Quantitative Trait Loci (QTL) Mapping and Kompetitive Allele Specific PCR (KASP) Marker Development for Powdery...

Powdery mildew, caused by Podosphaera xanthii, poses a significant threat to watermelon (Citrullus lanatus) cultivation. Development of resistant cultivars is one of the best strategies to manage powdery mildew. To elucidate the genetic basis of resistance, bulked segregant analysis (BSA) was conducted on an F₂ population derived from a cross between resistant (USVL608-PMR) and susceptible (USVL677-PMS) genotypes. A 570-kb region on chromosome 2 was identified using QTLseq, containing 99 single-nucleotide polymorphisms (SNP) and eight putative genes. A tightly linked kompetitive allele specific PCR (KASP) marker was developed and validated across three F₂ populations (USVL608-PMR × USVL677-PMS, USVL608-PMR × 'Sugar Baby,' USVL608-PMR × 'Dixie Lee'), showing a 3:1 segregation ratio and very strong linkage to resistance. Marker-disease resistance linkage was further validated in the F₃ generation of all three populations. RNAseq analysis revealed the upregulation of lipoxygenase (LOX), jasmonic acid (JA), and reactive oxygen species (ROS) pathways after inoculation, suggesting their role in powdery mildew resistance in watermelon. The development of tightly linked KASP markers in three different backgrounds for powdery mildew resistance and a molecular understanding of disease resistance will be useful for breeding and selecting new disease-resistant watermelon cultivars.