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

Commodities

Practices

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.