Abstract/Summary

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.