Determination of genetic diversity and population structure in common bean (Phaseolus vulgaris L.) genotypes using capillary electrophoresis-based SSR markers

Common bean ( Phaseolus vulgaris L.) is an important grain legume due to its contribution to plant-based protein intake and its broad adaptability to diverse agroecological conditions. Molecular characterization of common bean genetic resources is essential for conserving landraces and identifying suitable parental materials for breeding programs. In this study, the genetic diversity and population structure of 75 common bean genotypes, including landraces, breeding lines, and registered cultivars, were assessed using 14 SSR markers and capillary electrophoresis-based fragment analysis. The SSR markers generated a total of 527 polymorphic allelic variants, with an average of 37.64 polymorphic allelic variants per marker. Polymorphism information content (PIC) values ranged from 0.738 to 0.974, with a mean value of 0.90, while the mean genetic diversity value was also 0.90, indicating the high discriminatory capacity of the SSR marker set. STRUCTURE HARVESTER indicated that K = 2 represented the strongest primary level of population structure, while the K = 3 model provided an additional biologically informative substructure. The genetic relationships inferred by STRUCTURE analysis were broadly supported by UPGMA clustering and principal coordinate analysis (PCoA), with the first two principal coordinates explaining 41.74% of the total molecular variation. AMOVA showed that 85.52% of the total genetic variation was distributed within genetic clusters, whereas 14.48% was attributed to variation among clusters. The overall PhiPT value was statistically significant (PhiPT = 0.145, p = 0.005), indicating low-to-moderate genetic differentiation among the inferred genetic groups. Overall, these findings demonstrate that capillary electrophoresis-supported SSR analysis is an effective approach for assessing genetic diversity and population structure in common bean. The evaluated germplasm represents a valuable genetic resource for common bean breeding, germplasm characterization, DNA fingerprinting, and the conservation of genetic resources.