Molecular Diversity and Genetic Relationships among Melon (Cucumis melo L.) Genotypes Revealed by RAPD Markers

Abstract

Melon (Cucumis melo L.) is an economically important horticultural crop in Indonesia, and developing superior cultivars requires sufficient genetic diversity and effective germplasm characterization. This study aimed to assess genetic variation among melon genotypes, identify informative RAPD primers to distinguish melon from timun suri and blewah, and characterize genetic relationships among melon genotypes for breeding purposes. A combined field and laboratory study was conducted at the Plant Breeding Laboratory, UPN “Veteran” Yogyakarta. Eight RAPD primers were evaluated using 10 genetic materials comprising eight melon genotypes, timun suri, and blewah. Amplified DNA fragments were scored as binary data and analyzed using NTSYS-pc 2.1 software. The primers generated 69 loci, with 98.86% polymorphism, indicating substantial molecular variation among the evaluated materials. BC-388 and BC-551 showed the highest discriminatory capacity for separating timun suri and blewah from melon genotypes and were subsequently used to assess genetic relationships among the eight melon genotypes. UPGMA analysis separated the melon genotypes into two major groups at a similarity coefficient of 0.69. Cluster 1 comprised DGMC-2-5-16-1-5, DGMD-4-9-3-3-4, Pearl Lady, Dalmatian, and Golden Apollo, whereas Cluster 2 comprised Orange Melody, Silver Light, and Yuki Lady; both clusters showed a mean similarity coefficient of 0.77. The advanced breeding lines DGMC-2-5-16-1-5 and DGMD-4-9-3-3-4 showed substantial genetic divergence from several genotypes, indicating their potential as parental materials. Overall, RAPD markers revealed substantial genetic variation and relationships, providing preliminary molecular information for strategic parent selection in melon breeding.