Genome-Wide Association Analysis To Delineate High-Quality Snps For Seed Micronutrient Density In Chickpea (Cicer Arietinum L.)
Abstract Chickpea is the most important nutrient rich grain legume crop in the world. A diverse core set of 147 chickpea genotypes was genotyped with 50K Cicer SNP array and trait phenotyped in two different environments for four seed micro-nutrients (Cu, Fe, Mn, and Zn). The trait data and high-throughput 50K SNP genotypic data was used for genome-wide association study (GWAS) that led the discovery of gene/QTLs for seed Cu, Fe, Mn, and Zn concentrations in chickpea. The analysis of seed micronutrient data revealed significant differences for all the four micronutrient concentrations (P ≤ 0.05). The mean concentration of seed Fe, Zn, Cu, and Mn pooled over two-year data was 146.1 ppm, 45.9 ppm, 63.8 ppm and 27.0 ppm respectively. The analysis of results led to the identification of 35 SNPs significantly associated with seed Zn, Cu, Fe and Mn concentrations. Among these 35 MTAs, 5 were stable (consistently identified in different environments), 6 were major (explain more than 15% phenotypic variation for an individual trait) and 3 were both major and stable MTAs. The stable and major MTAs identified during the present study shall prove useful in molecular breeding programs aimed at enhancing seed nutrient density of chickpea.