title: Genome-Wide Scans for Delineation of Candidate Genes Regulating Seed-Protein Content in Chickpea.
abstract: 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.
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics Patancheru, India.
authors.forename: Hari D
authors.initials: HD
authors.lastname: Upadhyaya
authors.affiliation: National Institute of Plant Genome Research New Delhi, India.
authors.forename: Deepak
authors.initials: D
authors.lastname: Bajaj
authors.affiliation: National Institute of Plant Genome Research New Delhi, India.
authors.forename: Laxmi
authors.initials: L
authors.lastname: Narnoliya
authors.affiliation: National Institute of Plant Genome Research New Delhi, India.
authors.forename: Shouvik
authors.initials: S
authors.lastname: Das
authors.affiliation: National Research Centre on Plant Biotechnology New Delhi, India.
authors.forename: Vinod
authors.initials: V
authors.lastname: Kumar
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics Patancheru, India.
authors.forename: C L L
authors.initials: CL
authors.lastname: Gowda
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics Patancheru, India.
authors.forename: Shivali
authors.initials: S
authors.lastname: Sharma
authors.affiliation: National Institute of Plant Genome Research New Delhi, India.
authors.forename: Akhilesh K
authors.initials: AK
authors.lastname: Tyagi
authors.affiliation: National Institute of Plant Genome Research New Delhi, India.
authors.forename: Swarup K
authors.initials: SK
authors.lastname: Parida
keywords: GBS; GWAS; QTL; SNP; chickpea; seed-protein content