Global genomic population structure of wild and cultivated oat reveals signatures of chromosome rearrangements

Wubishet A. Bekele (), Raz Avni, Clayton L. Birkett, Asuka Itaya, Charlene P. Wight, Justin Bellavance, Sophie Brodführer, Francisco J. Canales, Craig H. Carlson, Anne Fiebig, Yongle Li, Steve Michel, Raja Sekhar Nandety, David J. Waring, Juan D. Arbelaez, Aaron D. Beattie, Melanie Caffe, Isabel A. Blanco, Jason D. Fiedler, Rajeev Gupta, Lucia Gutierrez, John C. Harris, Stephen A. Harrison, Matthias H. Herrmann, Yung-Fen Huang, Julio Isidro y Sanchez, Michael S. McMullen, Jennifer W. Mitchell Fetch, Kirby T. Nilsen, Isobel A. P. Parkin, YuanYing Peng, Kevin P. Smith, Tim Sutton, Weikai Yan, Pamela Zwer, Axel Diederichsen, Kathy Esvelt Klos, Yong-Bi Fu, Catherine J. Howarth, Jean-Luc Jannink, Eric N. Jellen, Tim Langdon, Peter J. Maughan, Edyta Paczos-Grzeda, Elena Prats, Taner Z. Sen, Martin Mascher () and Nicholas A. Tinker ()
Additional contact information
Wubishet A. Bekele: Agriculture and Agri-Food Canada
Raz Avni: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
Clayton L. Birkett: R.W. Holley Center for Agriculture and Health, USDA-ARS
Asuka Itaya: Agriculture and Agri-Food Canada
Charlene P. Wight: Agriculture and Agri-Food Canada
Justin Bellavance: Agriculture and Agri-Food Canada
Sophie Brodführer: Institute for Breeding Research on Agricultural Crops
Francisco J. Canales: Institute for Sustainable Agriculture (IAS)
Craig H. Carlson: Edward T. Schafer Agricultural Research Center, USDA-ARS
Anne Fiebig: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
Yongle Li: Australian Grain Technologies (AGT)
Steve Michel: Western Regional Research Center
Raja Sekhar Nandety: Edward T. Schafer Agricultural Research Center, USDA-ARS
David J. Waring: Cornell University
Juan D. Arbelaez: University of Illinois
Aaron D. Beattie: University of Saskatchewan
Melanie Caffe: South Dakota State University
Isabel A. Blanco: University of California, Davis
Jason D. Fiedler: Edward T. Schafer Agricultural Research Center, USDA-ARS
Rajeev Gupta: Edward T. Schafer Agricultural Research Center, USDA-ARS
Lucia Gutierrez: University of Wisconsin—Madison
John C. Harris: Department of Primary Industries and Regions
Stephen A. Harrison: Louisiana State University
Matthias H. Herrmann: Institute for Breeding Research on Agricultural Crops
Yung-Fen Huang: National Taiwan University
Julio Isidro y Sanchez: Universidad Politécnica de Madrid (UPM)
Michael S. McMullen: North Dakota State University
Jennifer W. Mitchell Fetch: Agriculture and Agri-Food Canada
Kirby T. Nilsen: Agriculture and Agri-Food Canada
Isobel A. P. Parkin: Agriculture and Agri-Food Canada
YuanYing Peng: Sichuan Agricultural University
Kevin P. Smith: University of Minnesota
Tim Sutton: Department of Primary Industries and Regions
Weikai Yan: Agriculture and Agri-Food Canada
Pamela Zwer: Department of Primary Industries and Regions
Axel Diederichsen: Agriculture and Agri-Food Canada
Kathy Esvelt Klos: USDA-ARS
Yong-Bi Fu: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
Catherine J. Howarth: Aberystwyth University
Jean-Luc Jannink: R.W. Holley Center for Agriculture and Health, USDA-ARS
Eric N. Jellen: Brigham Young University
Tim Langdon: Aberystwyth University
Peter J. Maughan: Brigham Young University
Edyta Paczos-Grzeda: University of Life Sciences in Lublin
Elena Prats: Institute for Sustainable Agriculture (IAS)
Taner Z. Sen: Western Regional Research Center
Martin Mascher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
Nicholas A. Tinker: Agriculture and Agri-Food Canada

Nature Communications, 2025, vol. 16, issue 1, 1-14

Abstract: Abstract The genus Avena consists of approximately 30 wild and cultivated oat species. Cultivated oat is an important food crop, yet the broader genetic diversity within the Avena gene pool remains underexplored and underexploited. Here, we characterize over 9000 wild and cultivated hexaploid oat accessions of global origin using genotyping-by-sequencing and explore population structure using multidimensional scaling and population-based clustering methods. We also conduct analyses to reveal chromosome regions associated with local adaptation, sometimes resulting from large-scale chromosome rearrangements. We report four distinct genetic populations within the wild species A. sterilis, a distinct population of cultivated A. byzantina, and multiple populations within cultivated A. sativa. Some chromosome regions associated with local adaptation are also associated with confirmed structural rearrangements on chromosomes 1A, 1C, 3C, 4C, and 7D. This work provides evidence suggesting multiple polyploid origins, multiple domestications, and/or reproductive barriers amongst Avena populations caused by differential chromosome structure.

Date: 2025
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DOI: 10.1038/s41467-025-57895-3

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