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.