Development of Genome-Wide Simple Sequence Repeat Markers from Whole-Genome Sequence of Mungbean (Vigna radiata)

Mungbean (Vigna radiata L.) is a major pulse crop cultivated extensively across Asia and is considered an important model species among legumes because of its diploid genome and relatively small genome size. The availability of reliable, economical, and highly polymorphic molecular markers is critical for assessing genetic diversity, constructing linkage maps, and implementing functional genomics-based breeding programs. Among the available marker systems, simple sequence repeat (SSR) markers are highly polymorphic, abundant, co-dominant, and extensively used for allelic characterization across diverse crop species. This chapter describes the methodology for developing SSR markers and their use in genetic diversity studies in mungbean. Genome-wide SSR screening is performed to identify SSR motifs in the mungbean whole-genome sequence using the Phobos tandem repeat detection tool. The identified SSR motifs are annotated and categorized based on motif length, repeat type, and chromosomal location to facilitate the selection of informative loci for marker development. Primers are designed for selected SSR loci using appropriate flanking sequences and subsequently validated through PCR amplification across a panel of diverse mungbean genotypes. The polymorphism of these SSR markers is assessed by analyzing distinct and reproducible amplification patterns. The developed SSR markers constitute a valuable genomic resource for genetic diversity studies, molecular characterization, and genomics-assisted breeding applications in mungbean.