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Genome-wide scans for delineation of candidate genes regulating seed-protein content in chickpea

By Hari Deo eUpadhyaya, Deepak eBajaj, Laxmi eNaroliya, Shouvik eDas, Vinod eKumar, CLL Laxmipathi Gowda, Shivali eSharma, Akhilesh eTyagi and SWARUP KUMAR PARIDA


Identification of potential genes/alleles governing complex seed-protein content (SPC) trait 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 to 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 x ICC 4958) by selective genotyping. The seed-specific expression, including differential up-regulation (> 4-fold) of six SPC-associated genes particularly in accessions, parents and homozygous individuals of the aforementioned mapping population with high level of contrasting seed-protein content (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 seed-protein content

Topics: GWAS, SNP, QTL, GBS, chickpea, seed protein content, Plant culture, SB1-1110
Publisher: Frontiers Media S.A.
Year: 2016
DOI identifier: 10.3389/fpls.2016.00302
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