Downy mildew in hop (Humulus lupulus L.) is caused by Pseudoperonospora humuli and generates significant losses in quality and yield. To identify the biochemical processes that confer natural downy mildew resistance (DMR), a metabolome‐ and genome‐wide association study was performed. Inoculation of a high density genotyped F1 hop population (n = 192) with the obligate biotrophic oomycete P. humuli led to variation in both the levels of thousands of specialized metabolites and DMR. We observed that metabolites of almost all major phytochemical classes were induced 48 hr after inoculation. But only a small number of metabolites were found to be correlated with DMR and these were enriched with phenylpropanoids. These metabolites were also correlated with DMR when measured from the non‐infected control set. A genome‐wide association study revealed co‐localization of the major DMR loci and the phenylpropanoid pathway markers indicating that the major contribution to resistance is mediated by these metabolites in a heritable manner. The application of three putative prophylactic phenylpropanoids led to a reduced degree of leaf infection in susceptible genotypes, confirming their protective activity either directly or as precursors of active compounds.

Hop is an essential ingredient in brewing, providing beer with its characteristic bitterness and aroma. Most modern hop cultivars are hybrids between European and North American hop lineages, but how these ancestries contribute to bitter acid content, the most important trait in hop breeding, remains unclear. Here, we report chromosome-scale, haplotype-resolved assemblies of the hybrid hop cultivar Apollo, assign European and North American ancestry across the genome, and identify varying levels of recombination suppression between chromosomes of either origin. Using this reference, we uncover genetic and chemical diversity in core bittering pathways between European and North American hops. We further show additive effects of beneficial European and North American alleles on bitter acid content, providing a foundation for genomics-assisted hop breeding.

Verticillium wilt of hop (Humulus lupulus L.), caused by the soil-borne pathogen Verticillium nonalfalfae, is a devastating disease with no effective chemical control. In European hop-growing regions, breeding resistant cultivars is the most effective strategy. The lack of response differences in earlier studies suggests constitutive resistance. We therefore conducted a genome-wide association study (GWAS) using a phased hop genome assembly to improve detection of Verticillium resistance loci. A bi-parental population of 142 genotypes, derived from a cross between resistant Wye Target and susceptible BL2/1, was phenotyped for Verticillium wilt resistance and genotyped by sequencing. Association analyses with five statistical models (MLM in TASSEL 5, MLM, MLMM, FarmCPU and BLINK in GAPIT) did not identify any significant SNPs; however, several candidate loci were identified using exploratory threshold, particularly in the phase 2 genome assembly, including a wall-associated kinase (WAK) consistently detected across both genome phases and all models. GWAS results were further assessed with a Random Forest model, which identified SNPs of high feature importance and showed adequate predictive power (accuracy ≈ 0.4, correlation ≈ 0.8) for preliminary breeding screening. These findings provide an initial set of candidate markers and exploratory prediction models for Verticillium wilt resistance in hop, representing a valuable genomic resource for future marker-assisted selection and breeding strategies.