Towards the identification of retrotransposon-based and ISSR molecular markers associated with populations resistant to ZYMV in melon

• Retrotransposon-based markers validated as reliable markers for genetic structure and diversity studies in melon.
• Varieties Dublone, PI414723 and Meanhno were confirmed as the sources for ZYMV resistance in melon breeding programs.
• Seven REMAP and 4 ISSR markers were found to be associated with populations resistant to ZYMV (P ≤ 0.01).

Melon (Cucumis melo L.) is one of the most important commercial vegetable crops grown in Iran. Very few studies on the genetic structure and diversity of melon landraces of Iran are available in the literature. In addition, it is susceptible to a number of diseases causing reduction in both productivity and quality of the crop. In this study we applied inter retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP) and inter simple sequence repeat (ISSR) molecular markers to investigate genetic diversity and its association with populations resistant to ZYMV in 11 Iranian melon populations and 12 commercial lines. Significant differences (P ≤ 0.01) were detected among populations for reaction to ZYMV infection. No symptoms observed on inbred line PI414723, while variety Charentais T showed the highest value of virus infection (1.87). Based on five IRAP, 15 REMAP and 20 ISSR primers, a total of 656 reproducible and scorable loci were generated, among them 75.41% were polymorphic. Population structure analysis using STRUCTURE software identified K = 10 as the reliable value for the number of clusters. Associations between molecular markers and populations resistant to ZYMV were tested using mixed linear model (MLM) approach that accounts for population structure. Highly significant associations were found for seven REMAP and four ISSR markers affecting ZYMV resistance (P ≤ 0.01). This study provides evidence that using natural germplasms, the diversity can be enhanced for marker-trait associations that can be validated in segregating populations and exploited through marker-assisted selection.