Genetic mapping and QTL analysis of multigenic resistance to powdery mildew (Podosphaera macularis) in hop (Humulus lupulus L.)

Hop powdery mildew (PM) (Podosphaera macularis) causes substantial losses if left uncontrolled. Most resistant hop cultivars possess qualitative resistance based on R-genes. One cultivar, Comet, has uncharacterized resistance that may be polygenic. This study focused on identifying genomic regions controlling PM resistance in Comet and ascertaining putative genetic mechanisms behind such resistance. A cross between Comet and susceptible male, USDA 64035M, was made. Offspring were screened for resistance under greenhouse conditions and genotyped using genotyping-by-sequencing. Genome-wide analysis using mixed linear model analysis along with quantitative trait locus (QTL) analysis using either composite interval mapping or stepwise regression analyses was performed to identify QTLs. All analyses identified a region on chromosome 6 covering positions 308–314 Mb on the physical map. Analysis of the putative genes within this region identified 140 genes with 27 plant resistance-like genes found in nine clusters. Six sulfur-rich protein genes with homology to patatins, thionins, and agglutinins were identified in two clusters. Two glucan-endo-1,3-beta-glucosidase genes were identified bordering different R-gene clusters. Finally, putative upregulators of transcription and stress-response genes were identified. The 10 most highly associated single-nucleotide polymorphisms for PM resistance were subsequently developed as KASP markers. The combination of R-gene clusters, sulfur-rich proteins, endo-1,3-beta-glucosidase genes, and stress-response genes may be responsible for resistance to PM in the cultivar Comet.