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A pangenome and pantranscriptome of hexaploid oat

Avni, Raz ; Kamal, Nadia ; Bitz, Lidija ; Jellen, Eric N. ; Bekele, Wubishet A. ; Angessa, Tefera T. ; Auvinen, Petri ; Bitz, Oliver ; Boyle, Brian and Canales, Francisco J. , et al. (2025) In Nature
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... (More)

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 status
epub
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in
Nature
publisher
Nature Publishing Group
external identifiers
  • pmid:41162711
  • scopus:105020189979
ISSN
0028-0836
DOI
10.1038/s41586-025-09676-7
language
English
LU publication?
yes
additional info
Publisher Copyright: © The Author(s) 2025.
id
6689cf94-c732-4694-9742-bc4d51935570
date added to LUP
2025-11-06 12:03:33
date last changed
2025-11-13 12:27:27
@article{6689cf94-c732-4694-9742-bc4d51935570,
  abstract     = {{<p>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.</p>}},
  author       = {{Avni, Raz and Kamal, Nadia and Bitz, Lidija and Jellen, Eric N. and Bekele, Wubishet A. and Angessa, Tefera T. and Auvinen, Petri and Bitz, Oliver and Boyle, Brian and Canales, Francisco J. and Carlson, Craig H. and Chapman, Brett and Chawla, Harmeet Singh and Chen, Yutang and Copetti, Dario and Correia de Lemos, Samara and Dang, Viet and Eichten, Steven R. and Klos, Kathy Esvelt and Fenn, Amit M. and Fiebig, Anne and Fu, Yong-Bi and Gundlach, Heidrun and Gupta, Rajeev and Haberer, Georg and He, Tianhua and Herrmann, Matthias H. and Himmelbach, Axel and Howarth, Catherine J. and Hu, Haifei and Isidro y Sánchez, Julio and Itaya, Asuka and Jannink, Jean-Luc and Jia, Yong and Kaur, Rajvinder and Knauft, Manuela and Langdon, Tim and Lux, Thomas and Marmon, Sofia and Marosi, Vanda and Mayer, Klaus F.X. and Michel, Steve and Nandety, Raja Sekhar and Nilsen, Kirby T. and Paczos-Grzęda, Edyta and Pasha, Asher and Prats, Elena and Provart, Nicholas J. and Ravagnani, Adriana and Reid, Robert W. and Schlueter, Jessica A. and Schulman, Alan H. and Sen, Taner Z. and Singh, Jaswinder and Singh, Mehtab and Sirijovski, Nick and Stein, Nils and Studer, Bruno and Viitala, Sirja and Vronces, Shauna and Walkowiak, Sean and Wang, Penghao and Waters, Amanda J. and Wight, Charlene P. and Yan, Weikai and Yao, Eric and Zhang, Xiao-Qi and Zhou, Gaofeng and Zhou, Zhou and Tinker, Nicholas A. and Fiedler, Jason D. and Li, Chengdao and Maughan, Peter J. and Spannagl, Manuel and Mascher, Martin}},
  issn         = {{0028-0836}},
  language     = {{eng}},
  month        = {{10}},
  publisher    = {{Nature Publishing Group}},
  series       = {{Nature}},
  title        = {{A pangenome and pantranscriptome of hexaploid oat}},
  url          = {{http://dx.doi.org/10.1038/s41586-025-09676-7}},
  doi          = {{10.1038/s41586-025-09676-7}},
  year         = {{2025}},
}