 613 30.3 8.20E−08 
    1230 CGPG6785 Molybdop_Fe4S4 44 105 86.1 1.10E−22 
    1230 CGPG6785 Molybdopterin 108 660 93.7 5.70E−25 
    1230 CGPG6785 Molydop_binding 892 1011 60.2 6.90E−15 
    1231 CGPG6800 PGI 52 541 1093.7 0
    1232 CGPG686 RRM_1 9 80 101 3.50E−27 
    1232 CGPG686 zf-CCHC 118 135 37.8 3.90E−08 
    1233 CGPG6898 Hin1 28 163 112.4 1.30E−30 
    1234 CGPG6900 Pkinase 97 365 172.1 1.40E−48 
    1236 CGPG6920 Dehydrin 14 128 165.3 1.50E−46 
    1237 CGPG6921 CorA 48 440 576.8 2.10E−170
    1240 CGPG6945 SNARE 37 99 67.1 5.60E−17 
    1241 CGPG6946 MATH 13 133 30.7 5.10E−06 
    1242 CGPG6948 PAP2 100 233 71.2 3.40E−18 
    1243 CGPG6974 DUF538 7 146 248.7 1.20E−71 
    1244 CGPG6976 DUF926 293 406 220 5.20E−63 
    1245 CGPG6996 CPDase 1 179 275.9 7.80E−80 
    1246 CGPG7002 zf-C3HC4 123 157 25 0.00026
    1247 CGPG7013 zf-C3HC4 115 156 26.2 0.00011
    1248 CGPG7021 Invertase_neut 98 564 1154 0
    1248 CGPG7021 GDE_C 151 537 −212.6 0.0022
    1251 CGPG7075 DUF1749 77 349 217.1 3.80E−62 
    1252 CGPG7080 Glutaredoxin 44 106 97.2 5.10E−26 
    1253 CGPG7094 DUF300 6 281 574.1 1.40E−169
    1254 CGPG7095 Abhydrolase_3 107 321 295.6 9.10E−86 
    1255 CGPG7104 Saccharop_dh 13 445 35.1 6.50E−09 
    1256 CGPG7118 F-box 25 73 25 0.00026
    1257 CGPG7122 Pkinase 20 280 206.6 5.70E−59 
    1257 CGPG7122 Pkinase_Tyr 20 280 199.1 1.10E−56 
    1258 CGPG713 Cyclin_N 5 135 6.2 4.30E−05 
    1259 CGPG7130 CS 145 220 109.9 7.50E−30 
    1260 CGPG7145 Transthyretin 191 310 185.5 1.30E−52 
    1261 CGPG7166 DnaJ 79 141 29.6 5.80E−06 
    1262 CGPG7179 ByStin 127 423 795.6 2.90E−236
    1263 CGPG7184 PBD 27 127 24 0.0002
    1264 CGPG7185 GAF 190 346 32.9 1.10E−06 
    1264 CGPG7185 HisKA 382 445 24.6 0.00036
    1265 CGPG7192 2OG-FeII_Oxy 201 301 136.6 6.60E−38 
    1266 CGPG7199 RWD 3 122 126.7 6.30E−35 
    1267 CGPG72 Amino_oxidase 66 528 217.5 3.10E−62 
    1268 CGPG7231 B3_4 118 280 89.3 1.10E−23 
    1268 CGPG7231 B5 305 378 94.9 2.40E−25 
    1269 CGPG7241 Peptidase_C26 58 281 149 1.20E−41 
    1272 CGPG7265 ARM_1 12 296 531.9 6.60E−157
    1273 CGPG7274 DUF640 36 168 312.1 1.00E−90 
    1274 CGPG7291 elF-1a 20 91 71.9 2.00E−18 
    1275 CGPG7303 Aldedh 20 484 779 2.80E−231
    1276 CGPG7315 Y_phosphatase2 116 280 346.6 4.00E−101
    1278 CGPG7327 Actin 2 470 33.2 5.40E−16 
    1280 CGPG7347 Tcp11 648 1133 261.8 1.40E−75 
    1281 CGPG7348 CorA 90 467 408.2 1.20E−119
    1283 CGPG7356 Metallophos 2 120 28.1 3.10E−05 
    1284 CGPG7359 Methyltransf_11 38 135 43.8 5.80E−10 
    1284 CGPG7359 Methyltransf_12 38 133 46 1.30E−10 
    1286 CGPG7372 zf-C3HC4 119 160 38.8 1.90E−08 
    1287 CGPG7379 zf-C3HC4 36 76 39.6 1.10E−08 
    1288 CGPG7398 DUF212 22 167 141.6 2.10E−39 
    1289 CGPG7403 TLD 203 341 176.8 5.30E−50 
    1290 CGPG7404 PBP 25 170 217.5 2.90E−62 
    1291 CGPG7410 HLH 36 83 14 0.0047
    1292 CGPG7417 MMR_HSR1 131 252 120.2 6.00E−33 
    1293 CGPG7423 Gln-synt_N 102 183 171.5 2.10E−48 
    1293 CGPG7423 Gln-synt_C 190 471 581.1 1.10E−171
    1294 CGPG7424 FBPase 92 424 521.2 1.20E−153
    1297 CGPG7443 DUF1001 92 274 425.2 9.10E−125
    1298 CGPG7449 ScpA_ScpB 104 347 405 1.10E−118
    1301 CGPG7459 DUF1350 90 360 812.2 2.80E−241
    1303 CGPG7481 Abhydrolase_1 113 361 29.1 1.50E−05 
    1304 CGPG7483 GTP_EFTU 62 260 227.2 3.70E−65 
    1304 CGPG7483 GTP_EFTU_D2 281 355 38.5 2.30E−08 
    1304 CGPG7483 EFG_C 461 551 54.5 3.60E−13 
    1306 CGPG7503 PBP 19 170 159.9 6.70E−45 
    1307 CGPG7504 MSF1 15 187 125.9 1.10E−34 
    1309 CGPG7516 DUF783 25 229 255.1 1.40E−73 
    1312 CGPG7524 Isy1 1 292 519.5 3.70E−153
    1313 CGPG7525 UFD1 10 184 417.5 1.90E−122
    1315 CGPG7537 KTI12 1 291 406.2 4.80E−119
    1317 CGPG7575 efhand 95 123 31.4 3.20E−06 
    1318 CGPG7577 TP_methylase 1 213 89.5 1.00E−23 
    1319 CGPG7590 Ribonuc_L-PSP 61 179 210.1 5.20E−60 
    1321 CGPG7601 CCT 237 275 74 4.80E−19 
    1322 CGPG7605 RRM_1 88 158 65 2.40E−16 
    1323 CGPG7607 Amidohydro_2 10 289 102.2 1.50E−27 
    1325 CGPG7632 zf-Tim10_DDP 12 77 105 2.30E−28 
    1326 CGPG7673 zf-MYND 76 113 47.5 4.40E−11 
    1326 CGPG7673 UCH 468 774 192.5 1.00E−54 
    1327 CGPG7683 zf-LSD1 28 52 40.3 6.70E−09 
    1327 CGPG7683 zf-LSD1 67 91 54.8 2.80E−13 
    1327 CGPG7683 zf-LSD1 105 129 54.1 4.70E−13 
    1328 CGPG773 H_PPase 64 798 1699.2 0
    1329 CGPG7776 DUF525 311 445 155.8 1.10E−43 
    1330 CGPG7781 SapB_1 45 83 37.9 3.60E−08 
    1330 CGPG7781 SapB_2 86 119 18.1 0.025
    1330 CGPG7781 SapB_1 131 169 27.7 4.20E−05 
    1330 CGPG7781 SapB_2 172 206 20.8 0.0049
    1331 CGPG7785 LRRNT_2 24 65 39.3 1.30E−08 
    1331 CGPG7785 LRR_1 93 115 11.4 2.1
    1331 CGPG7785 LRR_1 117 139 8.8 6.4
    1331 CGPG7785 LRR_1 141 163 12.5 1.3
    1331 CGPG7785 LRR_1 165 187 15.6 0.18
    1331 CGPG7785 LRR_1 189 211 8.7 6.8
    1331 CGPG7785 LRR_1 213 235 16.9 0.075
    1331 CGPG7785 Pkinase 415 682 18.7 1.10E−09 
    1332 CGPG7787 Aldose_epim 26 301 257.4 3.00E−74 
    1334 CGPG7796 WD40 50 88 32 2.10E−06 
    1334 CGPG7796 WD40 92 130 43 1.00E−09 
    1334 CGPG7796 WD40 134 174 47.8 3.70E−11 
    1334 CGPG7796 WD40 182 220 37.9 3.40E−08 
    1334 CGPG7796 WD40 391 432 33.3 8.40E−07 
    1334 CGPG7796 WD40 436 475 40.4 6.20E−09 
    1334 CGPG7796 WD40 489 527 28.9 1.80E−05 
    1334 CGPG7796 WD40 531 569 31 4.30E−06 
    1334 CGPG7796 WD40 573 611 43.9 5.30E−10 
    1334 CGPG7796 WD40 615 653 28.6 2.20E−05 
    1334 CGPG7796 Utp13 674 809 231.1 2.40E−66 
    1335 CGPG7797 GILT 35 144 133.6 5.40E−37 
    1336 CGPG7801 LRR_1 106 129 8.1 8.7
    1336 CGPG7801 LRR_1 132 154 16.9 0.071
    1336 CGPG7801 LRR_1 156 178 10.9 2.6
    1336 CGPG7801 LRR_1 180 199 9.2 5.4
    1336 CGPG7801 LRR_1 201 223 9.4 4.9
    1336 CGPG7801 LRR_1 225 246 17.1 0.062
    1336 CGPG7801 LRR_1 249 272 12.8 1.1
    1336 CGPG7801 LRR_1 273 294 10.3 3.4
    1336 CGPG7801 Pkinase 456 716 −45.5 7.60E−06 
    1337 CGPG7813 WD40 379 417 43.1 9.20E−10 
    1337 CGPG7813 WD40 421 459 39.8 9.60E−09 
    1337 CGPG7813 WD40 507 545 46.9 6.80E−11 
    1337 CGPG7813 WD40 549 587 29.5 1.20E−05 
    1337 CGPG7813 PWP2 785 900 243.1 5.70E−70 
    1341 CGPG7863 zf-CW 100 153 85.7 1.40E−22 
    1341 CGPG7863 MBD 162 237 43.4 7.80E−10 
    1342 CGPG7868 BCNT 165 244 123.2 7.40E−34 
    1343 CGPG7881 Aldedh 99 558 694.8 6.40E−206
    1344 CGPG7887 HEAT 191 222 12 1.5
    1344 CGPG7887 Arm 262 302 27.2 6.00E−05 
    1344 CGPG7887 HEAT 389 424 14.1 0.52
    1344 CGPG7887 Arm 423 463 32.8 1.20E−06 
    1345 CGPG7899 RRM_1 225 295 27.8 3.80E−05 
    1346 CGPG7901 IQ 107 127 30.9 4.40E−06 
    1346 CGPG7901 IQ 129 149 18.8 0.02
    1347 CGPG7909 DUF383 92 271 353 4.90E−103
    1347 CGPG7909 DUF384 272 330 107.8 3.20E−29 
    1348 CGPG7911 AAA 245 447 58.7 1.90E−14 
    1349 CGPG7919 Cullin 30 191 −9.6 7.00E−09 
    1350 CGPG7935 IQ 93 113 26.3 0.00011
    1350 CGPG7935 IQ 115 135 17.6 0.046
    1351 CGPG7940 RRM_1 96 161 37.7 3.90E−08 
    1352 CGPG7959 Cyclin_N 180 306 218.1 2.00E−62 
    1352 CGPG7959 Cyclin_C 308 428 179 1.20E−50 
    1353 CGPG7967 IQ 106 126 30.4 6.50E−06 
    1353 CGPG7967 IQ 128 148 15.1 0.26
    1354 CGPG7975 Arm 28 68 23.4 0.00079
    1354 CGPG7975 Arm 70 110 17.4 0.052
    1355 CGPG7996 efhand 136 164 22.7 0.0013
    1356 CGPG8006 AAA 241 440 50.9 4.10E−12 
    1357 CGPG801 Cyt-b5 74 171 81.3 3.00E−21 
    1358 CGPG8023 RRM_1 11 82 114.5 3.00E−31 
    1359 CGPG8025 IQ 93 113 27 6.80E−05 
    1359 CGPG8025 IQ 115 135 20.6 0.0056
    1360 CGPG8038 MFS_1 36 433 124.8 2.40E−34 
    1361 CGPG8053 DUF246 182 525 691.9 4.70E−205
    1364 CGPG8070 GILT 32 136 193.2 6.30E−55 
    1365 CGPG8073 Dirigent 17 183 330.8 2.30E−96 
    1366 CGPG8076 Tryp_alpha_amyl 32 107 47.1 5.90E−11 
    1369 CGPG8095 IPK 16 279 434.8 1.20E−127
    1370 CGPG8096 60KD_IMP 151 348 35.5 1.70E−13 
    1374 CGPG8129 Ank 49 81 32.1 1.90E−06 
    1374 CGPG8129 Ank 82 114 24.1 0.00049
    1374 CGPG8129 Ank 115 147 43.2 8.90E−10 
    1378 CGPG8165 Glutaredoxin 44 106 97.2 5.10E−26 
    1379 CGPG8169 Nol1_Nop2_Fmu 226 505 21.9 3.60E−09 
    1380 CGPG8203 Uricase 11 140 134.3 3.40E−37 
    1380 CGPG8203 Uricase 147 300 177.6 3.00E−50 
    1381 CGPG8205 DZC 113 148 81 3.70E−21 
    1383 CGPG8213 Phosphoesterase 27 388 519.9 2.70E−153
    1384 CGPG8225 FBPase 25 348 464.4 1.40E−136
    1385 CGPG8227 NIR_SIR_ferr 44 111 90.7 4.50E−24 
    1385 CGPG8227 NIR_SIR 119 275 207.5 3.00E−59 
    1385 CGPG8227 NIR_SIR_feu 331 399 57.3 5.00E−14 
    1385 CGPG8227 NIR_SIR 405 553 28.9 1.40E−05 
    1386 CGPG8235 Aldedh 12 471 791.5 4.70E−235
    1387 CGPG8236 Molybdop_Fe4S4 9 63 76 1.20E−19 
    1387 CGPG8236 Molybdopterin 66 495 428.7 8.00E−126
    1387 CGPG8236 Molydop_binding 593 703 111.8 2.00E−30 
    1387 CGPG8236 Fer2_BFD 852 903 50.3 6.50E−12 
    1388 CGPG8244 PAS_2 15 125 151.7 2.00E−42 
    1388 CGPG8244 GAF 152 320 93.4 7.10E−25 
    1388 CGPG8244 Phytochrome 331 513 88.8 1.70E−23 
    1388 CGPG8244 HisKA 528 596 43.1 9.40E−10 
    1388 CGPG8244 HATPase_c 637 747 127 5.20E−35 
    1389 CGPG8254 NIR_SIR_ferr 66 133 48.1 2.90E−11 
    1389 CGPG8254 NIR_SIR 166 347 198.6 1.40E−56 
    1389 CGPG8254 NIR_SIR_ferr 362 434 77.4 4.50E−20 
    1389 CGPG8254 NIR_SIR 443 591 15.1 0.00014
    1390 CGPG8255 PPDK_N 16 384 620.2 1.80E−183
    1390 CGPG8255 PEP-utilizers 439 531 141.1 3.00E−39 
    1390 CGPG8255 PEP-utilizers_C 559 914 485.9 4.80E−143
    1391 CGPG8262 ELFV_dehydrog_N 33 163 239.1 9.20E−69 
    1391 CGPG8262 ELFV_dehydrog 179 420 400.7 2.10E−117
    1392 CGPG8264 Aldedh 17 480 795.7 2.70E−236
    1393 CGPG8269 PGK 1 396 769.8 1.70E−228
    1394 CGPG8271 Gln-synt_N 16 97 149.9 6.70E−42 
    1394 CGPG8271 Gln-synt_C 104 386 584.6 9.60E−173
