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Avni, R.* ; Kamal, N. ; Bitz, L.* ; Jellen, E.N.* ; Bekele, W.A.* ; Angessa, T.T.* ; Auvinen, P.* ; Bitz, O.* ; Boyle, B.* ; Canales, F.J.* ; Carlson, C.H.* ; Chapman, B.* ; Chawla, H.* ; Chen, Y.* ; Copetti, D.* ; Correia de Lemos, S.* ; Dang, V.D.* ; Eichten, S.R.* ; Klos, K.E.* ; Fenn, A. ; Fiebig, A.* ; Fu, Y.B.* ; Gundlach, H. ; Gupta, R.* ; Haberer, G. ; He, T.* ; Herrmann, M.H.* ; Himmelbach, A.* ; Howarth, C.J.* ; Hu, H.* ; Isidro Y Sánchez, J.* ; Itaya, A.* ; Jannink, J.L.* ; Jia, Y.* ; Kaur, R.* ; Knauft, M.* ; Langdon, T.* ; Lux, T. ; Marmon, S.* ; Marosi, V.B. ; Mayer, K.F.X. ; Michel, S.* ; Nandety, R.S.* ; Nilsen, K.T.* ; Paczos-Grzęda, E.* ; Pasha, A.* ; Prats, E.* ; Provart, N.J.* ; Ravagnani, A.* ; Reid, R.W.* ; Schlueter, J.A.* ; Schulman, A.H.* ; Sen, T.Z.* ; Singh, J.* ; Singh, M.* ; Sirijovski, N.* ; Stein, N.* ; Studer, B.* ; Viitala, S.* ; Vronces, S.* ; Walkowiak, S.* ; Wang, P.* ; Waters, A.J.* ; Wight, C.P.* ; Yan, W.* ; Yao, E.* ; Zhang, X.Q.* ; Zhou, G.* ; Zhou, Z.* ; Tinker, N.A.* ; Fiedler, J.D.* ; Li, C.* ; Maughan, P.J.* ; Spannagl, M. ; Mascher, M.*

A pangenome and pantranscriptome of hexaploid oat.

Nature, DOI: 10.1038/s41586-025-09676-7 (2025)
Publ. Version/Full Text Research data DOI PMC
Open Access Hybrid
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Oat grain is a traditional human food that is rich in dietary fibre and contributes to improved human health1,2. Interest in the crop has surged in recent years owing to its use as the basis for plant-based milk analogues3. Oat is an allohexaploid with a large, repeat-rich genome that was shaped by subgenome exchanges over evolutionary timescales4. 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 type Article: Journal article
Document type Scientific Article
Keywords Linkage Map; Stem Rust; Identification; Germplasm; Markers; Genes
Language english
Publication Year 2025
HGF-reported in Year 2025
ISSN (print) / ISBN 0028-0836
e-ISSN 1476-4687
Journal Nature
Publisher Nature Publishing Group
Publishing Place London
Reviewing status Peer reviewed
Institute(s) Research Unit Plant Genome and Systems Biology (PGSB)
POF-Topic(s) 30202 - Environmental Health
Research field(s) Environmental Sciences
PSP Element(s) G-503500-002
Grants Australian Grains Research and Development Corporation (GRDC)
European Research Council (ERC) under the European Union's Horizon 2020 Research and Innovation programme
MICIU/AEI, FEDER, UE
Western Australia Oat Industry Partnership
Junta de Andalucia
Department of Primary Industry and Regional Development
Swedish Foundation for Strategic Research (ScanOats)
NSF
German Research Foundation (DFG)
McGill University
German Ministry of Food and Agriculture (BMEL, FUGE)
Alexander von Humboldt foundation
European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant
Agriculture and Agri-Food Canada (AAFC)
Canadian Field Crops Research Alliance
Prairie Oat Breeding Consortium
Genome Quebec
AAFC
ScanOats Research Center (Lantmaennen)
US Department of Agriculture (USDA) Agricultural Research Service
Severo Ochoa Program for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain

ERDF: 'A way of making Europe'
MCIN/AEI
ScanOats Research Center (Oatly AB)
Swedish National Genomics Infrastructure - Science for Life Laboratory
Knut and Alice Wallenberg Foundation
Swedish Research Council
BBSRC
Beatriz Galindo Program
Natural Resources Institute Finland (LUKE)
DOI 10.1038/s41586-025-09676-7
WOS ID 001603593800001
Scopus ID 105020189979
PubMed ID 41162711
Erfassungsdatum 2025-10-31
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