Hop ( Humulus lupulus L.) breeding programs seek to exploit genetic resources for bitter flavor, aroma, and disease resistance. However, these efforts have been thwarted by segregation distortion including female‐biased sex ratios. To better understand the transmission genetics of hop, we genotyped 4512 worldwide accessions of hop, including cultivars, landraces, and over 100 wild accessions using a genotyping‐by‐sequencing (GBS) approach. From the resulting ∼1.2 million single‐nucleotide polymorphisms (SNPs), prequalified GBS markers were validated by inferences in population structures and phylogeny. Analysis of pseudo‐testcross (Pt) mapping data from F ₁ families revealed mixed patterns of Mendelian and non‐Mendelian segregation. Three‐dimensional (3D) cytogenetic analysis of late meiotic prophase nuclei from two wild and two cultivated hop revealed conspicuous and prevalent occurrences of multiple, atypical, nondisomic chromosome complexes including autosomes. We used genome‐wide association studies (GWAS) and fixation index (F _st ) analysis to demonstrate selection mapping of genetic loci for key traits including sex, bitter acids, and drought tolerance. Among the possible mechanisms underlying the observed segregation distortion from the genomic data analysis, the cytogenetic analysis points to meiotic chromosome behavior as one of the contributing factors. The findings shed light on long‐standing questions on the unusual transmission genetics and phenotypic variation in hop, with major implications for breeding, cultivation, and the natural history of Humulus .

Hop (Humulus lupulus L.) is an important crop worldwide, known as the main flavoring ingredient in beer. The diversifying brewing industry demands variation in flavors, superior process properties, and sustainable agronomics, which are the focus of advanced molecular breeding efforts in hops. Hop breeders have been limited in their ability to create strains with desirable traits, however, because of the unusual and unpredictable inheritance patterns and associated non-Mendelian genetic marker segregation. Cytogenetic analysis of meiotic chromosome behavior has also revealed conspicuous and prevalent occurrences of multiple, atypical, non-disomic chromosome complexes, including those involving autosomes in late prophase. To explore the role of meiosis in segregation distortion, we undertook 3D cytogenetic analysis of hop pollen mother cells stained with DAPI and FISH. We used telomere FISH to demonstrate that hop exhibits a normal telomere clustering bouquet. We also identified and characterized a new sub-terminal 180 bp satellite DNA tandem repeat family called HSR0, located proximal to telomeres. Highly variable 5S rDNA FISH patterns within and between plants, together with the detection of anaphase chromosome bridges, reflect extensive departures from normal disomic signal composition and distribution. Subsequent FACS analysis revealed variable DNA content in a cultivated pedigree. Together, these findings implicate multiple phenomena, including aneuploidy, segmental aneuploidy, or chromosome rearrangements, as contributing factors to segregation distortion in hop.

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.

Hop (Humulus lupulusL.) is known for its use as a bittering agent in beer and has a rich history of cultivation, beginning in Europe and now spanning the globe. There are five wild varieties worldwide, which may have been introgressed with cultivated varieties. As a dioecious species, its obligate outcrossing, non-Mendelian inheritance, and genomic structural variability have confounded directed breeding efforts. Consequently, understanding genome evolution in Humulus represents a considerable challenge, requiring additional resources, including integrated genome maps. In order to facilitate cytogenetic investigations into the transmission genetics of hop, we report here the identification and characterization of 17 new and distinct tandem repeat sequence families. A tandem repeat discovery pipeline was developed using k-mer filtering and dot plot analysis of PacBio long-read sequences from the hop cultivar Apollo. We produced oligonucleotide FISH probes from conserved regions of HuluTR120 and HulTR225 and demonstrated their utility to stain meiotic chromosomes from wild hop, var. neomexicanus. The HuluTR225 FISH probe hybridized to several loci per nucleus and exhibited irregular, non-Mendelian transmission in male meiocytes of wild hop. Collectively, these tandem repeat sequence families not only represent unique and valuable new cytogenetic reagents but also have the capacity to inform genome assembly efforts and support comparative genomic analyses.