A pangenome and pantranscriptome of hexaploid oat

Authors: Esvelt Klos, Kathy; Fiedler, Jason; Gupta, Rajeev; Jannink, Jean Luc; MICHEL, STEVE - US Department Of Agriculture (USDA); Nandety, Raja Sekhar; Carlson, Craig; Sen, Taner; Yao, Eric; MASCHER, MARTIN - Leibniz Institute Of Plant Genetics And Crop Plant Research; TINKER, NICHOLAS - Agriculture And Agri-Food Canada; AVNI, RAZ - Leibniz Institute Of Plant Genetics And Crop Plant Research; CHAPMAN, BRETT - Murdoch University; HABERER, GEORG - German Research Center For Environmental Health; LANGDON, TIM - Aberystwyth University; RAVAGNANI, ADRIANA - Aberystwyth University; WALKOWIAK, SEAN - Canadian Grain Commission; SPANNAGL, MANUEL - German Research Center For Environmental Health

Submitted to: Nature
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/25/2025
Publication Date: 10/29/2025
Citation: Esvelt Klos, K.L., Fiedler, J.D., Gupta, R., Jannink, J., Michel, S., Nandety, R.S., Carlson, C.H., Sen, T.Z., Yao, E., Mascher, M., Tinker, N., Avni, R., Chapman, B., Haberer, G., Langdon, T., Ravagnani, A., Walkowiak, S., Spannagl, M. 2025. A pangenome and pantranscriptome of hexaploid oat. Nature. 649:131-139. https://doi.org/10.1038/s41586-025-09676-7.
DOI: https://doi.org/10.1038/s41586-025-09676-7

Interpretive Summary: Oat is an important cereal grain that has seen a contemporary resurgence due to its numerous health benefits and promise as a plant-based food ingredient. Its multi-copy genome is large and complex, with most of it containing repetitive and “junk” sequences with unknown function. This has limited the efficient use of molecular breeding tools for oat that have been very effective to push improvement of other crops such as soybean and corn. To overcome this bottleneck and understand more about this dynamic crop, we built up oat genomic infrastructure through the development of 31 individual genome sequences from domesticated and wild lines. This effort has highlighted large structural differences among the lines that have implications for breeders. Here we highlight a few examples of important differences in elite Australian lines and a variation that determines flowering time. Additionally, a gene expression atlas of 23 lines was developed that uncovers key characteristics of the almost 3 million genes in 90,000 families in these genomes. Analysis of this data has identified key interactions among important genes in oat and we show many instances where the loss of individual genes in one sub-genome is compensated by extra copies in the others. Taken together, these new resources will provide a solid framework for oat genetic research and will ensure the rapid deployment of this new information to develop elite oat varieties for producers.

Technical Abstract: Oat grains are important in breakfast cereal and are rich in dietary fibers. Interest in the crop has surged in recent years thanks to its role as the basis for plant-based milk analogs. Oat is an allohexaploid with a large, repeat-rich genome that was shaped by subgenome exchanges on an evolutionary timescale. 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 report annotated chromosome-scale sequence assemblies of 31 wild and domesticated oats along with an atlas of gene expression across six tissues in 23 genotypes. We describe the interplay of gene expression diversity across subgenomes, genotypes and tissues. Incipient gene loss in the hexaploid is accompanied by compensatory up-regulation of the remaining homeologs, but this process is constrained by subgenome divergence. Chromososomal rearrangements have had an impact on recent oat breeding. A large pericentric inversion associated with early flowering explains distorted segregation on chromosome 7D. A homeologous sequence exchange between chromosomes 2A and 2C in a semidwarf mutant has risen to prominence in Australian elite varieties. We expect that the oat pangenome will foster the adoption of genomic approaches and stimulate genetic inquiries into the evolution and adaptation of domesticated oats.