Genetic diversity assessment and marker-trait association for yield components in winter chickpea ( Cicer Arietinum L. ) genotypes using SSR markers

Increasing chickpea (Cicer arietinum L.) yield is of great importance in semi-arid regions such as Uzbekistan. This study evaluated genetic diversity and marker-trait associations (MTAs) for yield components in 38 winter chickpea varieties, including local cultivars Iftikhor, Mustakillik, and samples from the Chickpea International Elite Nursery. These samples demonstrated high phenotypic variability in yield components like pods per plant (48–100), seeds per pod (42–145), and 1000-seed weight (274.9–390.8 g), characterizing them as medium- and large-seeded. Using 48 polymorphic SSR markers, molecular analysis identified 150 alleles (2 to 8 per marker, averaging 3.0). Population structure analysis (K = 4) indicated genetic admixture. Importantly, SSR markers GA6, TA72, and TAASH showed significant correlations with grains per plant and seed weight. In silico analysis mapped these to yield-associated chromosomal regions, identifying candidate regulatory genes (ADNT1, DOF, WUSCHEL) to support marker-assisted selection (MAS) programs.