Extreme-phenotype genome-wide association study (XP-GWAS) of powdery mildew race 2 W tolerance in the USDA Citrullus germplasm collection
Abstract Powdery mildew outbreaks, caused by Podosphaera xanthii, cause reduced watermelon yields as the plants produce fewer and smaller fruits due to premature leaf senescence. The reduced leaf canopy can decrease fruit quality due to sun scalding. Sources of powdery mildew tolerance were previous...
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Nature Portfolio
2025-02-01
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| Online Access: | https://doi.org/10.1038/s41598-025-89445-8 |
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| author | Sandra E. Branham Venkata Rao Ganaparthi W. Patrick Wechter Younghoon Park Todd Wehner Angela Davis Antonia Tetteh Laura Massey Sue Hammar Rebecca Grumet Shaker Kousik Amnon Levi |
| author_facet | Sandra E. Branham Venkata Rao Ganaparthi W. Patrick Wechter Younghoon Park Todd Wehner Angela Davis Antonia Tetteh Laura Massey Sue Hammar Rebecca Grumet Shaker Kousik Amnon Levi |
| author_sort | Sandra E. Branham |
| collection | DOAJ |
| description | Abstract Powdery mildew outbreaks, caused by Podosphaera xanthii, cause reduced watermelon yields as the plants produce fewer and smaller fruits due to premature leaf senescence. The reduced leaf canopy can decrease fruit quality due to sun scalding. Sources of powdery mildew tolerance were previously identified by screening the USDA Citrullus germplasm collection with P. xanthii races 1 W and 2 W. However, not all gene loci associated with tolerance to race 2 W have been identified and markers tightly linked to such loci have not been developed. 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 2 W 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 tolerant and susceptible extremes resulted in 301,059 high-quality biallelic SNPs. Two adjacent SNPs on chromosome 7 were significantly associated with P. xanthii race 2 W 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. |
| format | Article |
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| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Nature Portfolio |
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| series | Scientific Reports |
| spelling | doaj-art-c91a3d87ebaa40c28009956c246394a92025-02-09T12:28:29ZengNature PortfolioScientific Reports2045-23222025-02-0115111010.1038/s41598-025-89445-8Extreme-phenotype genome-wide association study (XP-GWAS) of powdery mildew race 2 W tolerance in the USDA Citrullus germplasm collectionSandra E. Branham0Venkata Rao Ganaparthi1W. Patrick Wechter2Younghoon Park3Todd Wehner4Angela Davis5Antonia Tetteh6Laura Massey7Sue Hammar8Rebecca Grumet9Shaker Kousik10Amnon Levi11Coastal Research and Education Center, Clemson UniversityCoastal Research and Education Center, Clemson UniversityCoastal Research and Education Center, Clemson UniversityPusan National UniversityNorth Carolina State UniversityUnited States Department of AgricultureKwame Nkrumah University of Science and TechnologyAgricultural Research Service - Southeast AreaMichigan State UniversityMichigan State UniversityAgricultural Research Service - Southeast AreaAgricultural Research Service - Southeast AreaAbstract Powdery mildew outbreaks, caused by Podosphaera xanthii, cause reduced watermelon yields as the plants produce fewer and smaller fruits due to premature leaf senescence. The reduced leaf canopy can decrease fruit quality due to sun scalding. Sources of powdery mildew tolerance were previously identified by screening the USDA Citrullus germplasm collection with P. xanthii races 1 W and 2 W. However, not all gene loci associated with tolerance to race 2 W have been identified and markers tightly linked to such loci have not been developed. 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 2 W 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 tolerant and susceptible extremes resulted in 301,059 high-quality biallelic SNPs. Two adjacent SNPs on chromosome 7 were significantly associated with P. xanthii race 2 W 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.https://doi.org/10.1038/s41598-025-89445-8Disease resistanceXP-GWASPowdery mildewWatermelonResequencingKASP |
| spellingShingle | Sandra E. Branham Venkata Rao Ganaparthi W. Patrick Wechter Younghoon Park Todd Wehner Angela Davis Antonia Tetteh Laura Massey Sue Hammar Rebecca Grumet Shaker Kousik Amnon Levi Extreme-phenotype genome-wide association study (XP-GWAS) of powdery mildew race 2 W tolerance in the USDA Citrullus germplasm collection Scientific Reports Disease resistance XP-GWAS Powdery mildew Watermelon Resequencing KASP |
| title | Extreme-phenotype genome-wide association study (XP-GWAS) of powdery mildew race 2 W tolerance in the USDA Citrullus germplasm collection |
| title_full | Extreme-phenotype genome-wide association study (XP-GWAS) of powdery mildew race 2 W tolerance in the USDA Citrullus germplasm collection |
| title_fullStr | Extreme-phenotype genome-wide association study (XP-GWAS) of powdery mildew race 2 W tolerance in the USDA Citrullus germplasm collection |
| title_full_unstemmed | Extreme-phenotype genome-wide association study (XP-GWAS) of powdery mildew race 2 W tolerance in the USDA Citrullus germplasm collection |
| title_short | Extreme-phenotype genome-wide association study (XP-GWAS) of powdery mildew race 2 W tolerance in the USDA Citrullus germplasm collection |
| title_sort | extreme phenotype genome wide association study xp gwas of powdery mildew race 2 w tolerance in the usda citrullus germplasm collection |
| topic | Disease resistance XP-GWAS Powdery mildew Watermelon Resequencing KASP |
| url | https://doi.org/10.1038/s41598-025-89445-8 |
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