Genome-wide discovery of polymorphic simple sequence repeat (SSR) markers through comparative analysis of closely related hami melon cultivars

Simple sequence repeat (SSR) molecular markers are crucial for enhancing crop breeding programs. This study aimed to identify and validate polymorphic SSR markers in melon using genome sequencing data. By leveraging the melon reference genome and whole-genome sequences of multiple cultivars, we efficiently discovered 15,572 polymorphic SSR loci. Our analysis revealed that 38.17% of the polymorphic SSR were located within genic regions, with significant enrichment in functions related to organ development, transcription regulation, and plant hormones regulation. We validated a subset of randomly selected loci using PCR assays, confirming a polymorphism rate of 70.8% among the tested markers. Furthermore, population structure analysis, Principal Coordinate Analysis (PCoA), and neighbor-joining tree divided 30 melon cultivars into distinct genetic clusters, providing insights into their genetic diversity and evolutionary relationships. This development of polymorphic SSR markers offers valuable tools for melon breeding programs, facilitating the selection of desirable traits and accelerating cultivar.