    1395 CGPG8305 Sulfotransfer_1 70 336 352.4 7.40E−103
    1396 CGPG8320 DUF1005 282 487 545.7 4.80E−161
    1397 CGPG8326 Senescence 35 369 791.4 5.30E−235
    1398 CGPG8344 PPR 173 207 17.6 0.046
    1398 CGPG8344 PPR 208 242 19.4 0.013
    1398 CGPG8344 PPR 243 277 10.4 0.44
    1398 CGPG8344 PPR 279 312 13.4 0.19
    1398 CGPG8344 PPR 314 348 2 4.3
    1398 CGPG8344 PPR 349 383 8.3 0.79
    1398 CGPG8344 PPR 384 418 2.3 4
    1399 CGPG8347 Ribosomal_S8 5 130 214.4 2.60E−61 
    1400 CGPG8359 Tryp_alpha_amyl 85 167 93.5 6.40E−25 
    1401 CGPG8370 Tim17 40 156 129.2 1.10E−35 
    1402 CGPG8371 PseudoU_synth_1 62 167 44.3 4.10E−10 
    1402 CGPG8371 PseudoU_synth_1 324 431 18.3 0.00016
    1404 CGPG8378 LysM 78 121 22 0.0021
    1406 CGPG841 ArfGap 4 120 173.8 4.20E−49 
    1405 CGPG8383 DUF239 174 368 401.1 1.60E−117
    1409 CGPG8450 DUF793 1 390 976.4 1.10E−290
    1410 CGPG8451 IQ 105 125 21.2 0.0038
    1410 CGPG8451 IQ 127 147 21.5 0.0031
    1411 CGPG8459 ubiquitin 6 78 58.1 2.90E−14 
    1411 CGPG8459 UBA 145 187 49.6 1.10E−11 
    1411 CGPG8459 XPC-binding 242 298 56.4 9.40E−14 
    1411 CGPG8459 UBA 322 361 46 1.20E−10 
    1412 CGPG8461 Ribosomal_S8 5 130 219 1.10E−62 
    1413 CGPG8463 PI3_PI4_kinase 163 421 280.6 3.00E−81 
    1414 CGPG8471 F-box 1 46 36.9 6.90E−08 
    1414 CGPG8471 FBA_1 211 383 295.9 7.50E−86 
    1415 CGPG8474 Metallothio_PEC 12 85 150 6.10E−42 
    1416 CGPG8475 DAO 10 372 186.6 5.80E−53 
    1417 CGPG8476 IQ 84 104 30 8.20E−06 
    1417 CGPG8476 IQ 106 126 14.4 0.41
    1418 CGPG8490 ACT 21 85 3.9 1.3
    1418 CGPG8490 ACT 110 174 36.6 8.60E−08 
    1419 CGPG8510 DUF538 9 149 250.2 4.20E−72 
    1420 CGPG8530 Radical_SAM 119 283 51.3 3.30E−12 
    1421 CGPG8533 DUF212 27 172 104.1 4.20E−28 
    1425 CGPG8555 NUDIX 59 196 82 1.90E−21 
    1426 CGPG8561 zf-C3HC4 154 191 34 5.30E−07 
    1427 CGPG8569 2OG-FeII_Oxy 159 282 61.8 2.20E−15 
    1428 CGPG8573 DUF617 83 242 392.1 8.40E−115
    1431 CGPG8607 DUF862 69 219 244 3.20E−70 
    1432 CGPG8611 Stig1 13 154 165.9 1.00E−46 
    1434 CGPG8632 Sina 86 273 -41.1 0.00037
    1435 CGPG8634 FA_desaturase 55 278 132.1 1.60E−36 
    1436 CGPG8635 DUF59 36 117 47 6.30E−11 
    1438 CGPG8640 DUF581 119 176 133.1 7.60E−37 
    1439 CGPG8642 CRAL_TRIO_N 5 80 30.8 4.60E−06 
    1439 CGPG8642 CRAL_TRIO 93 266 84.7 2.80E−22 
    1441 CGPG8666 PetM 69 120 81.9 2.00E−21 
    1443 CGPG8688 Bet_v_l 55 192 −31.7 0.0014
    1443 CGPG8688 Polyketide_cyc 60 191 28.7 2.00E−05 
    1444 CGPG8689 DUF506 74 282 436 5.20E−128
    1445 CGPG8704 GHMP_kinases_N 24 93 39.2 1.40E−08 
    1445 CGPG8704 GHMP_kinases_C 166 249 32.3 1.70E−06 
    1448 CGPG8769 Self-incomp_S1 35 144 175.9 9.80E−50 
    1449 CGPG8774 Maf 1 207 −0.7 4.20E−09 
    1450 CGPG8778 PPR 13 47 5.4 1.7
    1450 CGPG8778 PPR 115 149 24.7 0.00032
    1450 CGPG8778 PPR 249 283 40.8 4.70E−09 
    1450 CGPG8778 PPR 284 318 12.2 0.27
    1450 CGPG8778 PPR 320 354 16.7 0.078
    1450 CGPG8778 PPR 386 420 9.5 0.56
    1451 CGPG8784 Snf7 16 189 208.6 1.50E−59 
    1452 CGPG879 ABC_tran 195 418 49.2 7.50E−12 
    1452 CGPG879 ABC2_membrane 520 733 231.7 1.60E−66 
    1452 CGPG879 PDR_assoc 738 812 107.4 4.30E−29 
    1452 CGPG879 ABC_tran 887 1077 109 1.40E−29 
    1452 CGPG879 ABC2_membrane 1174 1388 249.2 8.80E−72 
    1453 CGPG8797 AMP-binding 67 488 430.1 3.10E−126
    1454 CGPG8810 DUF1645 80 252 310.1 4.00E−90 
    1455 CGPG8827 DUF623 199 263 128.8 1.50E−35 
    1456 CGPG8853 DUF1635 1 218 517 2.10E−152
    1457 CGPG8873 p450 72 518 236.2 6.90E−68 
    1458 CGPG8877 Exo_endo_phos 33 310 121.7 2.10E−33 
    1459 CGPG8878 Pkinase 79 337. 343.8 2.80E−100
    1459 CGPG8878 efhand 400 428 24.9 0.00028
    1459 CGPG8878 efhand 434 462 34.5 3.60E−07 
    1460 CGPG8881 DUF1677 3 107 192.2 1.30E−54 
    1461 CGPG8895 RNA_poll_A14 1 137 277.8 2.20E−80 
    1462 CGPG8906 MCM 272 635 641.9 5.40E−190
    1463 CGPG8917 Pkinase 363 697 244 3.20E−70 
    1464 CGPG8919 Usp 11 141 43.4 8.00E−10 
    1464 CGPG8919 Pkinase_Tyr 405 676 88.6 1.90E−23 
    1464 CGPG8919 Pkinase 405 676 138.8 1.50E−38 
    1465 CGPG8925 DUF617 82 260 262.9 6.60E−76 
    1466 CGPG8930 Lectin_legB 26 261 232.7 8.20E−67 
    1466 CGPG8930 Pkinase 347 617 166.9 5.30E−47 
    1466 CGPG8930 Pkinase_Tyr 347 617 115.3 1.80E−31 
    1467 CGPG8937 LRR_1 440 461 13.9 0.57
    1467 CGPG8937 LRR_1 463 485 18.7 0.022
    1467 CGPG8937 LRR_1 487 510 14.6 0.36
    1467 CGPG8937 Pkinase 602 873 111.2 3.00E−30 
    1467 CGPG8937 Pkinase_Tyr 603 873 110.1 6.30E−30 
    1468 CGPG8942 RRM_1 23 94 105.3 1.80E−28 
    1469 CGPG8946 Pkinase 516 786 150.8 3.60E−42 
    1469 CGPG8946 Pkinase_Tyr 516 786 129.6 8.70E−36 
    1470 CGPG8990 V-SNARE 71 221 154.1 3.70E−43 
    1472 CGPG9008 TPK_catalytic 40 180 114.5 3.00E−31 
    1472 CGPG9008 TPK_B1_binding 191 259 94.4 3.40E−25 
    1473 CGPG9016 ETC_C1_NDUFA4 54 156 176.6 6.20E−50 
    1474 CGPG9036 MSP 93 329 549 4.70E−162
    1475 CGPG9060 LSM 22 101 66.3 1.00E−16 
    1477 CGPG908 PPR 62 96 9.9 0.5
    1477 CGPG908 PPR 125 158 20.9 0.0047
    1477 CGPG908 PPR 187 221 27 6.50E-05 
    1477 CGPG908 PPR 250 284 50.4 6.20E−12 
    1477 CGPG908 PPR 351 385 53.9 5.30E−13 
    1477 CGPG908 PPR 386 419 2.2 4
    1477 CGPG908 PPR 422 456 17.9 0.035
    1477 CGPG908 PPR 488 522 3.4 3
    1478 CGPG9093 AWPM-19 15 156 325.5 9.00E−95 
    1479 CGPG9096 OTU 11 121 104.8 2.50E−28 
    1482 CGPG9111 TB2_DP1_HVA22 4 101 157 5.10E−44 
    1483 CGPG9112 DUF778 10 177 350.3 3.20E−102
    1484 CGPG9123 DUF833 1 264 236.7 4.90E−68 
    1485 CGPG9124 Exo_endo_phos 20 427 39.2 1.40E−08 
    1485 CGPG9124 efhand 337 365 31.2 3.70E−06 
    1486 CGPG9138 ThiC 165 588 1118.5 0
    1488 CGPG9150 Pkinase 56 326 144.9 2.20E−40 
    1488 CGPG9150 Pkinase_Tyr 56 326 129.9 6.90E−36 
    1489 CGPG9152 elF2A 217 410 382.7 5.60E−112
    1490 CGPG9162 AAA_5 211 346 6.5 0.00057
    1490 CGPG9162 AAA 211 398 309.1 8.00E−90 
    1491 CGPG9165 GATase 11 201 185.4 1.40E−52 
    1491 CGPG9165 GMP_synt_C 432 524 210.5 3.80E−60 
    1492 CGPG9166 GATase 28 210 194.9 1.90E−55 
    1492 CGPG9166 GMP_synt_C 447 539 211.2 2.30E−60 
    1493 CGPG9171 Zip 5 266 60.5 5.40E−15 
    1494 CGPG9177 Complex1_30kDa 113 181 146.8 5.60E−41 
    1494 CGPG9177 Complex1_49kDa 329 600 639.1 3.70E−189
    1495 CGPG9178 PRA-CH 54 129 201 2.90E−57 
    1495 CGPG9178 PRA-PH 142 230 175.7 1.20E−49 
    1496 CGPG9179 Pkinase 4 283 341.9 1.10E−99 
    1496 CGPG9179 Pkinase_Tyr 4 283 96.5 7.90E−26 
    1497 CGPG9181 P21-Arc 17 187 370.6 2.40E−108
    1499 CGPG9189 SAC3_GANP 19 164 152.8 9.30E−43 
    1500 CGPG9201 TPT 201 350 168.8 1.40E−47 
    1501 CGPG9222 YjeF_N 34 199 271.5 1.70E−78 
    1501 CGPG9222 Carb_kinase 257 496 426.9 2.70E−125
    1502 CGPG9234 DUF393 65 183 109.6 9.00E−30 
    1503 CGPG9237 Tim17 18 146 112.4 1.30E−30 
    1504 CGPG9244 TOM20_plant 9 200 435.3 8.30E−128
    1506 CGPG9249 Pkinase 46 330 137.7 3.20E−38 
    1506 CGPG9249 Pkinase_Tyr 46 330 94.3 3.60E−25 
    1507 CGPG9251 Cyclin_N 54 186 115.8 1.30E−31 
    1507 CGPG9251 Cyclin_C 188 314 23.7 0.00055
    1508 CGPG9280 DUF1000 53 168 192 1.40E−54 
    1510 CGPG9302 Diphthamide_syn 30 398 118.1 2.50E−32 
    1511 CGPG931 Pkinase 114 398 303.3 4.30E−88 
    1512 CGPG9313 CN_hydrolase 5 200 75.3 2.00E−19 
    1512 CGPG9313 NAD_synthase 338 652 −11.3 1.20E−11 
    1514 CGPG9327 OPT 74 729 779.8 1.60E−231
    1515 CGPG933 WD40 46 84 23.2 0.00093
    1515 CGPG933 WD40 134 173 22.9 0.0012
    1515 CGPG933 WD40 177 215 33.6 7.00E−07 
    1515 CGPG933 WD40 222 260 42.8 1.10E−09 
    1515 CGPG933 WD40 314 353 21.7 0.0026
    1515 CGPG933 WD40 524 562 31.5 3.00E−06 
    1515 CGPG933 WD40 568 605 23.3 0.00085
    1516 CGPG9334 Sugar_tr 7 720 205.2 1.50E−58 
    1516 CGPG9334 MFS_1 11 679 116.5 7.90E−32 
    1517 CGPG967 BTB 38 135 7.2 0.00091
    1517 CGPG967 NPH3 218 460 370.2 3.20E−108
    1518 CGPG988 Cystatin 36 124 86.1 1.10E−22 
  • TABLE 19
    Pfam domain accession gathering
    name number cutoff domain description
    14-3-3 PF00244.10 25 14-3-3 protein
    2-oxoacid_dh PF00198.13 −112 2-oxoacid dehydrogenases acyltransferase (catalytic domain)
    2OG-FeII_Oxy PF03171.10 11.5 2OG-Fe(II) oxygenase superfamily
    60KD_IMP PF02096.11 −95 60 Kd inner membrane protein
    AAA PF00004.19 12.3 ATPase family associated with various cellular activities (AAA)
    AAA_5 PF07728.4 4 ATPase family associated with various cellular activities (AAA)
    AA_permease PF00324.11 −120.8 Amino acid permease
    ABC1 PF03109.7 −27.6 ABC1 family
    ABC2_membrane PF01061.14 −17.9 ABC-2 type transporter
    ABC_tran PF00005.17 9.5 ABC transporter
    ACT PF01842.15 0 ACT domain
    ADH_N PF08240.2 −14.5 Alcohol dehydrogenase GroES-like domain
    ADH_zinc_N PF00107.16 23.8 Zinc-binding dehydrogenase
    AHSA1 PF08327.1 16.3 Activator of Hsp90 ATPase homolog 1-like protein
    AMP-binding PF00501.18 0 AMP-binding enzyme
    AOX PF01786.8 25 Alternative oxidase
    AP2 PF00847.10 0 AP2 domain
    ARM_1 PF04683.4 25 Adhesion regulating molecule conserved region
    ATP_synt_H PF05493.3 25 ATP synthase subunit H
    AWPM-19 PF05512.2 25 AWPM-19-like family
    Aa_trans PF01490.8 −128.4 Transmembrane amino acid transporter protein
    Abhydrolase_1 PF00561.10 10.3 alpha/beta hydrolase fold
    Abhydrolase_3 PF07859.3 25.8 alpha/beta hydrolase fold
    Actin PF00022.9 −144 Actin
    Acyltransferase PF01553.11 −0.4 Acyltransferase
    Aha1_N PF09229.1 −19.7 Activator of Hsp90 ATPase, N-terminal
    AlaDh_PNT_C PF01262.12 −43.4 Alanine dehydrogenase/PNT, C-terminal domain
    AlaDh_PNT_N PF05222.5 25 Alanine dehydrogenase/PNT, N-terminal domain
    Aldedh PF00171.12 −209.3 Aldehyde dehydrogenase family
