Whole-genome simple sequence repeat development and genetic diversity analysis of sponge gourd ( <i>Luffa cylindrica</i> )

Sponge gourd (<i>Luffa cylindrica</i>) is a versatile economic crop with nutritional, medicinal, and industrial value, but its genetic research has long been limited by a lack of stable molecular markers. Although high-quality genomic data of the sponge gourd line P93075 is available, no comprehensive whole-genome simple sequence repeat (SSR) marker development and systematic genetic diversity analysis based on this genome have been reported to date. This study first developed SSR markers using the high-quality <i>L. cylindrica</i> P93075 genome as reference. Using a microsatellite identification tool (MISA), 128,557 genome-wide SSR loci were identified, with a density of 195.91 SSRs/Mb; dinucleotide repeats (41.25% of total loci) were the dominant type. Candidate polymorphic SSR markers were initially screened <i>via</i> TBtools, resulting in 8,557 potential polymorphic markers. These markers showed ≥3 bp differences in amplified fragment length between the P93075 and SG2019 genomes. For validation, 308 randomly selected markers evenly distributed across 13 chromosomes were tested by polyacrylamide gel electrophoresis (PAGE), with 232 showing clear polymorphism, corresponding to a 75.32% polymorphism rate. In this study, 15 highly polymorphic SSR markers with a mean polymorphism information content (<i>PIC</i>) of 0.6838 were employed to analyze the genetic diversity and population structure of 67 globally sourced sponge gourd germplasms. The analysis revealed high genetic diversity, with an average gene diversity of 0.7267 and an average Shannon-Weaver index of 1.4618. Population structure analysis using Structure 2.3.4, together with unweighted pair group method with arithmetic mean (UPGMA) clustering and principal coordinate analysis (PCoA), consistently grouped the 67 germplasms into three groups. The clustering pattern was closely correlated with geographical origin. Based on these analyses, India was identified as the core genetic diversity center of sponge gourd in this study, consistent with previous domestication research findings. These newly developed SSR markers and insights into genetic diversity fill the gap of genome-wide SSR resources for sponge gourd and provide a solid foundation for sponge gourd molecular breeding, germplasm utilization, and genetic research.