Genotyping-by-sequencing of a bi-parental mapping population segregating for downy mildew resistance in hop (Humulus lupulus L.)

Abstract

Downy mildew (caused by Pseudoperonospora humuli) causes significant losses in hop (Humulus lupulus L.) cone yield and quality, and potential crown death. Breeding for resistance has proved difficult presumably because of the highly quantitative nature of genetic control over expression. The objective of this study was to utilize multiple environments to ascertain downy mildew resistance and identify molecular markers linked to resistance. A widely segregating population, ‘Teamaker’ × USDA 21422M was inoculated and evaluated for downy mildew in field studies (Corvallis, OR and Yakima, WA) and a greenhouse study. Next generation sequencing using an Illumina HiSeq 2000 was performed on this population. Resulting reads were imported into UNEAK TASSEL 4.0 pipeline for processing and SNP-calls. Approximately 120,435 unfiltered SNP markers were identified and of these markers, 9081 high quality markers chosen for association analysis. Data analyses for field studies in OR and WA were performed separately using trait values averaged across blocks. Differential trait associated marker sets were identified across each physical environment with partial overlap between field environments. Mixed linear model analyses identified 39 markers (21 from OR, 10 from WA and eight overlapping) associated with response to downy mildew infection (p < 1 × 10−4). The most significant 17 markers were validated using high-resolution melting curve analysis and the resistant allele identified. Four SNP markers, along with the respective “resistant” alleles, were classified as highly selective for resistance (model adjusted R2 = 0.437). Multiplexing studies are underway to develop a simple PCR tool for selecting downy mildew resistance.