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SG11201811021YA - Method to screen for a mutant within a population of organisms by applying a pooling and splitting approach - Google Patents

Method to screen for a mutant within a population of organisms by applying a pooling and splitting approach

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Publication number
SG11201811021YA
SG11201811021YA SG11201811021YA SG11201811021YA SG11201811021YA SG 11201811021Y A SG11201811021Y A SG 11201811021YA SG 11201811021Y A SG11201811021Y A SG 11201811021YA SG 11201811021Y A SG11201811021Y A SG 11201811021YA SG 11201811021Y A SG11201811021Y A SG 11201811021YA
Authority
SG
Singapore
Prior art keywords
organisms
international
copenhagen
mutant
vej
Prior art date
Application number
SG11201811021YA
Inventor
Toni Wendt
Ole Olsen
Søren Knudsen
Hanne Thomsen
Alexander Striebeck
Birgitte Skadhauge
Magnus Wohlfahrt Rasmussen
Massimiliano Carciofi
Original Assignee
Carlsberg As
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
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Application filed by Carlsberg As filed Critical Carlsberg As
Publication of SG11201811021YA publication Critical patent/SG11201811021YA/en

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    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/6895Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for plants, fungi or algae
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    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844Nucleic acid amplification reactions
    • C12Q1/686Polymerase chain reaction [PCR]
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    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/01Preparation of mutants without inserting foreign genetic material therein; Screening processes therefor
    • AHUMAN NECESSITIES
    • A01AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01HNEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
    • A01H4/00Plant reproduction by tissue culture techniques ; Tissue culture techniques therefor
    • A01H4/005Methods for micropropagation; Vegetative plant propagation using cell or tissue culture techniques
    • AHUMAN NECESSITIES
    • A01AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01HNEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
    • A01H6/00Angiosperms, i.e. flowering plants, characterised by their botanic taxonomy
    • A01H6/46Gramineae or Poaceae, e.g. ryegrass, rice, wheat or maize
    • A01H6/4624Hordeum vulgarus [barley]
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    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/10Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/102Mutagenizing nucleic acids
    • C12N15/1024In vivo mutagenesis using high mutation rate "mutator" host strains by inserting genetic material, e.g. encoding an error prone polymerase, disrupting a gene for mismatch repair
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    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6806Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
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    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813Hybridisation assays
    • C12Q1/6827Hybridisation assays for detection of mutation or polymorphism
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    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844Nucleic acid amplification reactions
    • C12Q1/6858Allele-specific amplification
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    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
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    • C12Q2600/00Oligonucleotides characterized by their use
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    • C12Q2600/00Oligonucleotides characterized by their use
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    • C40COMBINATORIAL TECHNOLOGY
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    • C40B30/00Methods of screening libraries
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    • C40COMBINATORIAL TECHNOLOGY
    • C40BCOMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B40/00Libraries per se, e.g. arrays, mixtures
    • C40B40/02Libraries contained in or displayed by microorganisms, e.g. bacteria or animal cells; Libraries contained in or displayed by vectors, e.g. plasmids; Libraries containing only microorganisms or vectors

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Genetics & Genomics (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biochemistry (AREA)
  • Molecular Biology (AREA)
  • Microbiology (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • Biomedical Technology (AREA)
  • Analytical Chemistry (AREA)
  • Immunology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Plant Pathology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Developmental Biology & Embryology (AREA)
  • Botany (AREA)
  • Environmental Sciences (AREA)
  • Physiology (AREA)
  • Natural Medicines & Medicinal Plants (AREA)
  • Cell Biology (AREA)
  • General Chemical & Material Sciences (AREA)
  • Medicinal Chemistry (AREA)
  • Mycology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Breeding Of Plants And Reproduction By Means Of Culturing (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)

