Precision QTL mapping of downy mildew resistance in hop (Humulus lupulus L.)

Hop downy mildew (DM) is an obligate parasite causing severe losses in hop if not controlled. Resistance to this pathogen is a primary goal for hop breeding programs. The objective of this study was to identify QTLs linked to DM resistance. Next-generation-sequencing was performed on a mapping population segregating for DM resistance levels. Cloned plants were grown in a RCBD with three replicates under three environments: greenhouse (GH), field plots in Oregon (OR), Corvallis field plots in Washington (WA), Yakima). The linkage map of 3,341 SNP markers was determined with a four-stage process using Rqtl, TMAP, Joinmap v 4.0 and MERGEMAP. QTL analysis was performed using JMP Genomics and TASSEL 5.0. SNP markers were distributed across 11 linkage groups (LGs) with an average distance between markers of 0.2 cM and total distance of 745.9 cM. QTLs for all three environments were identified using multiple interval mapping. Overall heritability across the three environments varied from h(2) = 0.38 (GH) to 0.57 (OR). A total of 22 QTLs across 8 LG were identified for DM resistance: 5 identified from OR field data, 12 using WA data and five from GH DM data. No epistasis was observed. This study points out the complexity of genetic control of DM resistance in hop and identifies several markers that can be potentially be used to select for DM resistance in hop. It also provides the first linkage map suitable for genome sequencing due to the high density of SNP markers.