A pangenome and pantranscriptome of hexaploid oat

Oat grain is a traditional human food that is rich in dietary fibre and contributes to improved human health<sup>1,2</sup>. Interest in the crop has surged in recent years owing to its use as the basis for plant-based milk analogues<sup>3</sup>. Oat is an allohexaploid with a large, repeat-rich genome that was shaped by subgenome exchanges over evolutionary timescales<sup>4</sup>. In contrast to many other cereal species, genomic research in oat is still at an early stage, and surveys of structural genome diversity and gene expression variability are scarce. Here we present annotated chromosome-scale sequence assemblies of 33 wild and domesticated oat lines, along with an atlas of gene expression across 6 tissues of different developmental stages in 23 of these lines. We construct an atlas of gene-expression diversity across subgenomes, accessions and tissues. Gene loss in the hexaploid is accompanied by compensatory upregulation of the remaining homeologues, but this process is constrained by subgenome divergence. Chromosomal rearrangements have substantially affected recent oat breeding. A large pericentric inversion associated with early flowering explains distorted segregation on chromosome 7D and a homeologous sequence exchange between chromosomes 2A and 2C in a semi-dwarf mutant has risen to prominence in Australian elite varieties. The oat pangenome will promote the adoption of genomic approaches to understanding the evolution and adaptation of domesticated oats and will accelerate their improvement.

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Publication Details

Journal
Nature
Published
2025-10-29
DOI
https://doi.org/10.1038/s41586-025-09676-7
Citations
5
Primary Topic
Wheat and Barley Genetics and Pathology
Type
article
Field-Weighted Citation Impact
8.75
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article

A pangenome and pantranscriptome of hexaploid oat

Peter J. Maughan, Petri Auvinen, Yutang Chen, Rajeev Gupta et al.
5 citations
Nature
Wheat and Barley Genetics and Pathology
8.75
article

A pangenome and pantranscriptome of hexaploid oat

Peter J. Maughan, Petri Auvinen, Yutang Chen, Rajeev Gupta, Axel Himmelbach, Lidija Bitz, Tefera Tolera Angessa, Sean Walkowiak, Matthias Heinrich Herrmann, Eric N. Jellen, Kathy Esvelt Klos, Nicholas A. Tinker, Penghao Wang, Sofia Marmon, Edyta Paczos-Grzęda, Francisco J. Canales, Brett Chapman, Heidrun Gundlach, Martin Mascher, Taner Z. Sen, Thomas Lux, Haifei Hu, Craig H. Carlson, Steve Michel, Vanda Marosi, Samara Mireza Correia De Lemos, Viet Dang, Bruno Studer, Jessica A. Schlueter, Julio Isidro y Sánchez, Alan H. Schulman, Manuela Knauft, Nick Sirijovski, Jean‐Luc Jannink, Klaus Mayer, Sirja Viitala, Nils Stein, Brian Boyle, Yong Jia, Yong‐Bi Fu, Steven R. Eichten, Weikai Yan, Georg Haberer, Asher Pasha, Gaofeng Zhou, Anne Fiebig, Jason D. Fiedler, Asuka Itaya, Chengdao Li, Nadia Kamal, Mehtab Singh, Harmeet Singh Chawla, Charlene P. Wight, Dario Copetti, Tim Langdon, Wubishet A. Bekele, Robert W. Reid, Eric Yao, Elena Prats, Tianhua He, Kirby T. Nilsen, Nicholas J. Provart, Raja Sekhar Nandety, M. Spannagl, Raz Avni, Amit Fenn, Xiaoqi Zhang, Catherine J. Howarth, Jaswinder Singh, Zhou Zhou, Amanda J. Waters, Adriana Ravagnani, Rajvinder Kaur, Oliver Bitz, Shauna Vronces
article en
5 citations

Abstract

Oat grain is a traditional human food that is rich in dietary fibre and contributes to improved human health<sup>1,2</sup>. Interest in the crop has surged in recent years owing to its use as the basis for plant-based milk analogues<sup>3</sup>. Oat is an allohexaploid with a large, repeat-rich genome that was shaped by subgenome exchanges over evolutionary timescales<sup>4</sup>. In contrast to many other cereal species, genomic research in oat is still at an early stage, and surveys of structural genome diversity and gene expression variability are scarce. Here we present annotated chromosome-scale sequence assemblies of 33 wild and domesticated oat lines, along with an atlas of gene expression across 6 tissues of different developmental stages in 23 of these lines. We construct an atlas of gene-expression diversity across subgenomes, accessions and tissues. Gene loss in the hexaploid is accompanied by compensatory upregulation of the remaining homeologues, but this process is constrained by subgenome divergence. Chromosomal rearrangements have substantially affected recent oat breeding. A large pericentric inversion associated with early flowering explains distorted segregation on chromosome 7D and a homeologous sequence exchange between chromosomes 2A and 2C in a semi-dwarf mutant has risen to prominence in Australian elite varieties. The oat pangenome will promote the adoption of genomic approaches to understanding the evolution and adaptation of domesticated oats and will accelerate their improvement.

NatureVol. 649(8095)
Brigham Young University (US), University of North Carolina at Charlotte (US), PepsiCo (United Kingdom) (GB), Agricultural Research Service (US), Julius Kühn-Institut (DE), Agriculture and Agri-Food Canada (CA), University of Helsinki (FI), University of Arizona (US), University of Life Sciences in Lublin (PL), Aberystwyth University (GB), General Mills (United States) (US), Murdoch University (AU), University of Toronto (CA), Lund University (SE), Cornell University (US), Government of Western Australia (AU), German Centre for Integrative Biodiversity Research (DE), Natural Resources Institute Finland (FI), Helmholtz Zentrum München (DE), ETH Zurich (CH), Swedish e-Science Research Centre (SE), Department of Primary Industries and Regional Development (AU), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (ES), Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) (DE), Agriculture and Food (AU), Instituto de Agricultura Sostenible (ES), Robert W. Holley Center for Agriculture & Health (US), Institute of Biological, Environmental and Rural Sciences (GB), Institute of Plant Genetics, Polish Academy of Sciences (PL), Edward T. Schafer Agricultural Research Center (US), Université Laval (CA), Ottawa Research and Development Centre, Saskatoon Research and Development Centre, Canada Grain Commission, University of Manitoba (CA), McGill University (CA), Technical University of Munich (DE), Martin Luther University Halle-Wittenberg (DE), Shandong Agricultural University (CN), University of California, Berkeley (US)
Openalex Percentile: Top 2%
Wheat and Barley Genetics and Pathology
8.75
DOIOpen Access PDFOpenAlex
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