Taiwan’s climate is characterized by high temperatures and high humidity, making melon cultivation highly susceptible to diseases such as powdery mildew, downy mildew, bacterial fruit blotch, and viral infections. Under extreme climate conditions, additional stresses caused by low- and high-temperature extremes further exacerbate production risks, leading to increased disease management costs and reductions in yield and fruit quality. Because disease resistance and stress tolerance are generally quantitative traits influenced by polygenic interactions and environmental factors, conventional breeding requires multi-generational phenotypic evaluation, resulting in a prolonged breeding cycle. In contrast, molecular marker technologies enable genotype-based selection at early developmental stages, thereby improving selection efficiency and accuracy.

The objective of this project is to develop molecular markers associated with disease resistance and stress tolerance traits in melon and to integrate these markers with phenotypic data to establish an efficient molecular screening platform for resilience breeding. During the current phase, a total of 76 melon accessions were collected, and 25 accessions with known powdery mildew–resistant or –susceptible phenotypes were successfully propagated and purified through line multiplication (Figure 1), providing sufficient experimental materials with relatively stable genetic backgrounds for subsequent analyses.

For marker validation, the genomic DNA extraction protocol for melon was optimized, and multiple molecular markers associated with powdery mildew resistance QTLs were selected based on published literature, including candidate resistance genes such as MELO3C002403 and MELO3C002434. These markers were evaluated using AS-PCR and InDel assays (Figure 2). Although heterozygosity remained in some melon accessions, resulting in incomplete concordance between AS-PCR markers and sequence analysis of MELO3C00693 (Figure 3) with certain resistant or susceptible phenotypes, the results nonetheless provide a critical foundation for further marker optimization and trait–marker association analyses.

▲Figure 1. Melon cultivation during the autumn growing season.		▲Figure 2. AS-PCR primer pairs designed for the MELO3C002403 gene and PCR validation performed on 40 melon accessions with powdery mildew–resistant and –susceptible phenotypes.
▲Figure 3. Sequence alignment analysis of the MELO3C00693 gene in powdery mildew–resistant and –susceptible melon lines.