Multi-marker genetic diversity assessment of snake melon using iPBS, POGP and SRAP markers

Genetic diversity and population structure of snake melon (Cucumis melo subsp. melo var. flexuosus) remain insufficiently characterized, and available studies largely rely on single-marker systems, limiting cross-validation of genetic patterns. We hypothesized that integrating complementary marker types-iPBS (Inter-Primer Binding Site), POGP (Peroxidase Gene-based Polymorphism), and SRAP (Sequence-Related Amplified Polymorphism)-would provide a more robust and method-informed resolution of diversity and structure than any single marker approach. This study aimed to analyze the genetic diversity of 24 snake melon genotypes from Türkiye using iPBS, POGP, and SRAP markers. A total of 16 iPBS, 14 POGP, and 10 SRAP primers were used to assess polymorphism, genetic relationships, and population structure. The results revealed high polymorphism rates (iPBS: 93.4%, POGP: 90.0%, SRAP: 96.3%), with polymorphic information content (PIC) values ranging from 0.47 to 0.61. Genetic similarity analysis identified distinct and closely related genotypes, and UPGMA (Unweighted Pair Group Method with Arithmetic Mean) and PCoA (Principal Coordinate Analysis) supported clear clustering patterns. STRUCTURE analysis (K = 3) resolved three main subpopulations; approximately 50% of the genotypes (SM13-SM24) showed high membership in a single dominant cluster (Q ≥ 0.80), whereas the remaining genotypes were assigned to two minor clusters or exhibited admixed ancestry, consistent with pronounced genetic structuring accompanied by gene flow. Mantel correlation analysis indicated that iPBS and SRAP markers were the most consistent in detecting genetic variation. Overall, the combined marker analysis provides a comprehensive genetic framework for conservation and breeding strategies. This study represents the first multi-marker genetic characterization of snake melon, offering valuable insights into its genetic diversity and potential for crop improvement.