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Identification of SNPs in crucial starch biosynthesis genes in rice

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Abstract

Rice is the foremost crop catering to the major calorific requirement of the human population but has the disadvantage of having high glycaemic index (GI). The fine quality rice varieties, BPT and RNR have been recently identified as having low GI in nature and are grown mostly in southern parts of India. Starch (80%) is the major component of rice endosperm attributing to GI. The study aimed to unravel the molecular basis of low GI through targeted pooled amplicon sequencing of major starch biosynthetic genes. A total of 13 candidate genes involved in starch synthesis were amplified and pooled in equimolar proportion for sequencing. Single-nucleotide polymorphisms (SNPs) and insertions/deletions (Indels) were detected in both coding and noncoding regions. Among the genes that are under study, the highest number of variations were identified in starch synthase I (SSI) followed by starch synthase IIIA (SSIIIA) genes. Nonsynonymous SNPs with high probability of effecting gene function were validated by Sanger sequencing and molecular docking. Identified causative SNPs were mapped on 3000 rice genome database and their allele frequencies were obtained. The outcome of this study has a potential to be applied in breeding programmes to obtain low GI rice varieties with added beneficial traits.

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Acknowledgements

Authors would like to thank Dr Krishnan V., Chief Scientist, Research and Technology Innovation, ITC-LSTC, ITC Limited and Mr Chitranjan Dar (former), Mr Sanjiv Rangrass (present), member of CMC and Head of Quality Assurance, LSTC, CPO and EHS, ITC Limited for their encouragement and support. Authors also thank Dr Mahavishnan K. and Bhanuprakash H. R. for the help in procurement of certified seeds for each of the rice varieties from PJTSAU and field experiments.

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Author notes

  1. BNV is responsible for designing, conducting laboratory experiments and drafted the manuscript. AP and VK performed bioinformatics work including molecular docking and population genetics. HV executed SNP validation in Indian rice varieties. AM and CU were responsible for confocal and bright field microscopic studies, respectively. TVR played active role in conceptualization of the study. TV and HV edited the manuscript. GVS guided, supervised the project and provided critical suggestions on manuscript preparation.

Authors and Affiliations

  1. ITC Limited, ITC Life Sciences and Technology Centre, Peenya Industrial Area, 1st Phase, Bengaluru, 560 058, India

    B. N. V. PRIYA, I. ARUN PANDIYAN, M. AMARNATH, U. CHIDANAND, V. HEMANTH & G. V. S. SAIPRASAD

  2. ITC-ABD R&D Division, Rajahmundry, 53 3107, India

    T. V. REDDY

  3. Karolinska Institute, 17177, Stockholm, Sweden

    K. VINAY

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  1. B. N. V. PRIYA
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  2. I. ARUN PANDIYAN
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  3. T. V. REDDY
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  4. K. VINAY
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  5. M. AMARNATH
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  7. V. HEMANTH
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  8. G. V. S. SAIPRASAD
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Correspondence to B. N. V. PRIYA.

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Corresponding editor: Manoj Prasad

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PRIYA, B.N.V., ARUN PANDIYAN, I., REDDY, T.V. et al. Identification of SNPs in crucial starch biosynthesis genes in rice. J Genet 100, 8 (2021). https://doi.org/10.1007/s12041-020-01251-5

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  • DOI: https://doi.org/10.1007/s12041-020-01251-5

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