    Aldose_epim PF01263.10 −70.5 Aldose 1-epimerase
    Alpha-amylase PF00128.14 −92.6 Alpha amylase, catalytic domain
    Amidohydro_2 PF04909.4 −1.7 Amidohydrolase
    Amino_oxidase PF01593.14 −11.4 Flavin containing amine oxidoreductase
    Aminotran_1_2 PF00155.11 −57.5 Aminotransferase class I and II
    Aminotran_3 PF00202.11 −206.1 Aminotransferase class-III
    Aminotran_4 PF01063.9 −50 Aminotransferase class IV
    Aminotran_5 PF00266.9 −164.4 Aminotransferase class-V
    Ank PF00023.20 0 Ankyrin repeat
    Arf PF00025.11 40 ADP-ribosylation factor family
    ArfGap PF01412.9 −17 Putative GTPase activating protein for Arf
    Arm PF00514.13 17 Armadillo/beta-catenin-like repeat
    Asn_synthase PF00733.11 −52.8 Asparagine synthase
    AstE_AspA PF04952.5 −36.8 Succinylglutamate desuccinylase/Aspartoacylase family
    B3_4 PF03483.7 10 B3/4 domain
    B5 PF03484.5 25 tRNA synthetase B5 domain
    B56 PF01603.10 −210 Protein phosphatase 2A regulatory B subunit (B56 family)
    BCNT PF07572.3 25 Bucentaur or craniofacial development
    BNR PF02012.10 0.7 BNR/Asp-box repeat
    BRCT PF00533.16 27.8 BRCA1 C Terminus (BRCT) domain
    BTB PF00651.21 6.2 BTB/POZ domain
    Band_7 PF01145.15 −5 SPFH domain/Band 7 family
    Barwin PF00967.8 25 Barwin family
    Bet_v_I PF00407.9 −33 Pathogenesis-related protein Bet v I family
    Biotin_lipoyl PF00364.12 −2.3 Biotin-requiring enzyme
    Brix PF04427.8 11.4 Brix domain
    Bystin PF05291.2 25 Bystin
    C2 PF00168.20 3.7 C2 domain
    CAF1 PF04857.10 −100.5 CAF1 family ribonuclease
    CBS PF00571.18 17.5 CBS domain pair
    CCT PF06203.4 25 CCT motif
    CN_hydrolase PF00795.12 −13.9 Carbon-nitrogen hydrolase
    CPDase PF07823.2 −14.5 Cyclic phosphodiesterase-like protein
    CPSase_L_D2 PF02786.7 −48.9 Carbamoyl-phosphate synthase L chain, ATP binding domain
    CPSase_L_D3 PF02787.9 −56 Carbamoyl-phosphate synthetase large chain,
    oligomerisation domain
    CPSase_L_chain PF00289.12 14 Carbamoyl-phosphate synthase L chain, N-terminal domain
    CRAL_TRIO PF00650.10 −26 CRAL/TRIO domain
    CRAL_TRIO_N PF03765.5 16 CRAL/TRIO, N-terminus
    CS PF04969.6 8.6 CS domain
    CTP_transf_1 PF01148.10 −38.5 Cytidylyltransferase family
    Carb_kinase PF01256.8 −66.3 Carbohydrate kinase
    Chitin_bind_1 PF00187.9 25.1 Chitin recognition protein
    Citrate_synt PF00285.11 −101.5 Citrate synthase
    Complex1_30 kDa PF00329.9 −3 Respiratory-chain NADH dehydrogenase, 30 Kd subunit
    Complex1_49 kDa PF00346.9 −108 Respiratory-chain NADH dehydrogenase, 49 Kd subunit
    Copine PF07002.6 −36.5 Copine
    CorA PF01544.9 −61.3 CorA-like Mg2+ transporter protein
    Cornichon PF03311.4 25 Cornichon protein
    Cpn60_TCP1 PF00118.14 −223.4 TCP-1/cpn60 chaperonin family
    Cullin PF00888.12 −33.3 Cullin family
    Cyclin PF08613.1 −34.2 Cyclin
    Cyclin_C PF02984.9 −13 Cyclin, C-terminal domain
    Cyclin_N PF00134.13 −14.7 Cyclin, N-terminal domain
    Cys_Met_Meta_PP PF01053.10 −278.4 Cys/Met metabolism PLP-dependent enzyme
    Cystatin PF00031.11 17.5 Cystatin domain
    Cyt-b5 PF00173.18 4 Cytochrome b5-like Heme/Steroid binding domain
    Cytochrom_C PF00034.11 11.7 Cytochrome c
    DAGK_cat PF00781.14 −5.7 Diacylglycerol kinase catalytic domain (presumed)
    DAO PF01266.14 −35 FAD dependent oxidoreductase
    DEAD PF00270.19 7.2 DEAD/DEAH box helicase
    DHDPS PF00701.12 −90 Dihydrodipicolinate synthetase family
    DHquinase_I PF01487.6 25 Type I 3-dehydroquinase
    DJ-1_PfpI PF01965.14 −7 DJ-1/PfpI family
    DREPP PF05558.3 25 DREPP plasma membrane polypeptide
    DSHCT PF08148.2 −86.9 DSHCT (NUC185) domain
    DUF1000 PF06201.4 −20.8 Domain of Unknown Function (DUF1000)
    DUF1001 PF06206.2 −63.3 Protein of unknown function (DUF1001)
    DUF1005 PF06219.3 25 Protein of unknown function (DUF1005)
    DUF1350 PF07082.2 −145.7 Protein of unknown function (DUF1350)
    DUF1635 PF07795.2 −27.2 Protein of unknown function (DUF1635)
    DUF1639 PF07797.4 25 Protein of unknown function (DUF1639)
    DUF1644 PF07800.3 25 Protein of unknown function (DUF1644)
    DUF1645 PF07816.2 −35.3 Protein of unknown function (DUF1645)
    DUF1677 PF07911.4 25 Protein of unknown function (DUF1677)
    DUF1749 PF08538.1 −181.1 Protein of unknown function (DUF1749)
    DUF1984 PF09328.1 12.8 Domain of unknown function (DUF1984)
    DUF21 PF01595.10 −28.2 Domain of unknown function DUF21
    DUF212 PF02681.5 −30 Divergent PAP2 family
    DUF23 PF01697.17 −18.5 Domain of unknown function
    DUF231 PF03005.6 −58 Arabidopsis proteins of unknown function
    DUF239 PF03080.5 25 Arabidopsis proteins of unknown function
    DUF246 PF03138.5 −15 Plant protein family
    DUF26 PF01657.8 0 Domain of unknown function DUF26
    DUF260 PF03195.5 0.8 Protein of unknown function DUF260
    DUF300 PF03619.7 25 Domain of unknown function
    DUF313 PF03754.4 25 Domain of unknown function (DUF313)
    DUF383 PF04063.4 25 Domain of unknown function (DUF383)
    DUF384 PF04064.4 25 Domain of unknown function (DUF384)
    DUF393 PF04134.3 25 Protein of unknown function, DUF393
    DUF506 PF04720.3 25 Protein of unknown function (DUF506)
    DUF525 PF04379.5 25 Protein of unknown function (DUF525)
    DUF538 PF04398.3 25 Protein of unknown function, DUF538
    DUF581 PF04570.5 −3.1 Protein of unknown function (DUF581)
    DUF59 PF01883.9 −7.9 Domain of unknown function DUF59
    DUF6 PF00892.11 20.8 Integral membrane protein DUF6
    DUF617 PF04759.4 25 Protein of unknown function, DUF617
    DUF623 PF04844.4 25 Protein of unknown function, DUF623
    DUF640 PF04852.3 2.4 Protein of unknown function (DUF640)
    DUF676 PF05057.5 −60.7 Putative serine esterase (DUF676)
    DUF740 PF05340.3 25 Protein of unknown function (DUF740)
    DUF778 PF05608.2 25 Protein of unknown function (DUF778)
    DUF783 PF05615.3 25 Protein of unknown function (DUF783)
    DUF788 PF05620.2 25 Protein of unknown function (DUF788)
    DUF791 PF05631.4 −136.8 Protein of unknown function (DUF791)
    DUF793 PF05633.2 25 Protein of unknown function (DUF793)
    DUF827 PF05701.2 25 Plant protein of unknown function (DUF827)
    DUF833 PF05742.2 −63.1 Protein of unknown function (DUF833)
    DUF860 PF05898.4 25 Plant specific of unknown function (DUF860)
    DUF862 PF05903.5 −21.4 PPPDE putative peptidase domain
    DUF914 PF06027.3 −193 Eukaryotic protein of unknown function (DUF914)
    DUF926 PF06047.2 25 Domain of Unknown Function (DUF926)
    DZC PF08381.1 15.3 Disease resistance/zinc finger/chromosome
    condensation-like region
    Dehydrin PF00257.10 −4.4 Dehydrin
    Di19 PF05605.3 25 Drought induced 19 protein (Di19)
    Diphthamide_syn PF01866.8 25 Putative diphthamide synthesis protein
    Dirigent PF03018.5 25 Dirigent-like protein
    DnaJ PF00226.21 −8 DnaJ domain
    DnaJ_C PF01556.9 −24 DnaJ C terminal region
    DnaJ_CXXCXGXG PF00684.9 1 DnaJ central domain (4 repeats)
    E1_dh PF00676.10 −90 Dehydrogenase E1 component
    E3_binding PF02817.7 10 e3 binding domain
    EFG_C PF00679.14 6 Elongation factor G C-terminus
    ELFV_dehydrog PF00208.11 −27 Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
    ELFV_dehydrog_N PF02812.8 31.8 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain
    ETC_C1_NDUFA4 PF04800.3 25 ETC complex I subunit conserved region
    Enolase_C PF00113.12 −71.2 Enolase, C-terminal TIM barrel domain
    Enolase_N PF03952.6 11.3 Enolase, N-terminal domain
    Exo_endo_phos PF03372.13 11 Endonuclease/Exonuclease/phosphatase family
    F-box PF00646.23 13.9 F-box domain
    FAD_binding_2 PF00890.14 −124.8 FAD binding domain
    FAD_binding_4 PF01565.13 −8.1 FAD binding domain
    FAD_binding_8 PF08022.2 −10.4 FAD-binding domain
    FA_desaturase PF00487.14 −46 Fatty acid desaturase
    FBA_1 PF07734.3 −39.4 F-box associated
    FBA_3 PF08268.2 −17.1 F-box associated
    FBD PF08387.1 25 FBD
    FBPase PF00316.10 −170.3 Fructose-1-6-bisphosphatase
    FHA PF00498.16 25 FHA domain
    FKBP_C PF00254.18 −7.6 FKBP-type peptidyl-prolyl cis-trans isomerase
    FTHFS PF01268.9 −167 Formate--tetrahydrofolate ligase
    Fer2_BFD PF04324.5 25 BFD-like [2Fe—2S] binding domain
    Fer4 PF00037.17 9.3 4Fe—4S binding domain
    Ferric_reduct PF01794.9 −7 Ferric reductase like transmembrane component
    Fibrillarin PF01269.8 −86.6 Fibrillarin
    GAF PF01590.16 23 GAF domain
    GATase PF00117.18 −38.1 Glutamine amidotransferase class-I
    GATase_2 PF00310.11 −95.1 Glutamine amidotransferases class-II
    GDE_C PF06202.4 −218.8 Amylo-alpha-1,6-glucosidase
    GHMP_kinases_C PF08544.3 20.8 GHMP kinases C terminal
    GHMP_kinases_N PF00288.16 17.1 GHMP kinases N terminal domain
    GIDA PF01134.12 −226.7 Glucose inhibited division protein A
    GILT PF03227.6 25 Gamma interferon inducible lysosomal thiol reductase (GILT)
    GMP_synt_C PF00958.12 25 GMP synthase C terminal domain
    GRAM PF02893.10 24.4 GRAM domain
    GRP PF07172.2 16.8 Glycine rich protein family
    GTP_EFTU PF00009.17 8 Elongation factor Tu GTP binding domain
    GTP_EFTU_D2 PF03144.15 25 Elongation factor Tu domain 2
    Gal-bind_lectin PF00337.12 −30 Galactoside-binding lectin
    Galactosyl_T PF01762.12 −46 Galactosyltransferase
    Gar1 PF04410.5 25 Gar1 protein RNA binding region
    Gln-synt_C PF00120.14 −124 Glutamine synthetase, catalytic domain
    Gln-synt_N PF03951.9 9 Glutamine synthetase, beta-Grasp domain
    Globin PF00042.12 −8.8 Globin
    Glucokinase PF02685.6 −157.6 Glucokinase
    Glutaminase PF04960.6 −143.6 Glutaminase
    Glutaredoxin PF00462.14 17.2 Glutaredoxin
    Glyco_hydro_1 PF00232.9 −301.8 Glycosyl hydrolase family 1
