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.
Highlights
(mostly seeds/grains) of crops is tightly regulated through complex cellular and genetic mechanism
It is highly imperative to dissect the genetic basis of variability governing Fe and Zn concentrations in seeds of food crops
Considering the importance of this crop as a dietary element across a major part of global population, especially in developing countries, it is desirable to understand the complex genetic inheritance pattern and gene regulatory function of seed-Fe and Zn concentrations in chickpea leading to their bio-fortification through marker-assisted genetic enhancement
Summary
The GBS assay is advantageous in rapid large-scale mining and high-throughput genotyping of high-quality accurate genome-wide SNPs simultaneously for high-resolution genetic and association mapping[37,38,39,44,45] This NGS-based strategy has potential to identify genes/QTLs regulating important agronomic traits in chickpea. For generating an intra-specific high-resolution genetic linkage map, 536 SNPs (529 genome-wide GBS- and 7 known gene-based SNPs) exhibiting polymorphism between parental accessions (desi accession ICC 4958 and kabuli accession ICC 8261) were genotyped in 277 individuals of a RIL (recombinant inbred line) mapping population (ICC 4958 x ICC 8261).
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