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Journal article
A pangenome and pantranscriptome of hexaploid oat
Nature (London)
2025
Abstract
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.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.
Details
- Title
- A pangenome and pantranscriptome of hexaploid oat
- Authors/Creators
- Raz Avni - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)Nadia Kamal - Helmholtz Zentrum MünchenLidija Bitz - Natural Resources Institute FinlandEric N Jellen - Brigham Young UniversityWubishet A Bekele - Agriculture and Agri-Food CanadaTefera T Angessa - Murdoch UniversityPetri Auvinen - University of HelsinkiOliver Bitz - Natural Resources Institute FinlandBrian Boyle - Université LavalFrancisco J Canales - Instituto de Agricultura SostenibleCraig H Carlson - Edward T. Schafer Agricultural Research CenterBrett Chapman - Murdoch UniversityHarmeet Singh Chawla - University of ManitobaYutang Chen - ETH ZurichDario Copetti - University of ArizonaSamara Correia de LemosViet Dang - Murdoch UniversitySteven R Eichten - General MillsKathy Esvelt Klos - Agricultural Research ServiceAmit M Fenn - Helmholtz Zentrum MünchenAnne Fiebig - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)Yong-Bi FuHeidrun Gundlach - Helmholtz Zentrum MünchenRajeev Gupta - Edward T. Schafer Agricultural Research CenterGeorg Haberer - Helmholtz Zentrum MünchenTianhua He - Murdoch UniversityMatthias H Herrmann - Julius Kühn-InstitutAxel Himmelbach - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)Catherine J Howarth - Institute of Biological, Environmental and Rural SciencesHaifei Hu - Murdoch UniversityJulio Isidro Y SánchezAsuka Itaya - Agriculture and Agri-Food CanadaJean-Luc JanninkYong Jia - Murdoch UniversityRajvinder Kaur - McGill UniversityManuela Knauft - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)Tim Langdon - Aberystwyth UniversityThomas Lux - Helmholtz Zentrum MünchenSofia Marmon - Lund UniversityVanda Marosi - Helmholtz Zentrum MünchenKlaus F X MayerSteve Michel - Agricultural Research ServiceRaja Sekhar Nandety - Edward T. Schafer Agricultural Research CenterKirby T Nilsen - University of ManitobaEdyta Paczos-Grzęda - Institute of Plant Genetics, Polish Academy of SciencesAsher Pasha - University of TorontoElena Prats - Instituto de Agricultura SostenibleNicholas J Provart - University of TorontoAdriana Ravagnani - Aberystwyth UniversityRobert W Reid - University of North Carolina at CharlotteJessica A Schlueter - University of North Carolina at CharlotteAlan H Schulman - University of HelsinkiTaner Z Sen - Agricultural Research ServiceJaswinder Singh - McGill UniversityMehtab Singh - McGill UniversityNick Sirijovski - Lund UniversityNils Stein - Martin Luther University Halle-WittenbergBruno Studer - ETH ZurichSirja Viitala - Natural Resources Institute FinlandShauna Vronces - University of TorontoSean Walkowiak - Canada Grain CommissionPenghao Wang - Murdoch UniversityAmanda J Waters - PepsiCharlene P Wight - Agriculture and Agri-Food CanadaWeikai Yan - Ottawa Research and Development CentreEric Yao - Agricultural Research ServiceXiao-Qi ZhangGaofeng Zhou - Murdoch UniversityZhou Zhou - McGill UniversityNicholas A Tinker - Ottawa Research and Development CentreJason D Fiedler - Edward T. Schafer Agricultural Research CenterChengdao Li - Murdoch UniversityPeter J Maughan - Brigham Young UniversityManuel Spannagl - Murdoch UniversityMartin Mascher - German Centre for Integrative Biodiversity Research
- Publication Details
- Nature (London)
- Publisher
- NATURE PORTFOLIO
- Number of pages
- 31
- Identifiers
- 991005823313507891
- Copyright
- © The Author(s) 2025
- Murdoch Affiliation
- Centre for Crop and Food Innovation; School of Medical, Molecular and Forensic Sciences
- Language
- English
- Resource Type
- Journal article
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- Citation topics
- 1 Clinical & Life Sciences
- 1.54 Molecular & Cell Biology - Genetics
- 1.54.1543 Flow Cytometry
- Web Of Science research areas
- Plant Sciences
- ESI research areas
- Biology & Biochemistry