Genetic Diversity and Population Structure of Soybean (Glycine max L.) through Integrated Morphological and SSR Analyses

Background Soybean ( Glycine max L.Merr.) is an important crop for protein and oil production, and its genetic improvement relies on the availability of diverse germplasm. In this study, 20 soybean genotypes, including one locally adapted conventional cultivar (AARI-21) and nineteen exotic accessions from the USDA germplasm collection, were evaluated using morphological traits and validated 13 simple sequence repeat (SSR) markers to determine genetic diversity in oil composition and yield. This study was conducted to identify genetically diverse lines to be used in future soybean improvement programs. Results Significant phenotypic variation was observed, with PI-548512 and PI-556554 showing thicker stem diameters, while PI-556487 produced more branches and a distinct flowering pattern. Principal component analysis (PCA) indicated that the principal contributors to Dim1 were the stem diameter, cotyledon length, flowering days, seeds per pod, and the principal contributors to Dim2 were plant height, nodes, pods per plant, and 100-seed weight. On the molecular scale, SSR markers were highly polymorphic, with a mean PIC of 0.53. Markers like SR. SS001, SR.PR.1, and SR.OL4 were very informative (PIC > 0.5), and this indicates that they have high discriminatory ability. The genotypes were clustered according to the SSR banding patterns in a cluster analysis that identified three distinct clusters, indicating that there is a lot of genetic variation. Some of the most genetically variable identified lines were AARI-21 (local) and PI 232998 and PI 559393 (introductions). Conclusions The results reveal significant morphologgical and molecular diversity between the studied germplasm, which can be utilized in molecular-assisted breeding to enhance the adaptation, quality traits and yield potential of soybean.