Extreme-Phenotype Genome-Wide Association Study (XP-GWAS) and Marker Development for Powdery Mildew Race 2W Tolerance in the USDA Citrullus Germplasm Collection

Authors: BRANHAM, SANDRA - Clemson University; GANAPARTHI, VENKATA - Clemson University; WECHTER, WILLIAM - Clemson University; PARK, YOUNG-HOON - Pusan National University; WEHNER, TODD - North Carolina State University; DAVIS, ANGELA - Retired ARS Employee; TETTEH, ANTONIA - North Carolina State University; Massey, Laura; HAMMAR, SUE - Michigan State University; GRUMET, REBECCA - Michigan State University; Kousik, Chandrasekar; Levi, Amnon

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/5/2025
Publication Date: 2/8/2025
Citation: Branham, S., Ganaparthi, V., Wechter, W., Park, Y., Wehner, T., Davis, A., Tetteh, A.Y., Massey, L.M., Hammar, S., Grumet, R., Kousik, C.S., Levi, A. 2025. Extreme-Phenotype Genome-Wide Association Study (XP-GWAS) and Marker Development for Powdery Mildew Race 2W Tolerance in the USDA Citrullus Germplasm Collection. Scientific Reports. 15, Article number: 4781 (2025). https://doi.org/10.1038/s41598-025-89445-8.
DOI: https://doi.org/10.1038/s41598-025-89445-8

Interpretive Summary: Watermelon is an important vegetable crop grown in 44 states in the U.S.A. Powdery mildew PM) is the most common leaf disease affecting watermelon plants at all stages of development causing significant monetary losses to growers. Identifying genetic resources with resistance to PM and utilizing them for developing resistant varieties would be very effective in combating this major disease of watermelon. In this study we used a genomic technology known as “extreme-phenotype genome-wide association study (XP-GWAS)” to identify gene loci conferring resistance to PM. Using the “XP-GWAS”, we were able to identify several gene loci associated with PM-resistance and accordingly developed DNA markers that will be useful in breeding programs aiming to develop cultivars resistant to this common disease of watermelon.

Technical Abstract: Powdery mildew outbreaks, caused by Podosphaera xanthii, cause reduced watermelon yields, fewer fruits per plant and smaller fruits due to premature leaf senescence. The reduced leaf canopy can also decrease fruit quality due to sun scalding. Sources of powdery mildew tolerance were previously identified by screening the USDA Citrullus germplasm collection with multiple races of P. xanthii but not all gene loci associated with tolerance to race 2W have been identified and no markers tightly linked to such loci were developed. Here, we employed a bulked segregant analysis approach using historical data from the USDA Germplasm Resource Information Network for an extreme-phenotype genome-wide association study (XP-GWAS) of tolerance to P. xanthii race 2W in Citrullus accessions (N=1,147). XP-GWAS identifies variants that segregate between pools of individuals chosen from the extremes of a phenotypic distribution from a diversity panel. Whole-genome resequencing of 45 individuals bulked from each extreme (tolerant and susceptible) resulted in 301,059 high-quality biallelic SNPs. Two adjacent SNPs on chromosome 7 were significantly associated with P. xanthii race 2W tolerance in the bulks and two additional SNPs had a strong signal in the XP-GWAS analysis. Kompetitive Allele-Specific PCR (KASP) markers were designed for sixteen SNPs across the three genomic regions. The KASP markers were validated by genotyping 186 accessions from the extremes of the disease response distribution of the Citrullus collection. Analysis of variance determined that thirteen of the markers were significantly associated, with the best marker in each region explaining 21-31% of the variation in powdery mildew tolerance.