A Novel Grape Downy Mildew Resistance Locus from Vitis rupestris

The viticulture industry needs advanced grape cultivars with genes that enhance disease resistance and environmental stress tolerance to meet the challenges of a changing climate. To discover beneficial allelic variants of grape genes, we established an F1 mapping population from a cross between two North American grapevines, Vitis rupestris Scheele and Vitis riparia Michx. We generated genotyping-by-sequencing (GBS) markers and constructed parental linkage maps consisting of 1177 and 1115 GBS markers, respectively (LOD threshold ≥ 14), which were validated by mapping the sex-determining locus to chromosome 2. Taking advantage of loci heterozygous in both parents, we also constructed an integrated map containing 2583 markers. We mapped a major quantitative trait locus (QTL) for downy mildew (Plasmopara viticola) resistance to chromosome 10 of V. rupestris using both greenhouse- and in vitro-generated leaf resistance data. This QTL explains 66.5% of the phenotypic variance under greenhouse conditions, and its 2-LOD confidence interval corresponds to region 2,470,297 to 3,024,940 bp on chromosome 10 in the Vitis vinifera L. PN40024 reference genome sequence (assembly 12X.v2). We provide PN40024-projected positions of the GBS markers, which can be used as anchors to develop additional markers for the introgression of this V. rupestris haplotype into cultivated grape varieties.