Melon (Cucumis melo L.) is an essential dietary component in Iran and Iraq, making the understanding of its genetic diversity crucial for breeding and conservation efforts. However, limited studies have investigated the genetic diversity of melon populations in these regions. This study evaluated the genetic diversity and population structure of 80 melon genotypes collected from 20 regions across Iran and Iraq using Inter-Simple Sequence Repeat (ISSR) and Start Codon Targeted (SCoT) markers. A total of 11 ISSR and 14 SCoT primers generated 166 and 245 fragments, respectively. The mean percentage of polymorphism was higher for ISSR (77.67%) than SCoT (68.47%). However, SCoT markers exhibited a higher polymorphic information content (0.438) compared to ISSR markers (0.374), indicating superior discriminatory power. The resolving power of the primers was comparable between the two marker systems. Cluster analysis using the Jaccard similarity coefficient and UPGMA algorithm grouped the genotypes into two and four clusters based on ISSR and SCoT markers, respectively, a pattern further supported by principal component analysis. Analysis of molecular variance revealed greater intra-population variation than inter-population variation for both markers. A combined marker analysis classified the genotypes into three major groups. Overall, our findings indicate that SCoT markers are more effective than ISSR markers for assessing genetic diversity and population structure in melon genotypes. This study provides valuable insights for melon breeding and conservation programs in Iran and Iraq.
