Mining of microsatellite markers in legume crops

Microsatellites or Simple Sequence Repeats (SSRs) are short tandem repeats widely distributed across plant genomes and are considered highly informative molecular markers due to their abundance, co-dominant inheritance, and high polymorphism. In legume crops, SSR markers are extensively utilized for genetic diversity studies, linkage mapping, and marker-assisted breeding. However, comprehensive genome-wide mining and comparative analysis of SSRs across major legume species remain limited. In the present study, genome-wide mining of SSR markers was performed using publicly available genomic sequences of major legume crops, including Glycine max, Cicer arietinum, Phaseolus vulgaris, and Vigna radiata. Bioinformatics tools were employed to identify SSR loci, classify repeat motifs (di-, tri-, tetra-, penta-, and hexa-nucleotides), and analyze their genomic distribution. Primer pairs were designed for selected SSR loci to evaluate their potential applicability in molecular studies. A large number of SSR loci were identified across all analyzed genomes, with di-nucleotide and tri-nucleotide repeats being the most predominant classes. Tri-nucleotide repeats were mainly enriched in coding regions, indicating their possible functional and evolutionary significance, while di-nucleotide repeats were more abundant in non-coding regions, suggesting higher variability. Comparative analysis revealed species-specific differences in SSR density and motif distribution. The designed SSR primers demonstrated high potential for cross-species transferability and polymorphism, highlighting their utility in genetic diversity analysis and breeding applications.