QTL mapping and KASP Marker Development for Powdery Mildew Resistance in Watermelon

Authors: KUMAR, RAHUL - Clemson University; CHANDA, BIDISHA - Clemson University; MANDAL, MIHIR - California Department Of Agriculture; Ikerd, Jennifer; BRANHAM, SANDRA - Clemson University; WECHTER, WILLIAM - Clemson University; Wadl, Phillip; Levi, Amnon; SHAIK, AZEEZAHMED - Clemson University; REDDY, UMESH - West Virginia State University; KARTHIKEYAN, RAGHUPATHY - Clemson University; Kousik, Chandrasekar

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/12/2025
Publication Date: 5/16/2025
Citation: Kumar, R., Chanda, B., Mandal, M., Ikerd, J.L., Branham, S., Wechter, W., Wadl, P.A., Levi, A., Shaik, A., Reddy, U., Karthikeyan, R., Kousik, C.S. 2025. QTL mapping and KASP Marker Development for Powdery Mildew Resistance in Watermelon. Plant Disease. https://doi.org/10.1094/PDIS-04-25-0737-RE.
DOI: https://doi.org/10.1094/PDIS-04-25-0737-RE

Interpretive Summary: Watermelon is an important crop grown across 44 states in the US. There are many diseases and pests that attack watermelon and cause significant damage. Powdery mildew is a common plant disease that can seriously damage watermelon crops. It’s caused by a fungus and spreads easily, making it hard for farmers to grow healthy watermelons. Affected watermelon plants produce lower quality fruit or less fruit. One way to fight this disease is by growing watermelon varieties that are naturally resistant to it. Researchers at USDA ARS In Charleston, SC wanted to understand what makes some watermelons resistant to powdery mildew. They looked at the DNA of watermelon plants by crossing a resistant variety with one that gets the disease easily. They discovered a small section of the watermelon’s DNA that is linked to disease resistance. To help breed disease resistant watermelon, the scientists created a simple DNA test (called KASP marker) that can tell whether a young plant will be resistant to powdery mildew or not. They tested this in several types of watermelons and found it worked well. This research will help develop better watermelon varieties that stay healthy and reduce the need for chemicals to manage powdery mildew. The information developed by this research will be useful for seed-industry, University and USDA breeders and extension personnel.

Technical Abstract: 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 polymorphism (SNP) and 8 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 post-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.