Cucumber (Cucumis sativus L.) is an economically important vegetable crop that is cultivated around the world. Pickling cucumber production in the United States is greatly impacted by Phytophthora fruit rot, caused by a soil-born oomycete pathogen, Phytophthora capsici. With no resistant variety available, genetic resources are needed to develop resistant varieties. The goal of this work was to identify quantitative trait loci (QTL) associated with resistance to Phytophthora fruit rot using multiple genomic approaches and populations. Young fruit resistance, which is observed during the state of rapid fruit growth prior to harvest, is a quantitative trait for which multiple QTL were identified. The largest effect QTL, qPFR5.1, located on chromosome 5 was fine mapped to a 1-Mb region. Genome-wide association studies (GWAS) and extreme-phenotype genome-wide association study (XP-GWAS) for young fruit resistance also were performed on a resequenced cucumber core collection representing > 96% of the genetic diversity of the USDA cucumber germplasm. Several SNPs overlapped with the QTL identified from QTL-seq analysis on biparental populations. In addition, novel SNPs associated with the resistance were identified from the germplasm. The resistant alleles were found mostly in accessions from India and South Asia, the center of origin for cucumber. The results from this work can be applied to future disease resistance studies and marker-assisted selection in breeding programs. When introgressing disease resistant traits, the resulting varieties also need to meet market standards, which are defined by morphological characteristics. Disease resistance and other valuable traits are often found in landraces or wild accessions that have fruit quality traits that are undesirable in commercial markets. To provide morphological and genetic information for the diversity of fruit traits in the cucumber core collection, external and internal fruit quality traits including fruit shape, skin color, netting, spine density, curvature, seed cavity size, flesh thickness, hollowness, and flesh color, were measured in 2019-2022. The photographic and phenotypic data are deposited and publicly available on the Cucurbit Genome Database (GuGenDB, http://cucurbitgenomics.org/v2/). GWAS analyses were performed on all traits collected. The findings from the association analyses supported many previously identified QTL and candidate genes, suggested additional candidate genes, and provide genetic framework for morphological diversity of the core collection.
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