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Transcriptome wide identification and characterization of regulatory genes involved in EAA metabolism and validation through expression analysis in different developmental stages of finger millet spikes

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Abstract

Finger millet is a rich source of seed storage proteins (SSPs). Various regulatory genes play an important role to maintain the quality and accumulation of SSPs in crop seeds. In the present study, nine regulatory genes of EAAs metabolic pathway, i.e., aspartate kinase, homoserine dehydrogenase, threonine synthase, threonine dehydratase, dihydrodipicolinate synthase, cystathionine γ synthase, anthranilate synthase, acetolactate synthase and lysine 2-oxoglutarato reductase/saccharopine dehydrogenase (LOR/SD) were identified from the transcriptomic data of developing spikes of two finger millet genotypes, i.e., GP-45 and GP-1. Results of sequence alignment search and motif/domain analysis showed high similarity of nucleotide sequences of identified regulatory genes with their respective homologs in rice. Results of promoter analysis revealed the presence of various cis-regulatory elements, like nitrogen responsive cis-elements (O2-site and GCN4), light responsive cis-elements, and stress responsive cis-elements. The presence of nine regulatory genes identified from the transcriptomic data of GP-45 and GP-1 was further confirmed by real time expression analysis in high and low protein containing genotypes, i.e., GE-3885 and GE-1437. Results of real time expression analysis showed significantly higher expression (p ≤ 0.01) of regulatory genes in GE-3885 rather than GE-1437 under control and treatment condition. Crude protein content of GE-3885 was found to be significantly higher (p ≤ 0.01) in comparison to GE-1437 under control condition, while under treatment condition GE-1437 was found to be more responsive to KNO3 treatment rather than GE-3885.

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Abbreviations

EAAs:

Essential amino acids

SSPs:

Seed storage proteins

TFs:

Transcription factors

AK:

Aspartate kinase

HD:

Homoserine dehydrogenase

TS:

Threonine synthase

TD:

Threonine dehydratase

DHDPS:

Dihydrodipicolinate synthase

CS:

Cystathione γ synthase

AS:

Anthranilate synthase

ALS:

Acetolactate synthase

LOR/SD:

Lysine 2-oxoglutarato reductase/saccharopine dehydrogenase

CM:

Chorismate mutase

FPKM:

Fragments per kilobase of exon per million fragments mapped

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Acknowledgements

The authors wish to acknowledge University Grant Commission, Govt. of India, New Delhi for providing fellowship. Author is also thankful to the SUB-DIC Bioinformatics GBPUA&T, Pantnagar for providing valuable support.

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  1. Kavita Gururani and Anil Kumar equal contribution.

Authors and Affiliations

  1. Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, U.S. Nagar, Pantnagar, 263145, Uttarakhand, India

    Kavita Gururani, Apoorv Tiwari, Aparna Agarwal, Supriya Gupta & Dinesh Pandey

  2. Rani Laxmi Bai Central Agriculture University, Jhansi, Uttar Pradesh, 284003, India

    Anil Kumar

  3. Department of Computational Biology and Bioinformatics, Jacob Institute of Biotechnology and Bio-Engineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, 211007, Uttar Pradesh, India

    Apoorv Tiwari

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Contributions

AK, DP, and KG conceptualized the manuscript. KG, AT, and AA conducted the experiments. KG and AA wrote the manuscript. AK, DP, and SG assisted and edited the manuscript. KG and AT has statistically analyzed the data. AK and DP contributed in critically revising the draft and updating the manuscript for publication.

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Correspondence to Anil Kumar or Dinesh Pandey.

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Gururani, K., Kumar, A., Tiwari, A. et al. Transcriptome wide identification and characterization of regulatory genes involved in EAA metabolism and validation through expression analysis in different developmental stages of finger millet spikes. 3 Biotech 10, 347 (2020). https://doi.org/10.1007/s13205-020-02337-8

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