    Glyco_hydro_17 PF00332.9 −152.3 Glycosyl hydrolases family 17
    Glyco_tran_28_C PF04101.6 −10.4 Glycosyltransferase family 28 C-terminal domain
    Glyco_transf_8 PF01501.10 −43.2 Glycosyl transferase family 8
    Glycolytic PF00274.9 −174.5 Fructose-bisphosphate aldolase class-I
    Gp_dh_C PF02800.10 −64.1 Glyceraldehyde 3-phosphate dehydrogenase,
    C-terminal domain
    Gp_dh_N PF00044.14 −74.2 Glyceraldehyde 3-phosphate dehydrogenase,
    NAD binding domain
    HATPase_c PF02518.16 22.4 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
    HD PF01966.12 15.3 HD domain
    HEAT PF02985.12 11.5 HEAT repeat
    HIT PF01230.13 −4.5 HIT domain
    HLH PF00010.16 8.3 Helix-loop-helix DNA-binding domain
    HMA PF00403.16 19.5 Heavy-metal-associated domain
    HMG-CoA_red PF00368.9 −242 Hydroxymethylglutaryl-coenzyme A reductase
    H_PPase PF03030.7 −377 Inorganic H+ pyrophosphatase
    Helicase_C PF00271.21 2.1 Helicase conserved C-terminal domain
    Hexapep PF00132.14 0.3 Bacterial transferase hexapeptide (three repeats)
    Hin1 PF07320.4 25 Harpin-induced protein 1 (Hin1)
    HisKA PF00512.15 10.3 His Kinase A (phosphoacceptor) domain
    Histone PF00125.14 17.4 Core histone H2A/H2B/H3/H4
    Hydrolase PF00702.16 13.6 haloacid dehalogenase-like hydrolase
    IGPD PF00475.9 25 Imidazoleglycerol-phosphate dehydratase
    IPK PF03770.7 25 Inositol polyphosphate kinase
    IQ PF00612.17 11.9 IQ calmodulin-binding motif
    Invertase_neut PF04853.3 −233.6 Plant neutral invertase
    Iso_dh PF00180.10 −97 Isocitrate/isopropylmalate dehydrogenase
    Isoamylase_N PF02922.8 −6.5 Isoamylase N-terminal domain
    Isy1 PF06246.3 25 Isy1-like splicing family
    K-box PF01486.8 0 K-box region
    KR PF08659.1 −74.3 KR domain
    KTI12 PF08433.1 −109.1 Chromatin associated protein KTI12
    Kelch_1 PF01344.15 7.8 Kelch motif
    Kelch_2 PF07646.5 14 Kelch motif
    LRRNT_2 PF08263.3 18.6 Leucine rich repeat N-terminal domain
    LRR_1 PF00560.23 7.7 Leucine Rich Repeat
    LRR_2 PF07723.3 6 Leucine Rich Repeat
    LSM PF01423.12 13.7 LSM domain
    Lectin_legB PF00139.10 −110.1 Legume lectin domain
    Lipoxygenase PF00305.9 −211 Lipoxygenase
    Lung_7-TM_R PF06814.3 25 Lung seven transmembrane receptor
    LysM PF01476.10 20 LysM domain
    MATH PF00917.16 0.5 MATH domain
    MBD PF01429.10 12.9 Methyl-CpG binding domain
    MCM PF00493.13 25 MCM2/3/5 family
    MFS_1 PF07690.6 23.5 Major Facilitator Superfamily
    MGDG_synth PF06925.2 25 Monogalactosyldiacylglycerol (MGDG) synthase
    MGS PF02142.12 3 MGS-like domain
    MIP PF00230.10 −62 Major intrinsic protein
    MMR_HSR1 PF01926.13 31.2 GTPase of unknown function
    MSF1 PF04707.4 25 MSF1-like conserved region
    MSP PF01716.9 −71 Manganese-stabilising protein/photosystem II polypeptide
    Maf PF02545.5 −42 Maf-like protein
    Mago-bind PF09282.1 25 Mago binding
    Malic_M PF03949.5 −143.9 Malic enzyme, NAD binding domain
    Metalloenzyme PF01676.8 −14.4 Metalloenzyme superfamily
    Metallophos PF00149.18 22 Calcineurin-like phosphoesterase
    Metallothio_PEC PF02068.6 25 Plant PEC family metallothionein
    Methyltransf_11 PF08241.2 20.9 Methyltransferase domain
    Methyltransf_12 PF08242.2 23 Methyltransferase domain
    Miro PF08477.3 10.8 Miro-like protein
    Mito_carr PF00153.17 0 Mitochondrial carrier protein
    Mo25 PF08569.1 −73.5 Mo25-like
    Molybdop_Fe4S4 PF04879.6 13.6 Molybdopterin oxidoreductase Fe4S4 domain
    Molybdopterin PF00384.12 −50 Molybdopterin oxidoreductase
    Molydop_binding PF01568.11 1.1 Molydopterin dinucleotide binding domain
    Mov34 PF01398.11 −4 Mov34/MPN/PAD-1 family
    MtN3_slv PF03083.6 9.7 MtN3/saliva family
    Myb_DNA-binding PF00249.21 14 Myb-like DNA-binding domain
    NADPH_Ox PF08414.1 25 Respiratory burst NADPH oxidase
    NAD_binding_6 PF08030.2 −23.6 Ferric reductase NAD binding domain
    NAD_synthase PF02540.7 −93.3 NAD synthase
    NAF PF03822.5 4.5 NAF domain
    NDK PF00334.9 −59.9 Nucleoside diphosphate kinase
    NDUF_B7 PF05676.3 −25.7 NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7)
    NIF PF03031.8 −77.9 NLI interacting factor-like phosphatase
    NIR_SIR PF01077.12 −19.6 Nitrite and sulphite reductase 4Fe—4S domain
    NIR_SIR_ferr PF03460.7 2.4 Nitrite/Sulfite reductase ferredoxin-like half domain
    NLE PF08154.2 14 NLE (NUC135) domain
    NOI PF05627.2 0.3 Nitrate-induced NOI protein
    NOT2_3_5 PF04153.8 25 NOT2/NOT3/NOT5 family
    NPH3 PF03000.5 25 NPH3 family
    NTP_transferase PF00483.13 −90.5 Nucleotidyl transferase
    NUDIX PF00293.18 0.2 NUDIX domain
    NicO PF03824.6 −17 High-affinity nickel-transport protein
    Nol1_Nop2_Fmu PF01189.8 −68.2 NOL1/NOP2/sun family
    Not3 PF04065.5 25 Not1 N-terminal domain, CCR4-Not complex component
    Nramp PF01566.9 −217 Natural resistance-associated macrophage protein
    Nuc_sug_transp PF04142.6 −158.6 Nucleotide-sugar transporter
    OPT PF03169.6 −238.6 OPT oligopeptide transporter protein
    OUT PF02338.9 10 OTU-like cysteine protease
    Orn_Arg_deC_N PF02784.7 −76 Pyridoxal-dependent decarboxylase, pyridoxal binding domain
    Orn_DAP_Arg_deC PF00278.12 6.7 Pyridoxal-dependent decarboxylase, C-terminal sheet domain
    OstA PF03968.5 −12.1 OstA-like protein
    P21-Arc PF04062.5 −74.5 P21-ARC (ARP2/3 complex 21 kDa subunit)
    PADR1 PF08063.2 25 PADR1 (NUC008) domain
    PAP2 PF01569.12 8.3 PAP2 superfamily
    PARP PF00644.10 −55.5 Poly(ADP-ribose) polymerase catalytic domain
    PARP_reg PF02877.5 52.8 Poly(ADP-ribose) polymerase, regulatory domain
    PAS_2 PF08446.1 −2.1 PAS fold
    PB1 PF00564.15 12.3 PB1 domain
    PBD PF00786.18 12.2 P21-Rho-binding domain
    PBP PF01161.10 −20.6 Phosphatidylethanolamine-binding protein
    PCI PF01399.17 25 PCI domain
    PC_rep PF01851.12 0 Proteasome/cyclosome repeat
    PDR_assoc PF08370.2 25 Plant PDR ABC transporter associated
    PEARLI-4 PF05278.3 25 Arabidopsis phospholipase-like protein (PEARLI 4)
    PEP-utilizers PF00391.13 0.6 PEP-utilising enzyme, mobile domain
    PEP-utilizers_C PF02896.8 −173 PEP-utilising enzyme, TIM barrel domain
    PFK PF00365.10 −132 Phosphofructokinase
    PGAM PF00300.12 −3 Phosphoglycerate mutase family
    PGI PF00342.9 −168.9 Phosphoglucose isomerase
    PGK PF00162.9 −39.9 Phosphoglycerate kinase
    PGM_PMM_I PF02878.6 −37.5 Phosphoglucomutase/phosphomannomutase,
    alpha/beta/alpha domain I
    PGM_PMM_II PF02879.6 −20 Phosphoglucomutase/phosphomannomutase,
    alpha/beta/alpha domain II
    PGM_PMM_III PF02880.6 −7.1 Phosphoglucomutase/phosphomannomutase,
    alpha/beta/alpha domain III
    PGM_PMM_IV PF00408.10 7.4 Phosphoglucomutase/phosphomannomutase, C-terminal domain
    PI-PLC-X PF00388.9 18.8 Phosphatidylinositol-specific phospholipase C, X domain
    PI-PLC-Y PF00387.9 −11 Phosphatidylinositol-specific phospholipase C, Y domain
    PI3_PI4_kinase PF00454.17 14.8 Phosphatidylinositol 3- and 4-kinase
    PLAT PF01477.13 36.3 PLAT/LH2 domain
    PP2C PF00481.12 −44 Protein phosphatase 2C
    PPAK PF02818.5 0 PPAK motif
    PPDK_N PF01326.9 −150.2 Pyruvate phosphate dikinase, PEP/pyruvate binding domain
    PPR PF01535.11 0 PPR repeat
    PRA-CH PF01502.9 25 Phosphoribosyl-AMP cyclohydrolase
    PRA-PH PF01503.8 −18.3 Phosphoribosyl-ATP pyrophosphohydrolase
    PSI_PsaH PF03244.4 25 Photosystem I reaction centre subunit VI
    PTR2 PF00854.12 −50 POT family
    PWP2 PF04047.4 25 Periodic tryptophan protein 2 WD repeat associated presumed
    domain
    Peptidase_C26 PF07722.3 25 Peptidase C26
    Peptidase_C54 PF03416.9 −153.2 Peptidase family C54
    Peptidase_M22 PF00814.15 −53 Glycoprotease family
    PetM PF08041.2 25 PetM family of cytochrome b6f complex subunit 7
    PfkB PF00294.14 −67.8 pfkB family carbohydrate kinase
    Phi_1 PF04674.3 25 Phosphate-induced protein 1 conserved region
    Phosphoesterase PF04185.5 −71.5 Phosphoesterase family
    Phytochelatin PF05023.5 25 Phytochelatin synthase
    Phytochrome PF00360.10 13 Phytochrome region
    Pkinase PF00069.15 −70.3 Protein kinase domain
    Pkinase_Tyr PF07714.7 65 Protein tyrosine kinase
    Polyketide_cyc PF03364.10 20.6 Polyketide cyclase/dehydrase and lipid transport
    Pre-SET PF05033.6 3.9 Pre-SET motif
    Prefoldin PF02996.8 9.3 Prefoldin subunit
    Pribosyltran PF00156.17 2 Phosphoribosyl transferase domain
    Pro_CA PF00484.9 −45 Carbonic anhydrase
    Pro_dh PF01619.8 −120.5 Proline dehydrogenase
    Pro_isomerase PF00160.11 −37 Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
    PseudoU_synth_1 PF01416.10 11 tRNA pseudouridine synthase
    Pyr_redox PF00070.17 5 Pyridine nucleotide-disulphide oxidoreductase
    Pyr_redox_2 PF07992.4 −20 Pyridine nucleotide-disulphide oxidoreductase
    Pyr_redox_dim PF02852.12 −13 Pyridine nucleotide-disulphide oxidoreductase, dimerisation
    domain
    Pyridoxal_deC PF00282.9 −158.6 Pyridoxal-dependent decarboxylase conserved domain
    RNA_polI_A14 PF08203.2 25 Yeast RNA polymerase I subunit RPA14
    RNA_pol_A_bac PF01000.16 10 RNA polymerase Rpb3/RpoA insert domain
    RNA_pol_I_A49 PF06870.3 25 A49-like RNA polymerase I associated factor
    RNA_pol_L PF01193.14 16.9 RNA polymerase Rpb3/Rpb11 dimerisation domain
    RRM_1 PF00076.12 17.7 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
    RWD PF05773.12 18.4 RWD domain
    Radical_SAM PF04055.11 8.5 Radical SAM superfamily
    Ras PF00071.12 −69.9 Ras family
    RelA_SpoT PF04607.7 −6.7 Region found in RelA/SpoT proteins
    Response_reg PF00072.14 4 Response regulator receiver domain
    Reticulon PF02453.8 −40 Reticulon
    Rho_GDI PF02115.7 −55 RHO protein GDP dissociation inhibitor
