Structural variation in the pangenome of wild and domesticated barley

Murukarthick Jayakodi, Qiongxian Lu, Hélène Pidon, M. Timothy Rabanus-Wallace, Micha Bayer, Thomas Lux, Yu Guo, Benjamin Jaegle, Ana Badea, Wubishet Bekele, Gurcharn S. Brar, Katarzyna Braune, Boyke Bunk, Kenneth J. Chalmers, Brett Chapman, Morten Egevang Jørgensen, Jia-Wu Feng, Manuel Feser, Anne Fiebig, Heidrun Gundlach, Wenbin Guo, Georg Haberer, Mats Hansson, Axel Himmelbach, Iris Hoffie, Robert E. Hoffie, Haifei Hu, Sachiko Isobe, Patrick König, Sandip M. Kale, Nadia Kamal, Gabriel Keeble-Gagnère, Beat Keller, Manuela Knauft, Ravi Koppolu, Simon G. Krattinger, Jochen Kumlehn, Peter Langridge, Chengdao Li, Marina P. Marone, Andreas Maurer, Klaus F. X. Mayer, Michael Melzer, Gary J. Muehlbauer, Emiko Murozuka, Sudharsan Padmarasu, Dragan Perovic, Klaus Pillen, Pierre A. Pin, Curtis J. Pozniak, Luke Ramsay, Pai Rosager Pedas, Twan Rutten, Shun Sakuma, Kazuhiro Sato, Danuta Schüler, Thomas Schmutzer, Uwe Scholz, Miriam Schreiber, Kenta Shirasawa, Craig Simpson, Birgitte Skadhauge, Manuel Spannagl, Brian J. Steffenson, Hanne C. Thomsen, Josquin F. Tibbits, Martin Toft Simmelsgaard Nielsen, Corinna Trautewig, Dominique Vequaud, Cynthia Voss, Penghao Wang, Robbie Waugh, Sharon Westcott, Magnus Wohlfahrt Rasmussen, Runxuan Zhang, Xiao-Qi Zhang, Thomas Wicker (), Christoph Dockter (), Martin Mascher () and Nils Stein ()
Additional contact information
Murukarthick Jayakodi: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Qiongxian Lu: Carlsberg Research Laboratory
Hélène Pidon: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
M. Timothy Rabanus-Wallace: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Micha Bayer: The James Hutton Institute
Thomas Lux: Helmholtz Center Munich–German Research Center for Environmental Health
Yu Guo: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Benjamin Jaegle: University of Zurich
Ana Badea: Agriculture et Agri-Food Canada
Wubishet Bekele: Agriculture et Agri-Food Canada
Gurcharn S. Brar: The University of British Columbia
Katarzyna Braune: Carlsberg Research Laboratory
Boyke Bunk: DSMZ–German Collection of Microorganisms and Cell Cultures GmbH
Kenneth J. Chalmers: University of Adelaide
Brett Chapman: Murdoch University
Morten Egevang Jørgensen: Carlsberg Research Laboratory
Jia-Wu Feng: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Manuel Feser: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Anne Fiebig: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Heidrun Gundlach: Helmholtz Center Munich–German Research Center for Environmental Health
Wenbin Guo: The James Hutton Institute
Georg Haberer: Helmholtz Center Munich–German Research Center for Environmental Health
Mats Hansson: Lund University
Axel Himmelbach: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Iris Hoffie: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Robert E. Hoffie: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Haifei Hu: Murdoch University
Sachiko Isobe: Kazusa DNA Research Institute
Patrick König: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Sandip M. Kale: Carlsberg Research Laboratory
Nadia Kamal: Helmholtz Center Munich–German Research Center for Environmental Health
Gabriel Keeble-Gagnère: La Trobe University
Beat Keller: University of Zurich
Manuela Knauft: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Ravi Koppolu: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Simon G. Krattinger: King Abdullah University of Science and Technology (KAUST)
Jochen Kumlehn: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Peter Langridge: University of Adelaide
Chengdao Li: Murdoch University
Marina P. Marone: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Andreas Maurer: Martin Luther University Halle-Wittenberg
Klaus F. X. Mayer: Helmholtz Center Munich–German Research Center for Environmental Health
Michael Melzer: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Gary J. Muehlbauer: University of Minnesota
Emiko Murozuka: Carlsberg Research Laboratory
Sudharsan Padmarasu: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Dragan Perovic: Federal Research Centre for Cultivated Plants
Klaus Pillen: Martin Luther University Halle-Wittenberg
Pierre A. Pin: SECOBRA Recherches
Curtis J. Pozniak: University of Saskatchewan
Luke Ramsay: The James Hutton Institute
Pai Rosager Pedas: Carlsberg Research Laboratory
Twan Rutten: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Shun Sakuma: Tottori University
Kazuhiro Sato: Kazusa DNA Research Institute
Danuta Schüler: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Thomas Schmutzer: Martin Luther University Halle-Wittenberg
Uwe Scholz: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Miriam Schreiber: The James Hutton Institute
Kenta Shirasawa: Kazusa DNA Research Institute
Craig Simpson: The James Hutton Institute
Birgitte Skadhauge: Carlsberg Research Laboratory
Manuel Spannagl: Helmholtz Center Munich–German Research Center for Environmental Health
Brian J. Steffenson: University of Minnesota
Hanne C. Thomsen: Carlsberg Research Laboratory
Josquin F. Tibbits: La Trobe University
Martin Toft Simmelsgaard Nielsen: Carlsberg Research Laboratory
Corinna Trautewig: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Dominique Vequaud: SECOBRA Recherches
Cynthia Voss: Carlsberg Research Laboratory
Penghao Wang: Murdoch University
Robbie Waugh: The James Hutton Institute
Sharon Westcott: Murdoch University
Magnus Wohlfahrt Rasmussen: Carlsberg Research Laboratory
Runxuan Zhang: The James Hutton Institute
Xiao-Qi Zhang: Murdoch University
Thomas Wicker: University of Zurich
Christoph Dockter: Carlsberg Research Laboratory
Martin Mascher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Nils Stein: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben

Nature, 2024, vol. 636, issue 8043, 654-662

Abstract: Abstract 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.

Date: 2024
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DOI: 10.1038/s41586-024-08187-1

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