Extensive variation between chromosomes of North American and European hop

Article https://doi.org/10.1038/s41467-026-72379-8 Extensive variation between chromosomes of North American and European hop Received: 11 July 2025 Accepted: 15 April 2026 1234567890():,; 1234567890():,; Check for updates Sandip Mallikarjun Kale 1,15,16, Heidrun Gundlach2,16, Oliver Gericke 1,16, Nadia Kamal 2,3, Aldo Almeida 1, Nicholi Pitra 4, Nicholas Price4, Georg Haberer 2, Thomas Lux 2, Flavia Krsticevic1, Oliver Kemp 1, Louise de Bang 1, Axel Himmelbach 5, Sudharsan Padmarasu5, Mark-Timothy Rabanus-Wallace 5, Lucie Horáková 6, Václav Bačovský6, Kasper Nielsen 1, Nanna Bjarnholt 7,8, Nikola Micic 7,8, Isabella Kruse-Andersen 1,7, Birger Lindberg Møller 7,8, Christian Janfelt Birgitte Skadhauge 1, Paul D. Matthews4, Klaus F. X. Mayer2,10, Nils Stein Martin Mascher 5,12, Manuel Spannagl 2,13 , Alexander Feiner 14 & Ilka Braumann 1 9 , 5,11 , 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. Female plants of Humulus spp. L. (hop), member of the Cannabaceae family and sister to the genus Cannabis, have been cultivated for their cones (hops) since at least A.D. 859 when the practice of adding hops into beer developed in medieval Central Europe1. Hops contain α-acids that lend a characteristic bitter taste and, more importantly, made beer a durable food item suitable for transport and trade. After the mid-14th century, the demand for beer increased. It was preferred over water, as the latter was often polluted. Brewing became a professional craft and 1 Carlsberg Research Laboratory, Copenhagen, Denmark. 2Helmholtz Munich – German Research Center for Environmental Health, Plant Genome and Systems Biology (PGSB), Neuherberg, Germany. 3Technical University of Munich, TUM School of Life Sciences, Computational Plant Biology, Freising, Germany. 4Hopsteiner, S.S. Steiner, Inc, New York, NY, USA. 5Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany. 6Department of Plant Developmental Genetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czechia. 7Department of Plant and Environmental Sciences, Section for Plant Biochemistry, University of Copenhagen, Frederiksberg, Denmark. 8Department of Plant and Environmental Sciences, Copenhagen Plant Science Center, University of Copenhagen, Frederiksberg, Denmark. 9Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark. 10School of Life Sciences, Technical University Munich, Freising, Germany. 11Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany. 12German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany. 13Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Perth, WA, Australia. 14Hopsteiner, Simon H. Steiner, Hopfen, GmbH, Mainburg, Germany. 15Present address: Department of Agroecology, Aarhus University, Slagelse, Denmark. 16These authors contributed e-mail: ; ; equally: Sandip Mallikarjun Kale, Heidrun Gundlach, Oliver Gericke. Nature Communications | (2026)17:4110 1 Article subsequent municipal regulations like the Bavarian purity law (1516) limited beer ingredients to barley, water, and hops2. This shaped the conventional understanding of what is a beer and aided its rise to the most popular alcoholic beverage globally3 with $555 billion gross value-added contribution to global Gross Domestic Product4. The utility of hops however extends well beyond their role as a bittering agent, as they offer a plethora of highly valuable metabolites with diverse functionalities. These include flavor- and aromacontributing terpenes, natural preservatives (β-acids), and the antiinflammatory and anti-cancer prenylflavonoid xanthohumol5,6, along with its derivative 8-prenylnaringenin, the most potent phytoestrogen known7. Despite the obvious potential to broaden hop applications due to existing efficient fractionation technology, the absence of varieties with enhanced metabolite compositions for dual cropping limits hop use predominantly to beer production. These unmet breeding demands highlight the need for improved genetic resources to support hop improvement. The hop originally cultivated for brewing purposes was H. lupulus, a species native to Europe and parts of Asia. Beyond H. lupulus, the genus Humulus comprises the five additional perennial species H. cordifolius (Japan), H. neomexicanus (south and western North America), H. lupuloides (central and eastern North America), H. pubescens (midwestern North America), and H. yunnanensis (southcentral China), as well as one annual species, H. scandens (syn. H. japonicus, East Asia)8. The Asian-North American and European hop lineages separated more than a million years ago, likely in China9. After the introduction of European H. lupulus to North America in the 17th century, spontaneous hybrid offspring of European (Eu) and native North American (NAm) hop, termed “Cluster”, proved superior to Eu landraces in bittering compound content. Cluster varieties were widely cultivated and in the early 20th century imported into Europe10. With the establishment of the first scientific hop breeding program in the United Kingdom in 1904, breeders began to hybridize imported NAm with Eu germplasm. The first hybrid cultivars were released in 1934, 1939, and 194410. More recent work shows that wild NAm hops contain higher α-acid levels than Eu hops. However, α-acid content of NAm-Eu hybrid cultivars exceeds that of wild hops of either origin by far11. Consequently, although traditional Eu landraces remain valued for their distinct and traditional aromas, most current cultivars are monoploid hybrids of Eu and NAm hop or their descendants. Still, current draft hop genome assemblies12–14 leave the impact of this interspecific breeding strategy on genome structure largely imperceptible, because they lack phasing and haplotype resolution and miss information on species ancestry for regions associated with beneficial traits. Assembling reference-quality, phased haplotype-resolved assemblies of complex plant genomes, such as the highly heterozygous dioecious hop genome (haploid genome size:~2.5 Gb, ♀ 2n = (...truncated)