    Rib_5-P_isom_A PF06026.5 −84.5 Ribose 5-phosphate isomerase A (phosphoriboisomerase A)
    Ribonuc_L-PSP PF01042.11 −25 Endoribonuclease L-PSP
    Ribosomal_L19 PF01245.10 −31 Ribosomal protein L19
    Ribosomal_L37 PF08561.1 25 Mitochondrial ribosomal protein L37
    Ribosomal_S8 PF00410.9 −27 Ribosomal protein S8
    SAC3_GANP PF03399.6 −15.2 SAC3/GANP/Nin1/mts3/eIF-3 p25 family
    SET PF00856.18 23.5 SET domain
    SH3_1 PF00018.18 −8 SH3 domain
    SH3_2 PF07653.7 0 Variant SH3 domain
    SIR2 PF02146.8 −95 Sir2 family
    SIS PF01380.12 0 SIS domain
    SKI PF01202.12 −9.2 Shikimate kinase
    SNARE PF05739.9 23.8 SNARE domain
    SNARE_assoc PF09335.1 −12.1 SNARE associated Golgi protein
    SOR_SNZ PF01680.7 25 SOR/SNZ family
    SPOC PF07744.3 12.3 SPOC domain
    SPT2 PF08243.2 25 SPT2 chromatin protein
    SRF-TF PF00319.9 11 SRF-type transcription factor (DNA-binding and dimerisation
    domain)
    Saccharop_dh PF03435.8 −77.9 Saccharopine dehydrogenase
    Saccharop_dh_N PF04455.3 25 LOR/SDH bifunctional enzyme conserved region
    SapB_1 PF05184.5 3 Saposin-like type B, region 1
    SapB_2 PF03489.7 10.8 Saposin-like type B, region 2
    ScpA_ScpB PF02616.5 −39 ScpA/B protein
    Sel1 PF08238.2 6.2 Sel1 repeat
    Self-incomp_S1 PF05938.2 −12.7 Plant self-incompatibility protein S1
    Senescence PF06911.3 −53.5 Senescence-associated protein
    Shikimate_DH PF01488.10 −4.4 Shikimate/quinate 5-dehydrogenase
    Shikimate_dh_N PF08501.1 −12.2 Shikimate dehydrogenase substrate binding domain
    Sina PF03145.7 −48.4 Seven in absentia protein family
    Skp1 PF01466.9 −2 Skp1 family, dimerisation domain
    Skp1_POZ PF03931.5 14.9 Skp1 family, tetramerisation domain
    Snf7 PF03357.11 −22.9 Snf7
    Spermine_synth PF01564.7 −93.8 Spermine/spermidine synthase
    SpoIIE PF07228.3 −13.7 Stage II sporulation protein E (SpoIIE)
    Sterol_desat PF01598.8 −13 Sterol desaturase
    Stig1 PF04885.4 25 Stigma-specific protein, Stig1
    Str_synth PF03088.7 4.7 Strictosidine synthase
    Sugar_tr PF00083.14 −85 Sugar (and other) transporter
    Sulfotransfer_1 PF00685.17 −53.1 Sulfotransferase domain
    TB2_DP1_HVA22 PF03134.9 −25.1 TB2/DP1, HVA22 family
    TFIIF_alpha PF05793.3 25 Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)
    TFIIS PF08711.1 3 Transcription elongation factor S-II protein N terminal
    TFIIS_C PF01096.9 15 Transcription factor S-II (TFIIS)
    TFIIS_M PF07500.4 7.4 Transcription factor S-II (TFIIS), central domain
    TIM PF00121.9 −97 Triosephosphate isomerase
    TLD PF07534.6 25 TLD
    TMEM14 PF03647.4 −1 Transmembrane proteins 14C
    TOM20_plant PF06552.3 25 Plant specific mitochondrial import receptor subunit TOM20
    TPK_B1_binding PF04265.5 25 Thiamin pyrophosphokinase, vitamin B1 binding domain
    TPK_catalytic PF04263.7 −23.8 Thiamin pyrophosphokinase, catalytic domain
    TPR_2 PF07719.7 20.1 Tetratricopeptide repeat
    TPT PF03151.7 −15.3 Triose-phosphate Transporter family
    TP_methylase PF00590.10 −38 Tetrapyrrole (Corrin/Porphyrin) Methylases
    Tcp11 PF05794.4 25 T-complex protein 11
    Tetraspannin PF00335.10 −15.4 Tetraspanin family
    ThiC PF01964.9 25 ThiC family
    ThiF PF00899.11 −38.4 ThiF family
    ThiG PF05690.4 −186.9 Thiazole biosynthesis protein ThiG
    Thioredoxin PF00085.10 −25.7 Thioredoxin
    Tim17 PF02466.9 2.7 Tim17/Tim22/Tim23 family
    Transaldolase PF00923.9 −49 Transaldolase
    Transket_pyr PF02779.14 −49 Transketolase, pyrimidine binding domain
    Transketolase_C PF02780.10 −15.5 Transketolase, C-terminal domain
    Transketolase_N PF00456.11 −98 Transketolase, thiamine diphosphate binding domain
    Transthyretin PF00576.11 25 Transthyretin precursor (formerly prealbumin)
    Trehalose_PPase PF02358.7 −49.4 Trehalose-phosphatase
    Tryp_alpha_amyl PF00234.12 −4 Protease inhibitor/seed storage/LTP family
    UAA PF08449.2 −146.2 UAA transporter family
    UBA PF00627.21 20.7 UBA/TS-N domain
    UBX PF00789.11 10 UBX domain
    UCH PF00443.19 −8.6 Ubiquitin carboxyl-terminal hydrolase
    UDPGT PF00201.9 −151 UDP-glucoronosyl and UDP-glucosyl transferase
    UFD1 PF03152.5 25 Ubiquitin fusion degradation protein UFD1
    UQ_con PF00179.16 −30 Ubiquitin-conjugating enzyme
    Uricase PF01014.9 −10.6 Uricase
    Usp PF00582.16 21.6 Universal stress protein family
    Utp13 PF08625.1 −12.4 Utp13 specific WD40 associated domain
    V-SNARE PF05008.5 −16 Vesicle transport v-SNARE protein
    Voltage_CLC PF00654.10 −148 Voltage gated chloride channel
    WD40 PF00400.22 21.5 WD domain, G-beta repeat
    WGR PF05406.5 5.8 WGR domain
    WRKY PF03106.6 25 WRKY DNA -binding domain
    XG_FTase PF03254.4 25 Xyloglucan fucosyltransferase
    XPC-binding PF09280.1 27.6 XPC-binding domain
    Xan_ur_permease PF00860.11 −151.2 Permease family
    YDG_SRA PF02182.8 25 YDG/SRA domain
    Y_phosphatase2 PF03162.4 −47.6 Tyrosine phosphatase family
    YjeF_N PF03853.5 25 YjeF-related protein N-terminus
    Zip PF02535.12 −25.6 ZIP Zinc transporter
    adh_short PF00106.15 −40.2 short chain dehydrogenase
    cobW PF02492.9 −10 CobW/HypB/UreG, nucleotide-binding domain
    eIF-1a PF01176.9 20 Translation initiation factor 1A/IF-1
    eIF2A PF08662.1 0 Eukaryotic translation initiation factor eIF2A
    efhand PF00036.22 21.7 EF hand
    efhand_like PF09279.1 17.8 Phosphoinositide-specific phospholipase C, efhand-like
    iPGM_N PF06415.4 −263.4 BPG-independent PGAM N-terminus (iPGM_N)
    mTERF PF02536.5 −60 mTERF
    malic PF00390.9 25 Malic enzyme, N-terminal domain
    p450 PF00067.12 −105 Cytochrome P450
    polyprenyl_synt PF00348.8 −43 Polyprenyl synthetase
    tRNA-synt_1g PF09334.1 −272.5 tRNA synthetases class I (M)
    ubiquitin PF00240.13 19.4 Ubiquitin family
    zf-C3HC4 PF00097.15 16 Zinc finger, C3HC4 type (RING finger)
    zf-CCHC PF00098.13 17.9 Zinc knuckle
    zf-CW PF07496.5 25 CW-type Zinc Finger
    zf-LSD1 PF06943.3 25 LSD1 zinc finger
    zf-MYND PF01753.9 11 MYND finger
    zf-PARP PF00645.8 25 Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    zf-Tim10_DDP PF02953.6 −5 Tim10/DDP family zinc finger
    zf-UBR PF02207.10 25 Putative zinc finger in N-recognin (UBR box)
    • Example 5 Plasmid Contruction for Transferring Recombinant DNA
  • This example illustrates the construction of plasmids for transferring recombinant DNA into the nucleus of a plant cell which can be regenerated into a transgenic crop plant of this invention. Primers for PCR amplification of protein coding nucleotides of recombinant DNA are designed at or near the start and stop codons of the coding sequence, in order to eliminate most of the 5′ and 3′ untranslated regions. DNA of interest, i.e. each DNA identified in Table 2 and the DNA for the identified homologous genes, are cloned and amplified by PCR prior to insertion into the insertion site the base vector.
  • A. Plant Expression Constructs for Corn Transformation
  • Elements of an exemplary common expression vector, pMON93039 are illustrated in Table 20. The exemplary base vector which is especially useful for corn transformation is illustrated in FIG. 1 and assembled using technology known in the art.
  • TABLE 20
    pMON93039
    Coordinates of
    function name annotation SEQ ID NO: 67779
    Agrobacterium B-AGRtu.right border Agro right border 11364-11720
    T-DNA sequence, essential for
    trabsfer transfer of T-DNA.
    Gene of E-Os.Act1 upstream promoter  19-775
    interest region of the rice actin
    expression
    1 gene
    cassette E-CaMV.35S.2xA1-B3 duplicated35S A1-B3  788-1120
    domain without TATA
    box
    P-Os.Act1 promoter region of the 1125-1204
    rice actin 1 gene
    L-Ta.Lhcb1 5′ untranslated leader 1210-1270
    of wheat major
    chlorophyll a/b binding
    protein
    I-Os.Act1 first intron and flanking 1287-1766
    UTR exon sequences
    from the rice actin 1
    gene
    T-St.Pis4 3′ non-translated region 1838-2780
    of the potato proteinase
    inhibitor II gene which
    functions to direct
    polyadenylation of the
    mRNA
    Plant P-Os.Act1 Promoter from the rice 2830-3670
    selectable actin 1 gene
    marker L-Os.Act1 first exon of the rice 3671-3750
    expression actin 1 gene
    cassette I-Os.Act1 first intron and flanking 3751-4228
    UTR exon sequences
    from the rice actin 1
    gene
    TS-At.ShkG-CTP2 Transit peptide region 4238-4465
    of Arabidopsis EPSPS
    CR-AGRtu.aroA- coding region for 4466-5833
    CP4.nat bacterial strain CP4
    native arogA gene
    T-AGRtu.nos A 3′ non-translated 5849-6101
    region of the nopaline
    synthase gene of
    Agrobacterium
    tumefaciens Ti plasmid
    which functions to
    direct polyadenylation
    of the mRNA.
    Agrobacterium B-AGRtu.left border Agro left border 6168-6609
    T-DNA sequence, essential for
    transfer transfer of T-DNA.
    Maintenance OR-Ec.oriV-RK2 The vegetative origin 6696-7092
    in E. coli of replication from
    plasmid RK2.
    CR-Ec.rop Coding region for 8601-8792
    repressor of primer
    from the ColE1
    plasmid. Expression of
    this gene product
    interferes with primer
    binding at the origin of
    replication, keeping
    plasmid copy number
    low.
    OR-Ec.ori-ColE1 The minimal origin of 9220-9808
    replication from the E. coli
    plasmid ColE1.
    P-Ec.aadA-SPC/STR romoter for Tn7 10339-10380
    adenylyltransferase
    (AAD(3″))
    CR-Ec.aadA-SPC/STR Coding region for Tn7 10381-11169
    adenylyltransferase
    (AAD(3″)) conferring
    spectinomycin and
    streptomycin
    resistance.
    T-Ec.aadA-SPC/STR 3′ UTR from the Tn7 11170-11227
    adenylyltransferase
    (AAD(3″)) gene of E. coli.