Abstract

12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date 04 January 2018 (04.01.2018) W I PO I PCT IiiimmoimiolollmonoloolosolimmommovoimIE (10) International Publication Number WO 2018/001884 Al (51) International Patent Classification: C12N 15/01 (2006.01) Cl 2N 15/85 (2006.01) C12N 15/10 (2006.01) (21) International Application Number: PCT/EP2017/065516 (22) International Filing Date: 23 June 2017 (23.06.2017) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: PA 2016 70485 01 July 2016 (01.07.2016) DK (71) Applicant: CARLSBERG A/S [DK/DK]; Ny Carlsberg Vej 100, 1799 Copenhagen (DK). (72) Inventors: WENDT, Toni; Sankt Nikolaj Vej 30 st. tv., 1953 Frederiksberg (DK). OLSEN, Ole; Holmblads- gade 102, 2.tv., 2300 Copenhagen S (DK). KNUDSEN, Soren; Bakkesvinget 18, 2760 Malov (DK). THOMSEN, Hanne, Cecilie; Bodil Ipsens Vej 23, 2500 Valby (DK). STRIEBECK, Alexander; Sankt Nikolaj Vej 22, 3th, 1953 Frederiksberg C (DK). SKADHAUGE, Birgitte; Linde- hojvej 31B, 3460 Birkerod (DK). RASMUSSEN, Mag- nus Wohlfahrt; Eskildsgade 66, 3.th, 1657 Copenhagen V (DK). CARCIOFI, Massimiliano; Venedigvej 7, 02 tv., 2300 Copenhagen (DK). (74) Agent: HOIBERG P/S; Adelgade 12, 1304 Copenhagen K (DK). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG). (54) Title: METHOD TO SCREEN FOR A MUTANT WITHIN A POPULATION OF ORGANISMS BY APPLYING A POOLING AND SPLITTING APPROACH (57) : In traditional plant breeding approaches, chemical mutagen- esis may be utilized to introduce nucleotide substitutions at random in the genome of a plant, i.e. without possibilities to control the sites of nucleotide changes. Because of genome complexities, the statistical probability is ex- tremely little when it comes to fmding a predetermined nucleotide substitu- tion. The present invention, however, demonstrates how a novel, alternative use of digital polymerase chain reaction (dPCR), preferably droplet dPCR (ddPCR), is developed to exploit finding of specific nucleotide substitutions in mutated genes. The entire platform comprises a screening method with a library of mutagenized organisms, digital PCR -based systems and a set-up to propagate and analyze identified, mutated organisms. Organism library pool Fraction of organism library pool Secondary sub-pools of = organisms of library pool Sub pool total [D] i t M 1 2 / 3 I 4 Secondary sub-samples —.. from secondary sub-pools of organisms W O 20 18/00 188 4 Al Reproductio 000 0000 ( Mutant organism FIG. 1C Aliquots of secondary sub-samples gDNA analysis (Example of mutant signal in well) 9 [Continued on next page] WO 2018/001884 Al 1111111111111101110111111111111111111111011111111111110111111111111M11E110111111 Declarations under Rule 4.17: — of inventorship (Rule 4.17(iv)) Published: with international search report (Art. 21(3)) with sequence listing part of description (Rule 5.2(a))
SG11201811021YA 2016-07-01 2017-06-23 Method to screen for a mutant within a population of organisms by applying a pooling and splitting approach SG11201811021YA (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
DKPA201670485 2016-07-01
PCT/EP2017/065516 WO2018001884A1 (en) 2016-07-01 2017-06-23 Method to screen for a mutant within a population of organisms by applying a pooling and splitting approach

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US (2) US11884972B2 (en)
EP (3) EP3693458A1 (en)
JP (2) JP7208797B2 (en)
CN (2) CN114959098A (en)
AR (1) AR110103A1 (en)
AU (3) AU2017288960B2 (en)
BR (1) BR112018076429A2 (en)
CA (1) CA3026016A1 (en)
CL (1) CL2018003710A1 (en)
CO (1) CO2019000828A2 (en)
CR (1) CR20190040A (en)
CU (1) CU20180158A7 (en)
DK (1) DK3478832T3 (en)
EA (1) EA201892809A1 (en)
ES (1) ES2916221T3 (en)
IL (1) IL263451B (en)
MA (3) MA45531A (en)
MX (2) MX2018016110A (en)
PE (1) PE20190228A1 (en)
PL (1) PL3478832T3 (en)
PT (1) PT3478832T (en)
SG (1) SG11201811021YA (en)
UY (1) UY37312A (en)
WO (1) WO2018001884A1 (en)
ZA (3) ZA201808218B (en)

