Identification of quantitative trait loci involved in R1-mediated resistance to powdery mildew and sex determination in hop (Humulus lupulus L.)

Authors: HAVILL, JOSHUA - University Of Minnesota; RICHARDSON, BRIANA - Oregon State University; ROHWER, CHARLIE - University Of Minnesota; Gent, David - Dave; Henning, John; MUEHLBAUER, GARY - University Of Minnesota

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/1/2023
Publication Date: 6/15/2023
Citation: Havill, J.S., Richardson, B.J., Rohwer, C.L., Gent, D.H., Henning, J.A., Muehlbauer, G.J. 2023. Identification of quantitative trait loci involved in R1-mediated resistance to powdery mildew and sex determination in hop (Humulus lupulus L.). Journal of Theoretical and Applied Genetics. 136. Article 154. https://doi.org/10.1007/s00122-023-04399-7.
DOI: https://doi.org/10.1007/s00122-023-04399-7

Interpretive Summary: Hop breeding typically involves selection for resistance to the disease powdery mildew and identification of the sex of plants since only female hop plants are produced commercially. Identification of DNA based molecular markers linked to the genes controlling powdery mildew resistance and sex would be useful to breeders and potential speed the development of new powdery mildew resistant varieties. In this research, we identified genetic loci associated with powdery mildew resistance referred to as R1. We identified a region on chromosome 4 that explained most of the variation in powdery mildew resistance in the progeny derived from a female plant that possess R1-based resistance and a powdery mildew susceptible male. We also identified markers associated with the sex of the progeny. Easily selected markers for the loci associated with these traits were developed and validated. The markers worked well in progeny in our cross, but were less predictive in other hop germplasm. The basic discoveries here should be helpful in future genetic and breeding contexts.

Technical Abstract: Hop (Humulus lupulus L.) is a dioecious species cultivated for the female inflorescence or cones, which impart bitterness, flavor and aroma to beer. Hop powdery mildew, caused by the obligate parasite Podosphaera macularis, is a major disease problem in many hop growing regions of the world. There are a diminishing number of effective resistance genes that are available to hop breeders due to the widespread emergence of highly-virulent pathogen strains in Europe and the Pacific Northwestern United States. Thus, identifying markers associated with the remaining effective resistance genes will facilitate pyramiding of these genes and preserve their utility. In addition, since female and male flowers are on separate plants, genetic markers associated with sex determination can be used to reduce the number of plants grown during the breeding process. The objectives of this study were to characterize the genetic basis of R1-mediated resistance present in the female hop cultivar Zenith, identify quantitative trait loci associated with R1-mediated resistance and biological sex, and develop molecular breeding tools for rapid marker-assisted selection of genotypes for R1-mediated resistance and biological sex. We constructed a genetic map using 1,339 single nucleotide polymorphisms (SNPs) based upon genotype-by-sequencing of 128 progeny derived from a Zenith x USDA 21058M F1 population. These SNPs were assigned to 10 linkage groups comprising a map length of 1,204.97 cM with an average of 0.94 cM between markers. One QTL, qHl_Chr4.PMR1, associated with powdery mildew resistance was identified on chromosome 4 that explained 57.2% of the variation for resistance. Another QTL, qHl_Chr3.SDR1, associated with biological sex was identified on chromosome 3 that explained 24.96% of the variation. To examine the effectiveness of these QTL for future breeding efforts, we developed markers associated with both QTL using Kompetitive allele-specific PCR (KASP) assays and assessed them against a panel of diverse germplasm. Our results showed that the KASP marker utility may be limited to specific populations that contain Zenith in their pedigree. The high-density map, along with the identified QTLs and associated KASP markers provide valuable genetic resources for selecting for biological sex during the breeding process and breeding for powdery mildew resistance in hop.