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

Authors: Henning, John; WISEMAN, MICHELE - Oregon State University; Gent, David; PADGITT-COBB, LILLIAN - Salk Institute; APPIAH-KUBI, REGINALD - Oregon State University; HENDRIX, DAVID - Oregon State University

Submitted to: Journal of Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/18/2024
Publication Date: 7/31/2024
Citation: Henning, J.A., Wiseman, M.S., Gent, D.H., Padgitt-Cobb, L., Appiah-Kubi, R., Hendrix, D.A. 2024. Genetic mapping and QTL analysis of multi-genic resistance to powdery mildew (Podosphaera macularis) in hop (Humulus lupulus L.). Journal of Genetics and Genomics. https://doi.org/10.1002/csc2.21310.
DOI: https://doi.org/10.1002/csc2.21310

Interpretive Summary: Hop powdery mildew (Podosphaera macularis) causes substantial losses if left uncontrolled. Most resistant hop cultivars are thought to possess qualitative resistance based upon single R-genes. However, R-gene resistance breaks down rapidly under intensive production. One cultivar, ‘Comet’, has uncharacterized resistance that may be polygenic and resistant to pathogen breakdown. Plant resistance in Comet appears to be controlled by a single region on chromosome 6 covering 6 Mb of DNA. Approximately 140 genes with 27 plant R-genes found in nine clusters were found in this region. Eight additional unique genes with different plant resistance mechanisms were also observed in this region along with transcription regulator genes and stress response genes This combination of R-gene clusters, sulfur-rich proteins, endo-1,3-beta-glucosidase and stress-response genes may be responsible for polygenic resistance to powdery mildew in the cultivar Comet.

Technical Abstract: Hop powdery mildew (Podosphaera macularis) causes substantial losses if left uncontrolled. Most resistant hop cultivars possess qualitative resistance based upon R-genes. One cultivar, ‘Comet’, has uncharacterized resistance that may be polygenic. This study focused on identifying genomic regions controlling powdery mildew 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 loci (QTL) analysis using either composite interval mapping or stepwise regression analyses were used to identify QTL. 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 proteins genes with homology to patatins, thionins, agglutinin were identified in two clusters. Two glucan-endo-1,3-beta-glucosidase genes were identified bordering different R-gene clusters. Finally, putative up-regulators of transcription and stress-response genes were identified. The combination of R-gene clusters, sulfur-rich proteins, endo-1,3-beta-glucosidase and stress-response genes may be responsible for resistance to powdery mildew in the cultivar Comet.