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CA3085987A1 (en) 2017-12-28 2019-07-04 Carlsberg A/S Cereal plants with improved cell wall properties
CN108913698B (en) * 2018-07-25 2021-10-26 安徽农业大学 CAPS marker related to wheat ear germination resistance/sensibility and application thereof
CN110724741B (en) * 2019-07-24 2020-05-19 艾普拜生物科技(苏州)有限公司 Primer, probe and kit for detecting minimal residual leukemia related fusion gene
EP3785529A1 (en) 2019-08-28 2021-03-03 Carlsberg A/S Barley plants with altered protein content in grains
EP4040946A1 (en) 2019-10-10 2022-08-17 Carlsberg A/S Methods for preparing mutant plants
JP2023516327A (en) 2020-03-02 2023-04-19 カールスバーグ アグシャセルスガーブ Barley plants with high marginal dextrinase activity
EP4029935A1 (en) 2021-01-14 2022-07-20 Carlsberg A/S S. eubayanus strain and hybrids thereof
EP4423297A1 (en) * 2021-10-25 2024-09-04 GT Molecular, Inc. Off-target blocking sequences to improve target discrimination by polymerase chain reaction
WO2023118136A1 (en) 2021-12-22 2023-06-29 BASF Agricultural Solutions Seed US LLC Improved screening method for genome edited events
WO2023170272A1 (en) 2022-03-11 2023-09-14 Carlsberg A/S Modulation of protein levels
WO2024105148A1 (en) 2022-11-16 2024-05-23 University Of Copenhagen Plants with low seed glucosinolate content
WO2024133900A1 (en) 2022-12-22 2024-06-27 University Of Copenhagen Improved (-)-sparteine production
CN117965576B (en) * 2024-02-01 2024-08-27 北京林业大学 King lily glycoside biosynthesis gene LlHCT1 and application thereof

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EP3693458A1 (en) 2020-08-12
MA45531A (en) 2019-05-08
CL2018003710A1 (en) 2019-03-22
CN114959098A (en) 2022-08-30
CU20180158A7 (en) 2019-08-06
ZA201907774B (en) 2022-07-27
AU2019268102A1 (en) 2019-12-12
CN109477087B (en) 2022-06-24
UY37312A (en) 2018-02-28
PT3478832T (en) 2022-05-19
AR110103A1 (en) 2019-02-27
JP7208797B2 (en) 2023-01-19
US20240182961A1 (en) 2024-06-06
CO2019000828A2 (en) 2019-04-30
ZA201808218B (en) 2020-02-26
CA3026016A1 (en) 2018-01-04
AU2017288960B2 (en) 2019-12-12
ZA201907775B (en) 2022-09-28
EP3478832A1 (en) 2019-05-08
AU2019268103B2 (en) 2020-03-12
CR20190040A (en) 2019-05-09
ES2916221T3 (en) 2022-06-29
AU2019268102B2 (en) 2020-03-05
EP3478832B1 (en) 2022-02-23
BR112018076429A2 (en) 2019-10-01
US20190194723A1 (en) 2019-06-27
AU2017288960A1 (en) 2019-01-17
MX2018016110A (en) 2019-05-30
DK3478832T3 (en) 2022-05-30
PL3478832T3 (en) 2022-06-06
JP2022101703A (en) 2022-07-06
AU2019268103A1 (en) 2019-12-12
PE20190228A1 (en) 2019-02-13
JP2019524083A (en) 2019-09-05
CN109477087A (en) 2019-03-15
MA52594A (en) 2021-03-17
IL263451A (en) 2019-01-31
EP3792357A1 (en) 2021-03-17
US11884972B2 (en) 2024-01-30
WO2018001884A1 (en) 2018-01-04
JP7539428B2 (en) 2024-08-23
IL263451B (en) 2022-08-01
MX2022014965A (en) 2023-01-11
MA54568A (en) 2021-10-27
EA201892809A1 (en) 2019-06-28

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