%0 Journal Article
%@ 2045-2322
%A Upadhyaya, H D
%A Bajaj, D
%A Das, S
%A Kumar, V
%A Gowda, C L L
%A Sharma, S
%A Tyagi, A K
%A Parida, S K
%D 2016
%F icrisat:9436
%I Nature Publishing Group
%J Scientific Reports
%K Genetic markers, Genome-wide association studies, Genetics, QTL mapping, Chickpea
%N 24050
%P 01-12
%T Genetic dissection of seed-iron and zinc concentrations in chickpea
%U http://oar.icrisat.org/9436/
%V 06
%X The SNP-based high-resolution QTL mapping mapped eight major genomic regions harbouring robust QTLs governing seed-Fe and Zn concentrations (39.4% combined phenotypic variation explained/PVE) on six chromosomes of an intra-specific high-density genetic linkage map (1.56 cM map-density). 24620 SNPs discovered from genome-wide GBS (genotyping-by-sequencing) and 13 known cloned Fe and Zn contents-related chickpea gene-orthologs were genotyped in a structured population of 92 sequenced desi and kabuli accessions. The large-scale 16591 SNP genotyping- and phenotyping-based GWAS (genome-wide association study) identified 16 genomic loci/genes associated (29% combined PVE) with seed-Fe and Zn concentrations. Of these, 11 trait-associated SNPs in the genes linked tightly with eight QTLs were validated by QTL mapping. The seed-specific expression, including pronounced differential-regulation of 16 trait-associated genes particularly in accessions/mapping individuals with contrasting level of seed-Fe and Zn contents was apparent. Collectively, the aforementioned rapid integrated genomic strategy led to delineate novel functional non-synonymous and regulatory SNP allelic-variants from 16 known/candidate genes, including three strong trait-associated genes (encoding late embryogenesis abundant and yellow stripe-like 1 protein, and vacuolar protein sorting-associated protein) and eight major QTLs regulating seed-Fe and Zn concentrations in chickpea. These essential inputs thus have potential to be deployed in marker-assisted genetic enhancement for developing nutritionally-rich iron/zinc-biofortified chickpea cultivars.
%Z The authors gratefully acknowledge the financial support for this study provided by a research grant from the  Department of Biotechnology (DBT), Government of India (102/IFD/SAN/2161/2013-14). Shouvik Das  acknowledges the DBT for Senior Research Fellowship award