  • B. Plant Expression Constructs for Soybean or Canola Transformation
  • Plasmids for use in transformation of soybean are also prepared. Elements of an exemplary common expression vector plasmid pMON82053 are shown in Table 21 below. This exemplary soybean transformation base vector illustrated in FIG. 2 is assembled using the technology known in the art. DNA of interest, i.e. each DNA identified in Table 2 and the DNA for the identified homologous genes, is cloned and amplified by PCR prior to insertion into the insertion site the base vector at the insertion site between the enhanced 35S CaMV promoter and the termination sequence of cotton E6 gene.
  • TABLE 21
    pMON82053
    Coordinates of
    function name annotation SEQ ID NO: 67780
    Agrobacterium B-AGRtu.left Agro left border sequence, essential 6144-6585
    T-DNA border for transfer of T-DNA.
    transfer
    Plant P-At.Act7 Promoter from the arabidopsis actin 6624-7861
    selectable 7 gene
    marker L-At.Act7 5′UTR of Arabidopsis Act7 gene
    expression I-At.Act7 Intron from the Arabidopsis actin7
    cassette gene
    TS-At.ShkG- Transit peptide region of Arabidopsis 7864-8091
    CTP2 EPSPS
    CR-AGRtu.aroA- Synthetic CP4 coding region with 8092-9459
    CP4.nno_At dicot preferred codon usage.
    T-AGRtu.nos A 3′ non-translated region of the 9466-9718
    nopaline synthase gene of
    Agrobacterium tumefaciens Ti
    plasmid which functions to direct
    polyadenylation of the mRNA.
    Gene of P-CaMV.35S-enh Promoter for 35S RNA from CaMV  1-613
    interest containing a duplication of the −90
    expression to −350 region.
    cassette T-Gb.E6-3b 3′ untranslated region from the fiber  688-1002
    protein E6 gene of sea-island cotton;
    Agrobaterium B-AGRtu.right Agro right border sequence, essential 1033-1389
    T-DNA border for transfer of T-DNA.
    transfer
    Maintenance OR-Ec.oriV-RK2 The vegetative origin of replication 5661-6057
    in E. coli from plasmid RK2.
    CR-Ec.rop Coding region for repressor of 3961-4152
    primer from the ColE1 plasmid.
    Expression of this gene product
    interferes with primer binding at the
    origin of replication, keeping
    plasmid copy number low.
    OR-Ec.ori-ColE1 The minimal origin of replication 2945-3533
    from the E. coli plasmid ColE1.
    P-Ec.aadA- romoter for Tn7 adenylyltransferase 2373-2414
    SPC/STR (AAD(3″))
    CR-Ec.aadA- Coding region for Tn7 1584-2372
    SPC/STR adenylyltransferase (AAD(3″))
    conferring spectinomycin and
    streptomycin resistance.
    T-Ec.aadA- 3′ UTR from the Tn7 1526-1583
    SPC/STR adenylyltransferase (AAD(3″)) gene
    of E. coli.
  • C. Plant Expression Constructs for Cotton Transformation
  • Plasmids for use in transformation of cotton are also prepared. Elements of an exemplary common expression vector plasmid pMON99053 are shown in Table 22 below and FIG. 3. Primers for PCR amplification of protein coding nucleotides of recombinant DNA are designed at or near the start and stop codons of the coding sequence, in order to eliminate most of the 5′ and 3′ untranslated regions. Each recombinant DNA coding for a protein identified in Table 2 is amplified by PCR prior to insertion into the insertion site within the gene of interest expression cassette of one of the base.
  • TABLE 22
    pMON99053
    Coordinates of
    function name annotation SEQ ID NO: 67781
    Agrobacterium B-AGRtu.right border Agro right border sequence, 11364-11720
    T-DNA essential for transfer of T-
    transfer DNA.
    Gene of Exp-CaMV.35S- Enhanced version of the 35S 7794-8497
    interest enh + ph.DnaK RNA promoter from CaMV
    expression plus the petunia hsp70 5′
    cassette untranslated region
    T-Ps.RbcS2-E9 The 3′ non-translated region  67-699
    of the pea RbcS2 gene which
    functions to direct
    polyadenylation of the
    mRNA.
    Plant Exp-CaMV.35S Promoter and 5′ untranslated  730-1053
    selectable region of the 35S RNA from
    marker CaMV
    expression CR-Ec.nptII-Tn5 Neomycin Phosphotransferase 1087-1881
    cassette II gene that confers resistance
    to neomycin and kanamycin
    T-AGRtu.nos A 3′ non-translated region of 1913-2165
    the nopaline synthase gene of
    Agrobacterium tumefaciens
    Ti plasmid which functions to
    direct polyadenylation of the
    mRNA.
    Agrobacterium B-AGRtu.left border Agro left border sequence, 2211-2652
    T-DNA essential for transfer of T-
    transfer DNA.
    Maintenance OR-Ec.oriV-RK2 The vegetative origin of 2739-3135
    in E. coli replication from plasmid
    RK2.
    CR-Ec.rop Coding region for repressor of 4644-4835
    primer from the ColE1
    plasmid. Expression of this
    gene product interferes with
    primer binding at the origin of
    replication, keeping plasmid
    copy number low.
    OR-Ec.ori-ColE1 The minimal origin of 5263-5851
    replication from the E. coli
    plasmid ColE1.
    P-Ec.aadA-SPC/STR romoter for Tn7 6382-6423
    adenylyltransferase
    (AAD(3″))
    CR-Ec.aadA-SPC/STR Coding region for Tn7 6424-7212
    adenylyltransferase
    (AAD(3″)) conferring
    spectinomycin and
    streptomycin resistance.
    T-Ec.aadA-SPC/STR 3′ UTR from the Tn7 7213-7270
    adenylyltransferase
    (AAD(3″)) gene of E. coli.
    • Example 6 Corn Plant Tranformation
  • This example illustrates the production and identification of transgenic corn cells in seed of transgenic corn plants having an enhanced agronomic trait, i.e. enhanced nitrogen use efficiency, increased yield, enhanced water use efficiency, enhanced tolerance to cold and/or enhanced seed compositions as compared to control plants. Transgenic corn cells are prepared with recombinant DNA expressing each of the protein encoding DNAs listed in Table 2 by Agrobacterium-mediated transformation using the corn transformation constructs as disclosed in Example 5.
  • Corn transformation is effected using methods disclosed in U.S. Patent Application Publication 2004/0344075 A 1 where corn embryos are inoculated and co-cultured with the Agrobacterium tumefaciens strain ABI and the corn transformation vector. To regenerate transgenic corn plants the transgenic callus resulting from transformation is placed on media to initiate shoot development in plantlets which are transferred to potting soil for initial growth in a growth chamber followed by a mist bench before transplanting to pots where plants are grown to maturity. The plants are self fertilized and seed is harvested for screening as seed, seedlings or progeny R2 plants or hybrids, e.g., for yield trials in the screens indicated above.
  • Many transgenic events which survive to fertile transgenic plants that produce seeds and progeny plants do not exhibit an enhanced agronomic trait. The transgenic plants and seeds having the transgenic cells of this invention which have recombinant DNA imparting the enhanced agronomic traits are identified by screening for nitrogen use efficiency, yield, water use efficiency, cold tolerance and enhanced seed composition.
    • Example 7 Soybean Plant Transformation
  • This example illustrates the production and identification of transgenic soybean cells in seed of transgenic soybean plants having an enhanced agronomic trait, i.e. enhanced nitrogen use efficiency, increased yield, enhanced water use efficiency, enhanced tolerance to cold and/or enhanced seed compositions as compared to control plants. Transgenic soybean cells are prepared with recombinant DNA expressing each of the protein encoding DNAs listed in Table 1 by Agrobacterium-mediated transformation using the soybean transformation constructs disclosed in Example 5. Soybean transformation is effected using methods disclosed in U.S. Pat. No. 6,384,301 where soybean meristem explants are wounded then inoculated and co-cultured with the soybean transformation vector, then transferred to selection media for 6-8 weeks to allow selection and growth of transgenic shoots.
  • The transformation is repeated for each of the protein encoding DNAs identified in Table 2.
  • Transgenic shoots producing roots are transferred to the greenhouse and potted in soil. Many transgenic events which survive to fertile transgenic plants that produce seeds and progeny plants do not exhibit an enhanced agronomic trait. The transgenic plants and seeds having the transgenic cells of this invention which have recombinant DNA imparting the enhanced agronomic traits are identified by screening for nitrogen use efficiency, yield, water use efficiency, cold tolerance and enhanced seed composition.
    • Example 8 Selection of Transgenic Plants with Enhanced Agronomic Trait(s)
  • This example illustrates identification of plant cells of the invention by screening derived plants and seeds for enhanced trait. Transgenic seed and plants in corn, soybean, cotton or canola with recombinant DNA identified in Table 2 are prepared by plant cells transformed with DNA that is stably integrated into the genome of the corn cell. Transgenic corn plant cells are transformed with recombinant DNA from each of the genes identified in Table 2. Progeny transgenic plants and seed of the transformed plant cells are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil as compared to control plants
    • A. Selection for Enhanced Nitrogen Use Efficiency
  • Transgenic corn seeds provided by the present invention are planted in fields with three levels of nitrogen (N) fertilizer being applied, i.e. low level (0 N), medium level (80 lb/ac) and high level (180 lb/ac). A variety of physiological traits are monitored. Plants with enhanced NUE provide higher yield as compared to control plants.
    • B. Selection for Increased Yield
  • Effective selection of enhanced yielding transgenic plants uses hybrid progeny of the transgenic plants for corn, cotton, and canola, or inbred progeny of transgenic plants for soybeanplants plant such as corn, cotton, canola, or inbred plant such as soy, canola and cottoncotton over multiple locations with plants grown under optimal production management practices, and maximum pest control. A useful target for improved yield is a 5% to 10% increase in yield as compared to yield produced by plants grown from seed for a control plant. Selection methods may be applied in multiple and diverse geographic locations, for example up to 16 or more locations, over one or more planting seasons, for example at least two planting seasons, to statistically distinguish yield improvement from natural environmental effects
    • C. Selection for Enhanced Water Use Efficiency (WUE)
  • The selection process imposes a water withholding period to induce stressdrought followed by watering. For example, for corn, a useful selection process imposes 3 drought/re-water cycles on plants over a total period of 15 days after an initial stress free growth period of 11 days. Each cycle consists of 5 days, with no water being applied for the first four days and a water quenching on the 5th day of the cycle. The primary phenotypes analyzed by the selection method are the changes in plant growth rate as determined by height and biomass during a vegetative drought treatment.
    • D. Selection for Growth Under Cold Stress
  • (1) Cold germination assay—Trays of transgenic and control seeds are placed in a growth chamber at 9.7° C. for 24 clays (no light). Seeds having higher germination rates as compared to the control are identified.
  • (2) Cold field efficacy trial—A cold field efficacy trial is used to identify gene constructs that confer enhanced cold vigor at germination and early seedling growth under early spring planting field conditions in conventional-till and simulated no-till environments. Seeds are planted into the ground around two weeks before local farmers begin to plant corn so that a significant cold stress is exerted onto the crop, named as cold treatment. Seeds also are planted under local optimal planting conditions such that the crop has little or no exposure to cold condition, named as normal treatment. At each location, seeds are planted under both cold and normal conditions with 3 repetitions per treatment. Two temperature monitors are set up at each location to monitor both air and soil temperature daily.
  • Seed emergence is defined as the point when the growing shoot breaks the soil surface. The number of emerged seedlings in each plot is counted everyday from the day the earliest plot begins to emerge until no significant changes in emergence occur. In addition, for each planting date, the latest date when emergence is 0 in all plots is also recorded. Seedling vigor is also rated at V3-V4 stage before the average of corn plant height reaches 10 inches, with 1=excellent early growth, 5=Average growth and 9=poor growth. Days to 50% emergence, maximum percent emergence and seedling vigor are used to determine plants with enhanced cold tolerance.
  • E. Screens for Transgenic Plant Seeds with Increased Protein and/or Oil Levels
  • This example sets forth a high-throughput selection for identifying plant seeds with improvement in seed composition using the Infratec 1200 series Grain Analyzer, which is a near-infrared transmittance spectrometer used to determine the composition of a bulk seed sample (Table 23). Near infrared analysis is a non-destructive, high-throughput method that can analyze multiple traits in a single sample scan. An NIR calibration for the analytes of interest is used to predict the values of an unknown sample. The NIR spectrum is obtained for the sample and compared to the calibration using a complex chemometric software package that provides predicted values as well as information on how well the sample fits in the calibration.
  • Infratec Model 1221, 1225, or 1227 with transport module by Foss North America is used with cuvette, item #1000-4033, Foss North America or for small samples with small cell cuvette, Foss standard cuvette modified by Leon Girard Co. Corn and soy check samples of varying composition maintained in check cell cuvettes are supplied by Leon Girard Co. NIT collection software is provided by Maximum Consulting Inc. Software. Calculations are performed automatically by the software. Seed samples are received in packets or containers with barcode labels from the customer. The seed is poured into the cuvettes and analyzed as received.
  • TABLE 23
    Typical sample(s): Whole grain corn and soybean seeds
    Analytical time to run method: Less than 0.75 min per sample
    Total elapsed time per run: 1.5 minute per sample
    Typical and minimum sample Corn typical: 50 cc; minimum 30 cc
    size: Soybean typical: 50 cc; minimum 5 cc
    Typical analytical range: Determined in part by the specific
    calibration.
    Corn - moisture 5-15%, oil 5-20%,
    protein 5-30%, starch 50-75%, and
    density 1.0-1.3%.
    Soybean - moisture 5-15%, oil 15-25%,
    and protein 35-50%.
