Genetic dissection of seed-iron and zinc concentrations in chickpea

Upadhyaya, H D and Bajaj, D and Das, S and Kumar, V and Gowda, C L L and Sharma, S and Tyagi, A K and Parida, S K (2016) Genetic dissection of seed-iron and zinc concentrations in chickpea. Scientific Reports, 06 (24050). 01-12. ISSN 2045-2322

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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.

Item Type: Article
Divisions: RP-Grain Legumes
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Genetic markers, Genome-wide association studies, Genetics, QTL mapping, Chickpea
Subjects: Mandate crops > Chickpea
Others > Food Legumes
Others > Genetics and Genomics
Depositing User: Mr Ramesh K
Date Deposited: 18 Apr 2016 08:24
Last Modified: 21 Oct 2016 09:35
Official URL:
Funders: Department of Biotechnology (DBT), Government of India
Acknowledgement: 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
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