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

by Tinker, Nicholas A. , Bellavance, Justin , Gupta, Rajeev , Carlson, Craig H. , Harris, John C. , Avni, Raz , Parkin, Isobel A. P. , Sutton, Tim , Howarth, Catherine J. , Bekele, Wubishet A. , Arbelaez, Juan D. , Mitchell Fetch, Jennifer W. , Nandety, Raja Sekhar , Peng, YuanYing , Diederichsen, Axel , Fiebig, Anne , Jannink, Jean-Luc , Beattie, Aaron D. , Langdon, Tim , Gutierrez, Lucia , Smith, Kevin P. , Yan, Weikai , Maughan, Peter J. , Birkett, Clayton L. , Fiedler, Jason D. , del Blanco, Isabel A. , Jellen, Eric N. , Zwer, Pamela , Brodführer, Sophie , Waring, David J. , Esvelt Klos, Kathy , Canales, Francisco J. , McMullen, Michael S. , Isidro y Sanchez, Julio , Wight, Charlene P. , Sen, Taner Z. , Huang, Yung-Fen , Li, Yongle , Caffe, Melanie , Paczos-Grzeda, Edyta , Fu, Yong-Bi , Michel, Steve , Itaya, Asuka , Harrison, Stephen A. , Prats, Elena , Herrmann, Matthias H. , Nilsen, Kirby T. , Mascher, Martin

in 45 / 631/181/2474 / 631/208/711 / 631/208/8 / 631/449/2491 / Adaptation / Avena - classification / Avena - genetics / Chromosome rearrangements / Chromosomes / Chromosomes, Plant - genetics / Clustering / Crops / Cultivars / Cultivation / Datasets / Food / Gene pool / Genetic diversity / Genetic Variation / Genetics, Population / Genome, Plant / Genomes / Genomics / Genotype / Genotyping / Germplasm / Grain cultivation / Humanities and Social Sciences / Metadata / Multidimensional methods / Multidimensional scaling / multidisciplinary / Polyploidy / Population genetics / Population structure / Populations / Science / Science (multidisciplinary) / Signatures

2025

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

2025

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2025

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Journal Article

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

Tinker, Nicholas A.,

Bellavance, Justin,

Gupta, Rajeev,

Carlson, Craig H.,

Harris, John C.,

Avni, Raz,

Parkin, Isobel A. P.,

Sutton, Tim,

Howarth, Catherine J.,

Bekele, Wubishet A.,

Arbelaez, Juan D.,

Mitchell Fetch, Jennifer W.,

Nandety, Raja Sekhar,

Peng, YuanYing,

Diederichsen, Axel,

Fiebig, Anne,

Jannink, Jean-Luc,

Beattie, Aaron D.,

Langdon, Tim,

Gutierrez, Lucia,

Smith, Kevin P.,

Yan, Weikai,

Maughan, Peter J.,

Birkett, Clayton L.,

Fiedler, Jason D.,

del Blanco, Isabel A.,

Jellen, Eric N.,

Zwer, Pamela,

Brodführer, Sophie,

Waring, David J.,

Esvelt Klos, Kathy,

Canales, Francisco J.,

McMullen, Michael S.,

Isidro y Sanchez, Julio,

Wight, Charlene P.,

Sen, Taner Z.,

Huang, Yung-Fen,

Li, Yongle,

Caffe, Melanie,

Paczos-Grzeda, Edyta,

Fu, Yong-Bi,

Michel, Steve,

Itaya, Asuka,

Harrison, Stephen A.,

Prats, Elena,

Herrmann, Matthias H.,

Nilsen, Kirby T.,

Mascher, Martin

2025

Overview

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. Oat is an important food crop, but the genetic diversity within the gene pool remains unclear. Here, the authors report the analyses of worldwide diversity and population structure of hexaploid oat, and identify signatures of structural rearrangements within the germplasm collection.

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Publisher

Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio

Subject

/ Avena - classification

/ Avena - genetics