Structural variation in the pangenome of wild and domesticated barley

• 成果类型: Article
• 署名作者: Jayakodi, Murukarthick; Lu, Qiongxian; Pidon, Helene; Rabanus-Wallace, M. Timothy; Bayer, Micha; Lux, Thomas; Guo, Yu; Jaegle, Benjamin; Badea, Ana; Bekele, Wubishet; Brar, Gurcharn S.; Braune, Katarzyna; Bunk, Boyke; Chalmers, Kenneth J.; Chapman, Brett; Jorgensen, Morten Egevang; Feng, Jia-Wu; Feser, Manuel; Fiebig, Anne; Gundlach, Heidrun; Guo, Wenbin; Haberer, Georg; Hansson, Mats; Himmelbach, Axel; Hoffie, Iris; Hoffie, Robert E.; Hu, Haifei; Isobe, Sachiko; Koenig, Patrick; Kale, Sandip M.; Kamal, Nadia; Keeble-Gagnere, Gabriel; Keller, Beat; Knauft, Manuela; Koppolu, Ravi; Krattinger, Simon G.; Kumlehn, Jochen; Langridge, Peter; Li, Chengdao; Marone, Marina P.; Maurer, Andreas; Mayer, Klaus F. X.; Melzer, Michael; Muehlbauer, Gary J.; Murozuka, Emiko; Padmarasu, Sudharsan; Perovic, Dragan; Pillen, Klaus; Pin, Pierre A.; Pozniak, Curtis J.; Ramsay, Luke; Pedas, Pai Rosager; Rutten, Twan; Sakuma, Shun; Sato, Kazuhiro; Schueler, Danuta; Schmutzer, Thomas; Scholz, Uwe; Schreiber, Miriam; Shirasawa, Kenta; Simpson, Craig; Skadhauge, Birgitte; Spannagl, Manuel; Steffenson, Brian J.; Thomsen, Hanne C.; Tibbits, Josquin F.; Nielsen, Martin Toft Simmelsgaard; Trautewig, Corinna; Vequaud, Dominique; Voss, Cynthia; Wang, Penghao; Waugh, Robbie; Westcott, Sharon; Rasmussen, Magnus Wohlfahrt; Zhang, Runxuan; Zhang, Xiao-Qi; Wicker, Thomas; Dockter, Christoph; Mascher, Martin; Stein, Nils
• 署名单位: Leibniz Institut fur Pflanzengenetik und Kulturpflanzenforschung; Institut Agro; INRAE; Centre National de la Recherche Scientifique (CNRS); Universite de Montpellier; James Hutton Institute; Helmholtz Association; Helmholtz-Center Munich - German Research Center for Environmental Health; University of Zurich; Agriculture & Agri Food Canada; Agriculture & Agri Food Canada; University of British Columbia; Leibniz Association; Leibniz Institut fur Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ); University of Adelaide; Murdoch University; Western Crop Genetics Alliance; Lund University; Guangdong Academy of Agricultural Sciences; Kazusa DNA Research Institute; La Trobe University; King Abdullah University of Science & Technology; Department of Primary Industries & Regional Development NSW; Yangtze University; Martin Luther University Halle Wittenberg; Technical University of Munich; University of Minnesota System; University of Minnesota Twin Cities; Julius Kuhn-Institut; University of Saskatchewan; University of Saskatchewan; Tottori University; Okayama University; University of Minnesota System; University of Minnesota Twin Cities; University of Dundee; German Research Foundation (DFG); German Centre for Integrative Biodiversity Research (iDiv); University of Alberta; Aarhus University
• 刊物名称: Nature
• ISSN/ISSBN: 0028-5641
• DOI: 10.1038/s41586-024-08187-1
• 发表日期: 2024-12-19
• 关键词: mildew resistance locus; inflorescence architecture; molecular-biology; size variation; gene; rna; annotation; prediction; EVOLUTION; Mutation

摘要

Pangenomes are collections of annotated genome sequences of multiple individuals of a species1. The structural variants uncovered by these datasets are a major asset to genetic analysis in crop plants2. Here we report a pangenome of barley comprising long-read sequence assemblies of 76 wild and domesticated genomes and short-read sequence data of 1,315 genotypes. An expanded catalogue of sequence variation in the crop includes structurally complex loci that are rich in gene copy number variation. To demonstrate the utility of the pangenome, we focus on four loci involved in disease resistance, plant architecture, nutrient release and trichome development. Novel allelic variation at a powdery mildew resistance locus and population-specific copy number gains in a regulator of vegetative branching were found. Expansion of a family of starch-cleaving enzymes in elite malting barleys was linked to shifts in enzymatic activity in micro-malting trials. Deletion of an enhancer motif is likely to change the developmental trajectory of the hairy appendages on barley grains. Our findings indicate that allelic diversity at structurally complex loci may have helped crop plants to adapt to new selective regimes in agricultural ecosystems.