title: Molecular marker assisted resistance breeding in UK hop
Creators: name: Hajdu, Klara
Publisher: name: University of Reading
Year: 2026

description: The flower of the female European hop plant (Humulus lupulus var. lupulus) is one of the four principal 
ingredients that makes the world’s most consumed alcoholic beverage, beer. Beer drinking trends have 
transformed over time and so has the purpose of hop addition in beer. Hops were initially used to 
preserve beer, however in the past decades, hops have become a source of interesting new flavours and 
aromas that contribute to a wholesome tasting experience. This emphasis on a broad palate of distinct 
flavours drives the global craft beer market and hop breeding goals today. Beside the development hop 
aromas, breeding programmes simultaneously consider the improvement of a number of important 
characteristics such as yield, growing habit, alpha acid content and resistance to pests and diseases
however resistance breeding is broadly recognized as one of the primary objectives due to the high 
economic impact of disease on plant development and yield. Pest and disease resistance genes exist in
UK germplasm, however resistance breeding is a lengthy process which is currently achieved through 
classical breeding approaches, where characterisation of desirable traits is conducted exclusively 
through means of labour and time-consuming phenotyping. In current hop breeding, artificial infection 
assays are used to screen for resistance to three major hop diseases: powdery mildew (PM), downy
mildew (DM) and Verticillium wilt (VW) at different stages of the breeding programme. Hop breeders 
could leverage molecular markers to bypass the phenotype-based selection methods. Simple, low-cost 
laboratory tests on young hop seedlings would decouple the need for extensive phenotyping from the 
ability to confirm disease resistance/susceptibility status of breeding lines. With the rise of high 
throughput, cost effective next generation sequencing techniques and genome-assisted approaches are 
becoming more achievable in breeding programmes. This project establishes novel resources for the 
UK hop breeding programme via whole genome re-sequencing and genetic mapping of disease 
resistance traits to assess the prospects of implementing marker assisted breeding techniques in the 
UK’s national hop breeding programme. A bi-parental mapping population segregating for disease 
resistances between the significant female progenitor ‘Pilgrim’ with resistances to VW, PM and DM 
and a disease susceptible male breeding line ‘316/1/10’ was established for this study. The mapping 
population and parental genotypes were screened for PM R2 resistance. In total, parents and 171 
individuals from the mapping population were genotyped with high-throughput DArT sequencing 
technology. An initial set of 9,562 DArT-SNP markers were refined to 1,395 segregating markers 
providing high-quality markers for QTL analysis and linkage map construction. A Maximum 
Likelihood Method (MLM) was used to generate two integrated linkage maps with and without the 
inclusion of markers with significant distortion from expected Mendelian segregation ratios. The 
comparison of the “non-distorted” and “distorted” maps provided useful insights into possible 
chromosomal translocation patterns in hop. Kruskal-Wallis mapping of powdery mildew R2 resistance 
identified two DArT SNPs that were significantly associated with PM resistance. These co-localised on 
the same linkage group within our linkage map and on Scaffold 77 of the ‘Cascade’ reference genome 
near a cluster of putative resistance genes. Whole genome re-sequencing and genome wide variant 
calling of the two parental genotypes revealed an additional 2.8 M polymorphic SNPs which were 
filtered for further segregating polymorphisms in the region of putative powdery mildew resistance 
genes. A total of 25 parental SNPs markers were found to segregate in the QTL region between parental 
lines. These 25 SNPs, together with the two powdery mildew associated DArT SNPs, were converted 
into bi-allelic KASP genotyping markers for future fine mapping and validation of PM resistance. This 
work provides a foundation to characterise the genetic background of pathogen resistances, and for the 
development of transferrable molecular breeding tools into UK hop. Furthermore, the data generated 
here, will contribute towards future QTL mapping and genomic selection studies in hop and will form 
an important part of future analyses in the UK’s hop breeding programme.