Fine mapping, introgression, and KASP marker development for powdery mildew resistance in watermelon using an interspecific RIL population (Citrullus monospermous × C. lanatus)

Authors: KUMAR, RAHUL - Clemson University; Ikerd, Jennifer; KARTHIKEYAN, RAGHUPATHY - Clemson University; Kousik, Chandrasekar

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/23/2025
Publication Date: 11/8/2025
Citation: Kumar, R., Ikerd, J.L., Karthikeyan, R., Kousik, C.S. 2025. Fine mapping, introgression, and KASP marker development for powdery mildew resistance in watermelon using an interspecific RIL population (Citrullus monospermous × C. lanatus). Journal of Theoretical and Applied Genetics. https://doi.org/10.1007/s00122-025-05079-4.
DOI: https://doi.org/10.1007/s00122-025-05079-4

Interpretive Summary: Watermelon is an important crop grown across 44 states in the US with a market value of more than $780 million. Powdery mildew is a common fungal disease that harms watermelon plants and reduces yield. To manage this problem without heavy use of chemicals, scientists are working on developing naturally resistant watermelon varieties. In this study, researchers at USDA ARS in Charleston, SC, used a resistant wild watermelon and a old susceptible cultivated one to create a large family of plants. They found that resistance is controlled by a single dominant gene, which makes it easier to pass on to the next generation. They identified a small region of DNA on chromosome 2 that carries this resistance gene. Inside this region, they found four genes possibly linked to disease resistance. To help plant breeders, they also developed DNA markers (called KASP markers) that can quickly and accurately tell whether a plant has the resistance gene. These markers worked well in different types of watermelon populations. This research will help speed up the development of powdery mildew–resistant watermelon using marker-assisted selection. 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, is a major fungal disease affecting watermelon production worldwide. Development of resistant cultivars through marker-assisted selection (MAS) offers an effective strategy for disease management. A major quantitative trait locus (QTL) for powdery mildew resistance was mapped using an F11 recombinant inbred line (RIL) population derived from an interspecific cross between resistant Citrullus mucosospermus line USVL531-MDR and susceptible Citrullus lanatus line USVL677-PMS. Genetic analysis revealed that resistance is governed by a single dominant gene, supported by 3:1 segregation ratio observed in both RIL and F2 populations. A major 54,772 bp QTL was identified on chromosome 2 (30,111,475–30,166,247 bp), containing three lipoxygenase (LOX) genes and a 50S ribosomal protein L27-like gene. Four tightly linked KASP marker (CMPMR-1) were developed from a SNP located within the three LOX genes and 50S ribosomal protein L27-like gene, identified in the QTL region, and were validated across multiple segregating populations, including the RIL (USVL531-MDR × USVL677-PMS) and two additional F2 populations (USVL531-MDR × ‘Sugar Baby’ and PI 560003 × USVL677-PMS). These markers accurately differentiated resistant and susceptible individuals (R² = 0.68–0.82) and demonstrated tight co-segregation with the resistance trait across multiple populations. QTL mapping and KASP markers development will facilitate marker-assisted selection (MAS) for powdery mildew resistance breeding and facilitate future gene cloning efforts.