Structural variation in the pangenome of wild and domesticated barley

Pangenomes are collections of annotated genome sequences of multiple individuals of a species<sup>1</sup>. The structural variants uncovered by these datasets are a major asset to genetic analysis in crop plants<sup>2</sup>. 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.

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Publication Details

Journal
Nature
Published
2024-11-13
DOI
https://doi.org/10.1038/s41586-024-08187-1
Citations
102
Primary Topic
Wheat and Barley Genetics and Pathology
Type
article
Field-Weighted Citation Impact
61.16

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article

Structural variation in the pangenome of wild and domesticated barley

Jia‐Wu Feng, Peter Langridge, Curtis Jerry Pozniak, Klaus Pillen et al.
102 citations
Nature
Wheat and Barley Genetics and Pathology
61.16
article

Structural variation in the pangenome of wild and domesticated barley

Jia‐Wu Feng, Peter Langridge, Curtis Jerry Pozniak, Klaus Pillen, Thomas Wicker, Luke Ramsay, Murukarthick Jayakodi, Marina Püpke Marone, Mats Hansson, Andreas Maurer, Jochen Kumlehn, Cynthia Voss, Thomas Schmutzer, Penghao Wang, K. J. Chalmers, M. Timothy Rabanus‐Wallace, Martin Toft Simmelsgaard Nielsen, Danuta Schüler, Brett Chapman, Miriam Schreiber, Heidrun Gundlach, Martin Mascher, Robert E. Hoffie, Manuel Feser, Thomas Lux, Haifei Hu, Benjamin Jaegle, Gary J. Muehlbauer, Micha Bayer, Iris Hoffie, Ana Badea, Patrick König, Manuela Knauft, Sharon Westcott, Craig G. Simpson, Josquin Tibbits, Michael Melzer, Qiongxian Lu, Birgitte Skadhauge, Klaus Mayer, Nils Stein, Ravi Koppolu, Shun Sakuma, Hélène Pidon, Christoph Dockter, Twan Rutten, Dragan Perović, Uwe Scholz, Simon G. Krattinger, Georg Haberer, Hanne Cecilie Thomsen, Gabriel Keeble‐Gagnère, Pierre A. Pin, Anne Fiebig, Corinna Trautewig, Chengdao Li, Boyke Bunk, Nadia Kamal, Yu Guo, Sachiko Isobe, Pai Pedas, Kenta Shirasawa, Sudharsan Padmarasu, Beat Keller, Wubishet A. Bekele, Gurcharn S. Brar, Dominique Vequaud, Robbie Waugh, Kazuhiro Sato, Magnus Wohlfahrt Rasmussen, Emiko Murozuka, Sandip M. Kale, Runxuan Zhang, Axel Himmelbach, Wenbin Guo, M. Spannagl, Morten Egevang Jørgensen, Brian J. Steffenson, Katarzyna Braune, Xiao‐Qi Zhang
article en
102 citations

Abstract

Pangenomes are collections of annotated genome sequences of multiple individuals of a species<sup>1</sup>. The structural variants uncovered by these datasets are a major asset to genetic analysis in crop plants<sup>2</sup>. 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.

NatureVol. 636(8043)
Centre National de la Recherche Scientifique (FR), University of Minnesota (US), Julius Kühn-Institut (DE), Agriculture and Agri-Food Canada (CA), University of British Columbia (CA), University of Alberta (CA), James Hutton Institute (GB), Okayama University (JP), Texas A&M University System (US), Murdoch University (AU), University of Dundee (GB), Yangtze University (CN), Lund University (SE), La Trobe University (AU), Université de Montpellier (FR), University of Zurich (CH), Aarhus University (DK), Institut Agro Montpellier (FR), Government of Western Australia (AU), Carlsberg Laboratory (DK), German Centre for Integrative Biodiversity Research (DE), Helmholtz Zentrum München (DE), Weihenstephan-Triesdorf University of Applied Sciences (DE), University of Saskatchewan (CA), Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR), Rice Research Institute (CN), Carlsberg Group (Denmark) (DK), Guangdong Academy of Agricultural Sciences (CN), Agriculture Victoria (AU), Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) (DE), Kazusa DNA Research Institute (JP), Institut des Sciences des Plantes de Montpellier (FR), Ottawa Research and Development Centre, Brandon Research and Development Centre, Tottori University (JP), The University of Adelaide (AU), Martin Luther University Halle-Wittenberg (DE), King Abdullah University of Science and Technology (SA), Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures (DE)
Biotechnology and Biological Sciences Research Council
Zero hunger
Openalex Percentile: Top 0%
Wheat and Barley Genetics and Pathology
61.16
DOIOpen Access PDFOpenAlex
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