Genetic diversity, population structure and marker-trait association analysis for yield-related traits in chickpea (Cicer arietinum L.)

Chickpea (Cicer arietinum L.) serves as a vital protein and mineral source in vegetarian diets worldwide. We assessed 96 diverse chickpea genotypes for seven yield and yield-related traits, and investigated genetic diversity, population structure, and marker-trait associations for yield-contributing traits using 21 gene-based SSR markers. The simple sequence repeat (SSR) markers revealed substantial genetic diversity (He = 0.57) among the chickpea genotypes. Using unweighted pair group method with arithmetic mean (UPGMA)-based clustering, we identified three major clusters primarily based on geographical proximity and breeding origin. The analysis of molecular variance (AMOVA) indicated that 11% of the variation was between clusters, 84% among individuals, and 5% within individuals. Wright’s F statistical analysis showed the deviation from Hardy–Weinberg expectation within a cluster (F_IS) for all 21 SSR loci as 0.942, while the deviation from Hardy–Weinberg expectation (F_IT) was 0.948 across the clusters. Pairwise correlation of alleles between clusters (F_ST )  suggested significant differences between all cluster pairs, indicating distinctiveness among the three groups. STRUCTURE analysis delineated the population into five sub-groups. Comparison between UPGMA clustering and Bayesian STRUCTURE analysis generally showed agreement in population subdivisions and genetic relationships. However, certain geographically close populations were dispersed into different clusters, possibly due to shared morphological traits. Marker-trait association using gene-based SSR markers revealed significant association with the yield and yield-related traits. These markers hold potential for marker-assisted breeding programs aimed at enhancing chickpea cultivation.