Genetic diversity and structure analysis of melon (Cucumis melo L.) genotypes using URP, SRAP, and CDDP markers

Melon (Cucumis melo L.) is an ancient and indigenous crop that grows in Iraq's Kurdistan region, and research into its genetic diversity is needed to improve this important culinary plant while also promoting a healthy diet. This study assessed the genetic diversity of 57 melon genotypes using three types of molecular markers, namely universal rice primer (URP), inter-retrotransposon amplified polymorphism (IRAP), sequence-related amplified polymorphism (SRAP), and conserved DNA derived polymorphism (CDDP) markers. The URP + IRAP, SRAP, and CDDP primers yielded 143, 125, and 131 polymorphic alleles, respectively. The average polymorphic information content (PIC) was 0.29, 0.26, and 0.32 for URAP + IRAP, SRAP, and CDDP, respectively. Based on the average values of polymorphic bands per primer and PIC of three types of markers, the order of the power of discrimination of melon genotype was as follows: URP + IRAP > CDDP > SRAP. The URP-4R, Me1-Em2, and MYB-1 primers had the highest Shannon information index values. Based on the Ward method-based cluster and STRUCTURE analysis, URP + IRAP and SRAP markers grouped 57 genotypes into two primary clusters with various sub-clusters, whereas CDDP markers divided 57 genotypes into three groups. The genetic distances between genotypes ranged from 0.32 to 0.84 for URP + IRAP, 0.20 to 0.78 for SRAP, and 0.25 to 0.73 for CDDP. The analysis of molecular variance revealed an increase in genetic variation within groups, as well as significant gene exchange between populations. In the SRAP analysis, substantial genetic distinctiveness was identified among populations. However, in CDDP analysis, high Shannon's information index and predicted heterozygosity were observed among populations. The outcomes of this study indicated a high level of variability in Iraqi melon germplasm, which must be preserved and included in improvement programs for this ancient crop.