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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Abstract
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 |
| URI: | http://oar.icrisat.org/id/eprint/9436 |
| Official URL: | http://dx.doi.org/10.1038/srep24050 |
| Projects: | UNSPECIFIED |
| 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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