    • Example 9 Cotton Transgenic Plants with Enhanced Agronomic Traits
  • Cotton transformation is performed as generally described in WO0036911 and in U.S. Pat. No. 5,846,797. Transgenic cotton plants containing each of the recombinant DNA having a sequence of SEQ ID NO: 1 through SEQ ID NO: 759 are obtained by transforming with recombinant DNA from each of the genes identified in Table 1. Progeny transgenic plants are selected from a population of transgenic cotton events under specified growing conditions and are compared with control cotton plants. Control cotton plants are substantially the same cotton genotype but without the recombinant DNA, for example, either a parental cotton plant of the same genotype that was not transformed with the identical recombinant DNA or a negative isoline of the transformed plant. Additionally, a commercial cotton cultivar adapted to the geographical region and cultivation conditions, i.e. cotton variety ST474, cotton variety FM 958, and cotton variety Siokra L-23, are used to compare the relative performance of the transgenic cotton plants containing the recombinant DNA. The specified culture conditions are growing a first set of transgenic and control plants under “wet” conditions, i.e. irrigated in the range of 85 to 100 percent of evapotranspiration to provide leaf water potential of −14 to −18 bars, and growing a second set of transgenic and control plants under “dry” conditions, i.e. irrigated in the range of 40 to 60 percent of evapotranspiration to provide a leaf water potential of −21 to −25 bars. Pest control, such as weed and insect control is applied equally to both wet and dry treatments as needed. Data gathered during the trial includes weather records throughout the growing season including detailed records of rainfall; soil characterization information; any herbicide or insecticide applications; any gross agronomic differences observed such as leaf morphology, branching habit, leaf color, time to flowering, and fruiting pattern; plant height at various points during the trial; stand density; node and fruit number including node above white flower and node above crack boll measurements; and visual wilt scoring. Cotton boll samples are taken and analyzed for lint fraction and fiber quality. The cotton is harvested at the normal harvest timeframe for the trial area. Enhanced water use efficiency is indicated by increased yield, improved relative water content, enhanced leaf water potential, increased biomass, enhanced leaf extension rates, and improved fiber parameters.
  • The transgenic cotton plants of this invention are identified from among the transgenic cotton plants by agronomic trait screening as having increased yield and enhanced water use efficiency.
    • Example 10 Canola Plants with Enhanced Agrominic Traits
  • This example illustrates plant transformation useful in producing the transgenic canola plants of this invention and the production and identification of transgenic seed for transgenic canola having enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
  • Tissues from in vitro grown canola seedlings are prepared and inoculated with a suspension of overnight grown Agrobacterium containing plasmid DNA with the gene of interest cassette and a plant selectable marker cassette. Following co-cultivation with Agrobacterium, the infected tissues are allowed to grow on selection to promote growth of transgenic shoots, followed by growth of roots from the transgenic shoots. The selected plantlets are then transferred to the greenhouse and potted in soil. Molecular characterization are performed to confirm the presence of the gene of interest, and its expression in transgenic plants and progenies. Progeny transgenic plants are selected from a population of transgenic canola events under specified growing conditions and are compared with control canola plants. Control canola plants are substantially the same canola genotype but without the recombinant DNA, for example, either a parental canola plant of the same genotype that is not transformed with the identical recombinant DNA or a negative isoline of the transformed plant
  • Transgenic canola plant cells are transformed with recombinant DNA from each of the genes identified in Table 2. Transgenic progeny plants and seed of the transformed plant cells are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
    • Example 11 Selection of Transgenic Plants with Enhanced Agronomic Trait(s)
  • This example illustrates the preparation and identification by selection of transgenic seeds and plants derived from transgenic plant cells of this invention where the plants and seed are identified by screening for a transgenic plant having an enhanced agronomic trait imparted by expression or suppression of a protein selected from the group including the homologous proteins identified in Example 2. Transgenic plant cells of corn, soybean, cotton, canola, alfalfa, wheat and rice are transformed with recombinant DNA for expressing or suppressing each of the homologs identified in Example 2. Plants are regenerated from the transformed plant cells and used to produce progeny plants and seed that are screened for enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. Plants are identified exhibiting enhanced traits imparted by expression or suppression of the homologous proteins.
    • Example 12 Monocot and Dicot Plant Transformation for the Suppression of Endogeneous Protein
  • This example illustrates monocot and dicot plant transformation to produce nuclei of this invention in cells of a transgenic plant by transformation where the recombinant DNA suppresses the expression of an endogenous protein identified in Table 24.
  • Corn, soybean, cotton, or canola tissue are transformed as described in Examples 2-5 using recombinant DNA in the nucleus with DNA that is transcribed into RNA that forms double-stranded RNA targeted to an endogenous gene with DNA encoding the protein. The genes for which the double-stranded RNAs are targeted are the native gene in corn, soybean, cotton or canola that are homologs of the genes encoding the protein that has the function of the protein in Arabidopsis as identified in table 24.
  • Populations of transgenic plants prepared in Examples 6, 7, 9, 10 or 11 with DNA for suppressing a gene identified in Table 2 as providing an enhanced trait by gene suppression are screened to identify an event from those plants with a nucleus of the invention by selecting the trait identified in this specification.
  • TABLE 24
    PEP
    SEQ
    ID Gene_id Construct ID Traits
    760 CGPG1022.pep RRM_1 DS
    761 CGPG1035.pep Peptidase_C54 SS
    763 CGPG105.pep AP2 HS PEG
    764 CGPG1060.pep DUF788 LN
    771 CGPG1136.pep RRM_1 DS
    774 CGPG1145.pep LNDIX LN
    776 CGPG1173.pep adh_short LN
    779 CGPG122.pep PTR2 LN
    781 CGPG1262.pep Gar1 CK
    782 CGPG128.pep Response_reg LN
    784 CGPG1291.pep DUF862 DS
    794 CGPG1398.pep Glycolytic LN
    795 CGPG1399.pep Metallophos LN
    799 CGPG146.pep p450 CS PP SS
    801 CGPG1528.pep ATP_synt_H LN
    803 CGPG1535.pep SPT2 LN
    804 CGPG1546.pep CTP_transf_1 LN
    805 CGPG1567.pep Ribosomal_L19 LN
    807 CGPG1575.pep DUF740 DS
    810 CGPG1641.pep Di19 SP
    812 CGPG1656.pep Cyt-b5::FA_desaturase CS
    813 CGPG1668.pep DUF791::MFS_1 SS
    817 CGPG1785.pep PB1::Pkinase_Tyr CK
    829 CGPG1938.pep F-box::LRR_2 CS
    835 CGPG2005.pep NADPH_Ox::Ferric_reduct::FAD_binding_8::NAD_binding_6 CS PP HS SS PEG
    838 CGPG2059.pep LNc_sug_transp SS
    842 CGPG2074.pep HMA::HMA CK
    845 CGPG2142.pep MATH::MATH DS
    850 CGPG2213.pep RNA_pol_l__A49 CK PEG
    851 CGPG2247.pep DUF23 CK
    852 CGPG228.pep p450 SP
    858 CGPG2354.pep ABC1 PP
    863 CGPG240.pep Hydrolase DS
    869 CGPG2472.pep Band_7 LN
    877 CGPG274.pep WD40::WD40::WD40 PP LL
    879 CGPG277.pep IGPD LN
    893 CGPG309.pep Cyclin_N LN
    911 CGPG337.pep Glyco_transf_8 LN
    917 CGPG347.pep DREPP LN
    931 CGPG372.pep SET LN
    941 CGPG394.pep DUF6::TPT LN
    943 CGPG397.pep SOR_SNZ::ThiG CK
    957 CGPG421.pep Pkinase::efhand::efhand::efhand::efhand LN
    958 CGPG422.pep Pkinase LN
    968 CGPG430.pep Pkinase DS
    996 CGPG468.pep Fer4::Fer4 LN
    1031 CGPG510.pep Rho_GDI SS
    1040 CGPG519.pep Abhydrolase_1 PEG
    1058 CGPG532.pep Transket_pyr::Transketolase_C LN
    1078 CGPG557.pep Chitin_bind_1::Barwin LN
    1083 CGPG561.pep XG_FTase PP
    1091 CGPG568.pep FTHFS LN
    1108 CGPG580.pep MGDG_synth::Glyco_tran_28_C LN
    1134 CGPG604.pep PSI_PsaH LN
    1144 CGPG614.pep cobW LN
    1150 CGPG620.pep tRNA-synt_1g DS
    1212 CGPG663.pep Pro_CA LN
    1232 CGPG686.pep RRM_1::zf-CCHC LN
    1258 CGPG713.pep Cyclin_N LN
    1267 CGPG72.pep Amino_oxidase LN
    1328 CGPG773.pep H_PPase PP
    1357 CGPG801.pep Cyt-b5 LN
    1406 CGPG841.pep ArfGap LN
    1452 CGPG879.pep ABC_tran::ABC2_membrane::PDR_assoc::ABC_tran::ABC2_membrane LN
    1477 CGPG908.pep PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR LN
    1515 CGPG933.pep WD40::WD40::WD40::WD40::WD40::WD40::WD40 SP
    1517 CGPG967.pep BTB::NPH3 CS

Claims (14)

What is claimed is:
1. A plant cell nucleus with stably integrated, recombinant DNA, wherein said recombinant DNA comprises a promoter that is functional in said plant cell and that is operably linked to a protein coding DNA encoding a protein having an amino acid sequence comprising the Pfam domain DUF581 and wherein said plant cell nucleus is selected by screening a population of transgenic plants that have said recombinant DNA and enhanced water use efficiency as compared to control plants that do not have said recombinant DNA in their nuclei.
2. A recombinant DNA construct wherein
a. said recombinant DNA comprises a promoter that is functional in said plant cell and that is operably linked to a protein coding DNA encoding at least one protein having an amino acid sequence comprising a Pfam domain module selected from the group consisting of AOX, UBX, DUF1635, Senescence, zf-Tim10_DDP, IQ, Skp1_POZ::Skp1, NLE::WD40::WD40::WD40::WD40, ArfGap::C2, DUF1639, PBP, PPR::PPR::PPR::PPR::PPR::PPR, zf-C3HC4::YDG_SRA, AAA, F-box::Kelch—1::Kelch—1, PetM, CPDase, Iso_dh, OTU, Sugar_tr, Pro_dh, Pkinase::NAF, HEAT::HEAT::HEAT::HEAT::HEAT::HEAT::HEAT::HEAT::HEAT::HEA T::HEAT::HEAT, Pkinase, Nuc_sug_transp, eIF2A, cobW, DUF538, WD40::WD40::WD40, DUF393, ScpA_ScpB, PCI, SRF-TF, DUF1644, DUF1645, NIF, WD40::WD40::WD40::WD40, WD40::WD40::WD40::WD40::WD40::WD40::WD40, F-box::LRR—2, tRNA-synt—1g, Glutaminase, Dehydrin, TP_methylase, Band—7, LRR—1::LRR—1::LRR—1::LRR—1, Exo_endo_phos, Ank::Ank::Ank, HLH, DUF617, Uricase::Uricase, ABC_tran::ABC2_membrane::PDR_assoc::ABC_tran::ABC2_membrane, Bystin, AWPM-19, IGPD, PAS—2::GAF::Phytochrome::HisKA::HATPase_c, 