Identification of potential alleles contributing for yield attributing traits in common bean (Phaseolus vulgaris L.) grown under Western Himalayan Kashmir Valley

Common bean is increasingly recognized as a highly beneficial global food source due to its rich nutritional and medicinal properties. The present study assessed the genetic variability among unexplored common bean germplasm using morphological parameters. Phenotypic coefficient of variation values were consistently greater than genotypic coefficient of variation values in both the locations, Wadura and Shuhama emphasized the significant variation. For genotyping and association analysis, 100 SSR markers spanning all chromosomes were employed, which resulted in the amplification of 534 alleles, with an average of 5.34 alleles per marker. The Polymorphism Information Content (PIC) values ranged from 0.5325 to 0.8926, averaging 0.7553. Using both the Mixed Linear Model (MLM) and General Linear Model (GLM) approaches, 4 SSR markers were found to be associated with days to flowering, number of pods per plant, and harvest index, explaining 14–48% of phenotypic variation. Notably, markers BM185 and BMB742 were identified as common in both models. The findings provide valuable genetic insights that can support breeding programs focused on enhancing yield-related traits in the North-Indian Himalayan region.