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Genome-wide discovery of DNA polymorphisms among chickpea cultivars with contrasting seed size/weight and their functional relevance

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Title Genome-wide discovery of DNA polymorphisms among chickpea cultivars with contrasting seed size/weight and their functional relevance
 
Creator Rajkumar, Mohan Singh
Garg, Rohini
Jain, Mukesh
 
Subject DNA polymorphisms
chickpea cultivars
Genome-wide discovery
 
Description Accepted date: 31 October 2018
Seed size/weight is a major agronomic trait which determine crop productivity in legumes. To understand the genetic basis of seed size determination, we sought to identify DNA polymorphisms between two small (Himchana 1 and Pusa 362) and two large-seeded (JGK 3 and PG 0515) chickpea cultivars via whole genome resequencing. We identified a total of 75535 single nucleotide polymorphisms (SNPs), 6486 insertions and deletions (InDels), 1938 multi-nucleotide polymorphisms (MNPs) and 5025 complex variants between the two small and two large-seeded chickpea cultivars. Our analysis revealed 814, 244 and 72 seed-specific genes harboring DNA polymorphisms in promoter or non-synonymous and large-effect DNA polymorphisms, respectively. Gene ontology analysis revealed enrichment of cell growth and division related terms in these genes. Among them, at least 22 genes associated with quantitative trait loci, and those involved in cell growth and division and encoding transcription factors harbored promoter and/or large-effect/non-synonymous DNA polymorphisms. These also showed higher expression at late-embryogenesis and/or mid-maturation stages of seed development in the large-seeded cultivar, suggesting their role in seed size/weight determination in chickpea. Altogether, this study provided a valuable resource for large-scale genotyping applications and a few putative candidate genes that might play crucial role in governing seed size/weight in chickpea.
Tis work was fnancially supported by the Department of Biotechnology, Government of India, New Delhi, (BT/
AB/NIPGR/SEED BIOLOGY/2012). Te fnancial assistance provided by the Jawaharlal Nehru University for
publication charges is gratefully acknowledged. RG acknowledges INSPIRE Faculty Award from the Department
of Science & Technology, Government of India. Research fellowship from the Department of Biotechnology,
Government of India under Centre of Excellence in Bioinformatics to the School of Computational & Integrative
Sciences, Jawaharlal Nehru University, New Delhi, is gratefully acknowledged. We are thankful to A. Pole for help
in initial data analysis.
 
Date 2018-11-20T07:17:20Z
2018-11-20T07:17:20Z
2018
 
Type Article
 
Identifier Scientific Reports 8(1): 16795
2045-2322
http://223.31.159.10:8080/jspui/handle/123456789/899
https://www.nature.com/articles/s41598-018-35140-w
https://doi.org/10.1038/s41598-018-35140-w
 
Language en_US
 
Format application/pdf
 
Publisher Springer Nature