60KD_IMP, DUF6::TPT, Glyco_hydro—1, F-box::Sell::Sell::zf-MYND, Cyclin_N::Cyclin_C, MFS—1, Tetraspannin, Cyt-b5, HMA::HMA, zf-CW::MBD, IQ::IQ, PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR, eIF-1a, Pro_isomerase, DUF623, PGM_PMM_I::PGM_PMM_II::PGM_PMM_III::PGM_PMM_IV, Hydrolase, SKI, Aa_trans, Ribosomal_L19, Isoamylase_N::Alpha-amylase, zf-MYND::UCH, Spermine_synth, ABC1, LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1, MtN3_slv::MtN3_slv, TPR—2, UQ_con, NIR_SIR_ferr::NIR_SIR::NIR_SIR_ferr::NIR_SIR, Metallothio_PEC, F-box, NUDIX, HEAT::Arm:HEAT::Arm, P21-Arc, Tcp11, KT112, Acyltransferase, Glutaredoxin, TIM, FKBP_C, NTP_transferase::Hexapep::Hexapep, Transaldolase, Peptidase_M22, TFIIS, Cyclin_N, DZC, Methyltransf—12, PFK, DUF1749, DUF1677, Y_phosphatase2, B3—4::B5, MSF1, Hin1, mTERF, TMEM14, zf-PARP::zf-PARP::PADR1::BRCT::WGR::PARP_reg::PARP, DUF21::CBS, Ribosomal_S8, LysM, Ank::Ank::Ank::Pkinase, SNARE_assoc, DUF640, iPGM_N::Metalloenzyme, Cullin, Glyco_transf—8, GAF::HisKA, Ribosomal_L37, Phi—1, OstA, HD::RelA_SpoT, Pyr_redox—2, Isy1, Peptidase_C26, WRKY, LRRNT—2::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::Pkinase, DUF212, PGI, Pyr_redox—2::efhand, Aminotran—1—2, PGK, FTHFS, PBI::Pkinase_Tyr, GRP, Arf, Radical_SAM, Cystatin, Stig1, UDPGT, Sulfotransfer—1, NADPH_Ox::Ferric_reduct::FAD_binding—8::NAD_binding—6, LRRNT—2::LRR—1::LRR—1::LRR—1::LRR—1::Pkinase, Ank::Ank::Pkinase_Tyr, AMP-binding, DEAD::Helicase_C, LSM, NTP_transferase, DHDPS, Mo25, DUF581, DREPP, Mito_carr:Mito_carr:Mito_carr, ThiC, Aminotran—3, Nramp, Aminotran—4, Pkinase::efhand::efhand::efhand::efhand, MMR_HSR1, B56, Transket_pyr::Transketolase_C, malic::Malic_M, PSI_PsaH, F-box::LRR—2::FBD, BNR::BNR::BNR, ADH_N::ADH_zinc_N, HMG-CoA_red, Pkinase::efhand::efhand, Cyclin, efhand::efhand::efhand, Fer4::Fer4, PTR2, Rib—5-P_isom_A, LRRNT—2::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::Pkinase, Pyr_redox, TLD, Voltage_CLC::CBS, DJ-1_Pfp1::DJ-1_Pfp1, SIR2, GATase::GMP_synt_C, Citrate_synt, DUF300, DUF231, Molybdop_Fe4S4::Molybdopterin::Molydop_binding, LRR—1::LRR—1::LRR—1::Pkinase, NOI, DAGK_cat, DUF239, V-SNARE, ELFV_dehydrog_N::ELFV_dehydrog, MCM, LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::Pkinase, FAD_binding—4, SpoIIE, DUF740, Gp_dh_N::Gp_dh_C, FHA::PP2C, Pyr_redox—2::Pyr_redox_dim, CBS, GRAM, DUF676, GILT, AlaDh_PNT_N::AlaDh_PNT_C::Saccharop_dh_N::Saccharop_dh, Peptidase_C54, ArfGap, Metallophos, SH3—1, DUF313, DUF383::DUF384, Brix, Ras, Maf, DUF246, RNA_pol_I_A49, C2, CRAL_TRIO_N::CRAL_TRIO, DUF1350, p450, PP2C, Histone, Enolase_N::Enolase_C, GTP_EFTU::GTP_EFTU_D2::EFG_C, MSP, NTP_transferase::Hexapep::Hexapep::Hexapep::Hexapep, RRM—1::RRM—1, ETC_C1_NDUFA4, Amino_oxidase, DUF827, CCT, BCNT, ubiquitin::UBA::XPC-binding::UBA, Tryp_alpha_amyl, FBPase, ACT::ACT, IPK, Usp::Pkinase, Sina, CTP_transf—1, PPR::PPR::PPR::PPR::PPR::PPR::PPR, PfkB, Sterol_desat, Zip, ADH_zinc_N, WD40::WD40::WD40::WD40::PWP2, Globin, BTB::NPH3, Amidohydro—2, CS, PAP2, Cys_Met_Meta_PP, Gar1, DAO, NDUF_B7, RNA_poll_A14, DUF833, MATH::BTB, DUF1000, DUF1001, TFIIS_C, PLAT::Lipoxygenase, Self-incomp_S1, Thioredoxin, DUF1005, DUF791::MFS—1, DUF6::DUF6, Gal-bind_lectin::Galactosyl_T, Invertase_neut, SAC3_GANP, DUF260, Polyketide_cyc, polyprenyl_synt, DUF23, GHMP_kinases_N::GHMP_kinases_C, Complex1—30 kDa::Complex1—49 kDa, Transthyretin, TB2_DP1_HVA22, Aldose_epim, H_PPase, SIS::CBS, YjeF_N::Carb_kinase, DUF914, Mov34, UFD1, Aha1_N::AHSA1, Dirigent, Response_reg, 14-3-3; Rho_GDI, Di19, SNARE, DUF778, efhand, Chitin_bind—1::Barwin, Phosphoesterase, zf-CCHC, LRRNT—2::LRR—1::LRR—1::Pkinase, TPT, SOR_SNZ::ThiG, CN_hydrolase::NAD_synthase, PPDK_N::PEP-utilizers::PEP-utilizers_C, PRA-CH::PRA-PH, Glucokinase, adh_short, SapB—1::SapB—2::SapB—1::SapB—2, DEAD::Helicase_C::DSHCT, Fibrillarin, AA_permease, NDK, RRM—1, GATase—2::Asn_synthase, Mago-bind, DHquinase—1::Shikimate_dh_N::Shikimate_DH, OPT, Orn_Arg_deC_N::Orn_DAP_Arg_deC, DUF926, Not3::NOT2—3—5, Pro_CA, Copine, DUF783, RWD, MATH, TOM20_plant, zf-UBR, Cyt-b5::FA_desaturase, DUF788, E1_dh, Saccharop_dh, Glycolytic, Actin, AstE_AspA, ATP_synt_H, SET, Cornichon, Pyridoxal_deC, MGDG_synth::Glyco_tran—28_C, Arm::Arm, DUF860, CorA, DnaJ::DnaJ_CXXCXGXG::DnaJ_C, DUF862, Prefoldin, PEARL1-4, PGAM, Gln-synt_N::Gln-synt_C, DUF793, CPSase_L_chain::CPSase_L_D2::CPSase_L_D3::CPSase_L_chain::CPSase_L_D2::MGS, Abhydrolase—1, Lung—7-TM_R, Abhydrolase—3, Glyco_hydro—17, F-box::FBA—1, DUF506, F-box::FBA—3, efhand_like::PI-PLC-X::PI-PLC-Y::C2, 2OG-Fell_Oxy, Pribosyltran, TFIIS_M::SPOC, FA_desaturase, Nol1_Nop2_Fmu, DUF59, LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1, Cytochrom_C, TPK_catalytic::TPK_B1_binding, DnaJ, Pkinase_Tyr, MIP, Ribonuc_L-PSP, NicO, zf-LSD1::zf-LSD1::zf-LSD1, PC_rep::PC_rep::PC_rep::PC_rep::PC_rep::PC_rep, Trehalose_PPase, LRR—1, WD40::WD40::WD40::WD40::WD40::WD40::WD40::WD40::WD40::WD40::Utp13, Phytochelatin::DUF1984, RNA_pol_A_bac, LRRNT—2::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::L RR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::LRR—1::Pkinas e, Reticulon, XG_FTase, RRM—1::zf-CCHC, Pre-SET::SET, MATH::MATH, Str_synth, SPT2, Lectin_legB::Pkinase, Snf7, Aldedh, HIT, zf-C3HC4, TFIIF_alpha, Transketolase_N::Transket_pyr::Transketolase_C, WD40::WD40, ARM—1, DUF26::DUF26::Pkinase, SRF-TF::K-box, PseudoU_synth—1::PseudoU_synth—1, PI3_PI4_kinase, CAF1, Tim17, Cpn60_TCP1, Xan_ur_permease, Biotin_lipoyl::E3_binding::2-oxoacid_dh, Myb_DNA-binding, AP2, Diphthamide_syn, DUF525, PBD, and Molybdop_Fe4S4::Molybdopterin::Molydop_binding::Fer2_BFD;
b. said recombinant DNA comprises a promoter that is functional in said plant cell and that is operably linked to a protein coding DNA encoding a protein comprising an amino acid sequence with at least 90% identity to a consensus amino acid sequence selected from the group consisting of SEQ ID NO: 67782 through 67894;
c. said recombinant DNA comprises a promoter that is functional in plant cells and that is operably linked to a protein coding DNA encoding a protein comprising an amino acid sequence selected from the group consisting of 918, 932, 1208, 1305, 1375, 1407, and homologs thereof listed in table 16;
d. said recombinant DNA comprises a promoter that is functional in said plant cell and that is operably linked to a protein coding recombinant DNA encoding a protein having an amino acid sequence having at least 70% identity to an amino acid sequence selected from the group consisting of 762, 846 and 1055;
e. said recombinant DNA suppresses comprises a promoter that is functional in said plant cell and operably linked to DNA that transcribe into RNA that suppresses the level of at least one endogenous protein wherein said endogenous protein has an amino acid sequence comprising a pfam domain module selected from the group consisting of RRM—1, Peptidase_C54, AP2, DUF788, RRM—1, NUDIX, adh_short, PTR2, Gar1, Response_reg, DUF86, Glycolytic, Metallophos, ATP_synt_H, SPT2, CTP_transf—1, Ribosomal_L19, DUF740, Di19, Cyt-b5::FA_desaturase, DUF791::MFS—1, PB1::Pkinase_Tyr, F-box::LRR—2, NADPH_Ox::Ferric_reduct::FAD_binding—8::NAD_binding—6, Nuc_sug_transp, HMA::HMA, MATH::MATH, RNA_pol_I_A49, DUF23, p450, ABC1, Hydrolase, Band—7, WD40::WD40::WD40, IGPD, Cyclin_N, Glyco_transf—8, DREPP, SET, DUF6::TPT, SOR_SNZ::ThiG, Pkinase::efhand::efhand::efhand::efhand, Pkinase, Fer4::Fer4, Rho_GDI, bhydrolase—1, Transket_pyr:Transketolase_C, Chitin_bind—1::Barwin, XG_FTase, FTHFS, MGDG_synth::Glyco_tran—28_C, PSI_PsaH, cobW, tRNA-synt—1g, Pro_CA, RRM—1::zf-CCHC, Cyclin_N, Amino_oxidase, H_PPase, Cyt-b5, ArfGap, ABC_tran::ABC2_membrane::PDR_assoc::ABC_tran::ABC2_membrane, PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR, WD40::WD40::WD40::WD40::WD40::WD40::WD40, BTB::NPH3RRM—1, Peptidase_C54, AP2, DUF788, RRM—1, NUDIX, adh_short, PTR2, Gar1, Response_reg, DUF86, Glycolytic, Metallophos, ATP_synt_H, SPT2, CTP_transf—1, Ribosomal_L19, DUF740, Di19, Cyt-b5::FA_desaturase, DUF791::MFS—1, PB1::Pkinase_Tyr, F-box::LRR—2, NADPH_Ox::Ferric_reduct::FAD_binding—8::NAD_binding—6, Nuc_sug_transp, HMA::HMA, MATH::MATH, RNA_pol_I_A49, DUF23, p450, ABC1, Hydrolase, Band—7, WD40::WD40::WD40, IGPD, Cyclin_N, Glyco_transf—8, DREPP, SET, DUF6::TPT, SOR_SNZ::ThiG, Pkinase::efhand::efliand::efhand::efhand, Pkinase, Fer4::Fer4, Rho_GDI, bhydrolase—1, Transket_pyr:Transketolase_C, Chitin_bind—1::Barwin, XG_FTase, FTHFS, MGDG_synth::Glyco_tran—28_C, PSI_PsaH, cobW, tRNA-synt—1g, Pro_CA, RRM—1::zf-CCHC, Cyclin_N, Amino_oxidase, H_PPase, Cyt-b5, ArfGap, ABC_tran::ABC2_membrane::PDR_assoc::ABC_tran::ABC2_membrane, PPR::PPR::PPR::PPR::PPR::PPR::PPR::PPR, WD40::WD40::WD40::WD40::WD40::WD40::WD40, and BTB::NPH3;
f. said recombinant DNA comprises a promoter that is functional in said plant cell and operably linked to DNA that transcribe into RNA that suppresses the level of an endogenous protein wherein said endogenous protein has an amino acid sequence with at least 70% identity to an amino acid sequence selected from the group consisting of SEQ ID NO: 767, 768, 772, 792, 809, 814, 821, 822, 836, 840, 848, 866, and homologs thereof listed in table 16;
and wherein said recombinant DNA construct is stably integrated into a chromosome in a plant cell nucleus which is selected by screening a population of transgenic plants that have said recombinant DNA and an enhanced trait as compared to control plants that do not have said recombinant DNA in their nuclei; and wherein said enhanced trait is selected from group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced high salinity tolerance, enhanced shade tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil.
3. The plant cell nucleus comprising a recombinant DNA construct of claim 2 wherein said protein coding DNA encodes a protein having an amino acid sequence selected from the group consisting of SEQ ID NO: 760 through SEQ ID NO: 67778.
4. The plant cell nucleus comprising a recombinant DNA construct of claim 2 further comprising DNA expressing a protein that provides tolerance from exposure to an herbicide applied at levels that are lethal to a wild type of said plant cell.
5. The plant cell nucleus of claim 4 wherein the agent of said herbicide is a glyphosate, dicamba, or glufosinate compound.
6. A transgenic plant cell or plant comprising a plurality of plant cells with the plant cell nucleus of claim 2.
7. The transgenic plant cell or plant of claim 6 which is homozygous for said recombinant DNA.
8. A transgenic seed comprising a plurality of plant cells with a plant cell nucleus comprising a recombinant DNA construct of claim 2.
9. The transgenic seed of claim 8 from a corn, soybean, cotton, canola, alfalfa, wheat or rice plant.
10. A transgenic pollen grain comprising a haploid derivative of a plant cell nucleus comprising a recombinant DNA construct of claim 2.
11. A method for manufacturing non-natural, transgenic seed that can be used to produce a crop of transgenic plants with an enhanced trait resulting from expression of recombinant DNA in a nucleus comprising a recombinant DNA construct of claim 2, wherein said method for manufacturing said transgenic seed comprising:
(a) screening a population of plants for said enhanced trait and said recombinant DNA, wherein individual plants in said population can exhibit said trait at a level less than, essentially the same as or greater than the level that said trait is exhibited in control plants which do not contain the recombinant DNA, wherein said enhanced trait is selected from the group of enhanced traits consisting of enhanced water use efficiency, enhanced cold tolerance, enhanced heat tolerance, enhanced high salinity tolerance, enhanced shade tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil,
(b) selecting from said population one or more plants that exhibit said trait at a level greater than the level that said trait is exhibited in control plants, and
(c) collecting seeds from selected plant selected from step b.
12. The method of claim 11 wherein said method for manufacturing said transgenic seed further comprising
(a) verifying that said recombinant DNA is stably integrated in said selected plants, and
(b) analyzing tissue of said selected plant to determine the expression or suppression of a protein having the function of a protein having an amino acid sequence selected from the group consisting of one of SEQ ID NO:760-1518.
13. The method of claim 11 wherein said seed is corn, soybean, cotton, alfalfa, canola wheat or rice seed.
14. A method of producing hybrid corn seed comprising:
(a) acquiring hybrid corn seed from a herbicide tolerant corn plant which also has stably-integrated, recombinant DNA construct of claim 2;
(b) producing corn plants from said hybrid corn seed, wherein a fraction of the plants produced from said hybrid corn seed is homozygous for said recombinant DNA, a fraction of the plants produced from said hybrid corn seed is hemizygous for said recombinant DNA, and a fraction of the plants produced from said hybrid corn seed has none of said recombinant DNA;
(c) selecting corn plants which are homozygous and hemizygous for said recombinant DNA by treating with an herbicide;
(d) collecting seed from herbicide-treated-surviving corn plants and planting said seed to produce further progeny corn plants;
(e) repeating steps (c) and (d) at least once to produce an inbred corn line; and
(f) crossing said inbred corn line with a second corn line to produce hybrid seed.
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