Leveraging Genomics-enabled Breeding to Improve Resistance to Powdery Mildew in Summer Squash for Southeastern U.S.

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Commodities

• Vegetables: cucurbits

Practices

• Crop Production: plant breeding and genetics

Powdery mildew is a major fungal disease that causes significant yield and quality losses in squash (Cucurbita spp.) production. Conventional growers rely on routine fungicide application to manage the disease, costing an average of $350/ acre per season. Organic growers have limited control options leading to heavy yield losses when the disease pressure is high. The availability of squash cultivars resistant to powdery mildew would reduce yield losses for growers and promote environmental stewardship through reduced pesticide application. However, resistance to powdery mildew in most commercial squash cultivars is lacking or, at best, weak, necessitating complementary and substantial fungicide applications to ensure profitability. Recently, we conducted a single greenhouse screen of the USDA core squash collection (n= 207) in Florida and identified several novel sources of genetic resistance to powdery mildew. Using the screening data, we performed a preliminary genome-wide association study (GWAS) analysis, revealing potential markers that could be useful for marker-assisted selection. Building upon this preliminary work, we propose to i) conduct a second greenhouse screening of the entire core collection and validate the new resistance sources,  ii) perform a comprehensive GWAS analysis using multi-screening phenotype data and validate  molecular markers linked to resistance, iii) transfer powdery mildew resistance into elite squash cultivars using marker-assisted selection, and iv) characterize the inheritance mechanism of resistance in novel resistant sources. The novel powdery-mildew-resistant germplasm will be evaluated for yield and horticultural performance under field conditions, and the findings will be communicated to growers through extension outreach.

1. Conduct a second greenhouse screening of the USDA squash core collection and validate new resistance sources: It builds on preliminary findings to confirm resistance traits under controlled conditions, ensuring that identified resistance is robust and reproducible.
2. Conduct a comprehensive GWAS analysis using multi-screening phenotype data and validate molecular markers linked to resistance: The rationale here is to utilize advanced genomic tools to decipher the genetic basis of resistance to powdery mildew in squash. Unlike traditional breeding, which relies on multiple growing seasons to confirm traits, thus utilizing many resources (soil, fertilizers, manual labor), GWAS enables quicker and more accurate identification of resistant genotypes.
3. Transfer powdery mildew resistance into elite squash cultivars using marker-assisted selection: This objective seeks to apply the findings from genomic analyses to practical breeding. The justification lies in its direct impact on developing commercially viable, disease-resistant squash varieties, reducing reliance on fungicides, and lowering production costs.
4. Characterize the mode of inheritance in the novel resistant sources: Understanding how resistance traits are inherited is fundamental for effective breeding. This objective aims to inform breeding strategies by elucidating the genetic mechanisms through which resistance is passed from one generation to the next, which is critical for predicting the behavior of these traits in breeding programs and ensuring the stability of resistance in future cultivars.