Genome-Wide Scans for Delineation of Candidate Genes Regulating Seed-Protein Content in Chickpea

Upadhyaya, H D and Bajaj, D and Narnoliya, L and Das, S and Kumar, V and Gowda, C L L and Sharma, S and Tyagi, A K and Parida, S K (2016) Genome-Wide Scans for Delineation of Candidate Genes Regulating Seed-Protein Content in Chickpea. Frontiers in Plant Science, 07 (302). 01-13. ISSN 1664-462X

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Identification of potential genes/alleles governing complex seed-protein content (SPC) is essential in marker-assisted breeding for quality trait improvement of chickpea. Henceforth, the present study utilized an integrated genomics-assisted breeding strategy encompassing trait association analysis, selective genotyping in traditional bi-parental mapping population and differential expression profiling for the first-time to understand the complex genetic architecture of quantitative SPC trait in chickpea. For GWAS (genome-wide association study), high-throughput genotyping information of 16376 genome-based SNPs (single nucleotide polymorphism) discovered from a structured population of 336 sequenced desi and kabuli accessions [with 150–200 kb LD (linkage disequilibrium) decay] was utilized. This led to identification of seven most effective genomic loci (genes) associated [10–20% with 41% combined PVE (phenotypic variation explained)] with SPC trait in chickpea. Regardless of the diverse desi and kabuli genetic backgrounds, a comparable level of association potential of the identified seven genomic loci with SPC trait was observed. Five SPC-associated genes were validated successfully in parental accessions and homozygous individuals of an intra-specific desi RIL (recombinant inbred line) mapping population (ICC 12299 × ICC 4958) by selective genotyping. The seed-specific expression, including differential up-regulation (>four fold) of six SPC-associated genes particularly in accessions, parents and homozygous individuals of the aforementioned mapping population with a high level of contrasting SPC (21–22%) was evident. Collectively, the integrated genomic approach delineated diverse naturally occurring novel functional SNP allelic variants in six potential candidate genes regulating SPC trait in chickpea. Of these, a non-synonymous SNP allele-carrying zinc finger transcription factor gene exhibiting strong association with SPC trait was found to be the most promising in chickpea. The informative functionally relevant molecular tags scaled-down essentially have potential to accelerate marker-assisted genetic improvement by developing nutritionally rich chickpea cultivars with enhanced SPC.

Item Type: Article
Divisions: RP-Grain Legumes
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Chickpea, GBS, GWAS, QTL, SNP, Seed-Protein Content
Subjects: Mandate crops > Chickpea
Others > Genetics and Genomics
Depositing User: Mr Ramesh K
Date Deposited: 01 Apr 2016 09:16
Last Modified: 05 Jan 2017 17:32
Official URL:
Acknowledgement: The authors gratefully acknowledge the financial support by the core grant of National Institute of Plant Genome Research (NIPGR), New Delhi, India. SD and LN acknowledge the UGC (University Grants Commission) and DBT (Department of Biotechnology) for Junior/Senior Research Fellowship awards.
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