Multiple wheat genomes reveal global variation in modern breeding

Sean Walkowiak, Liangliang Gao, Cecile Monat, Georg Haberer, Mulualem T. Kassa, Jemima Brinton, Ricardo H. Ramirez-Gonzalez, Markus C. Kolodziej, Emily Delorean, Dinushika Thambugala, Valentyna Klymiuk, Brook Byrns, Heidrun Gundlach, Venkat Bandi, Jorge Nunez Siri, Kirby Nilsen, Catharine Aquino, Axel Himmelbach, Dario Copetti, Tomohiro Ban, Luca Venturini, Michael Bevan, Bernardo Clavijo, Dal-Hoe Koo, Jennifer Ens, Krystalee Wiebe, Amidou N’Diaye, Allen K. Fritz, Carl Gutwin, Anne Fiebig, Christine Fosker, Bin Xiao Fu, Gonzalo Garcia Accinelli, Keith A. Gardner, Nick Fradgley, Juan Gutierrez-Gonzalez, Gwyneth Halstead-Nussloch, Masaomi Hatakeyama, Chu Shin Koh, Jasline Deek, Alejandro C. Costamagna, Pierre Fobert, Darren Heavens, Hiroyuki Kanamori, Kanako Kawaura, Fuminori Kobayashi, Ksenia Krasileva, Tony Kuo, Neil McKenzie, Kazuki Murata, Yusuke Nabeka, Timothy Paape, Sudharsan Padmarasu, Lawrence Percival-Alwyn, Sateesh Kagale, Uwe Scholz, Jun Sese, Philomin Juliana, Ravi Singh, Rie Shimizu-Inatsugi, David Swarbreck, James Cockram, Hikmet Budak, Toshiaki Tameshige, Tsuyoshi Tanaka, Hiroyuki Tsuji, Jonathan Wright, Jianzhong Wu, Burkhard Steuernagel, Ian Small, Sylvie Cloutier, Gabriel Keeble-Gagnère, Gary Muehlbauer, Josquin Tibbets, Shuhei Nasuda, Joanna Melonek, Pierre J. Hucl, Andrew G. Sharpe, Matthew Clark, Erik Legg, Arvind Bharti, Peter Langridge, Anthony Hall, Cristobal Uauy, Martin Mascher, Simon G. Krattinger, Hirokazu Handa, Kentaro K. Shimizu, Assaf Distelfeld, Ken Chalmers, Beat Keller, Klaus F. X. Mayer, Jesse Poland, Nils Stein, Curt A. McCartney (), Manuel Spannagl (), Thomas Wicker () and Curtis J. Pozniak ()
Additional contact information
Sean Walkowiak: University of Saskatchewan
Liangliang Gao: Kansas State University
Cecile Monat: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Georg Haberer: Helmholtz Zentrum München—German Research Center for Environmental Health
Mulualem T. Kassa: National Research Council Canada
Jemima Brinton: John Innes Centre
Ricardo H. Ramirez-Gonzalez: John Innes Centre
Markus C. Kolodziej: University of Zurich
Emily Delorean: Kansas State University
Dinushika Thambugala: Agriculture and Agri-Food Canada
Valentyna Klymiuk: University of Saskatchewan
Brook Byrns: University of Saskatchewan
Heidrun Gundlach: Helmholtz Zentrum München—German Research Center for Environmental Health
Venkat Bandi: University of Saskatchewan
Jorge Nunez Siri: University of Saskatchewan
Kirby Nilsen: University of Saskatchewan
Catharine Aquino: Functional Genomics Center Zurich
Axel Himmelbach: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Dario Copetti: University of Zurich
Tomohiro Ban: Yokohama City University
Luca Venturini: Life Sciences Department, Natural History Museum
Michael Bevan: John Innes Centre
Bernardo Clavijo: Earlham Institute, Norwich Research Park
Dal-Hoe Koo: Kansas State University
Jennifer Ens: University of Saskatchewan
Krystalee Wiebe: University of Saskatchewan
Amidou N’Diaye: University of Saskatchewan
Allen K. Fritz: Kansas State University
Carl Gutwin: University of Saskatchewan
Anne Fiebig: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Christine Fosker: Earlham Institute, Norwich Research Park
Bin Xiao Fu: Grain Research Laboratory, Canadian Grain Commission
Gonzalo Garcia Accinelli: Earlham Institute, Norwich Research Park
Keith A. Gardner: NIAB
Nick Fradgley: NIAB
Juan Gutierrez-Gonzalez: University of Minnesota
Gwyneth Halstead-Nussloch: University of Zurich
Masaomi Hatakeyama: Functional Genomics Center Zurich
Chu Shin Koh: Global Institute for Food Security, University of Saskatchewan
Jasline Deek: Tel Aviv University
Alejandro C. Costamagna: University of Manitoba
Pierre Fobert: National Research Council Canada
Darren Heavens: Earlham Institute, Norwich Research Park
Hiroyuki Kanamori: Institute of Crop Science, NARO
Kanako Kawaura: Yokohama City University
Fuminori Kobayashi: Institute of Crop Science, NARO
Ksenia Krasileva: Earlham Institute, Norwich Research Park
Tony Kuo: University of Guelph
Neil McKenzie: John Innes Centre
Kazuki Murata: Kyoto University
Yusuke Nabeka: Kyoto University
Timothy Paape: University of Zurich
Sudharsan Padmarasu: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Lawrence Percival-Alwyn: NIAB
Sateesh Kagale: National Research Council Canada
Uwe Scholz: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Jun Sese: National Institute of Advanced Industrial Science and Technology (AIST)
Philomin Juliana: Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT)
Ravi Singh: Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT)
Rie Shimizu-Inatsugi: University of Zurich
David Swarbreck: Earlham Institute, Norwich Research Park
James Cockram: NIAB
Hikmet Budak: Montana BioAg
Toshiaki Tameshige: Yokohama City University
Tsuyoshi Tanaka: Institute of Crop Science, NARO
Hiroyuki Tsuji: Yokohama City University
Jonathan Wright: Earlham Institute, Norwich Research Park
Jianzhong Wu: Institute of Crop Science, NARO
Burkhard Steuernagel: John Innes Centre
Ian Small: University of Western Australia
Sylvie Cloutier: Agriculture and Agri-Food Canada
Gabriel Keeble-Gagnère: Agriculture Victoria, AgriBio, Centre for AgriBioscience
Gary Muehlbauer: University of Minnesota
Josquin Tibbets: Agriculture Victoria, AgriBio, Centre for AgriBioscience
Shuhei Nasuda: Kyoto University
Joanna Melonek: University of Western Australia
Pierre J. Hucl: University of Saskatchewan
Andrew G. Sharpe: Global Institute for Food Security, University of Saskatchewan
Matthew Clark: Life Sciences Department, Natural History Museum
Erik Legg: Syngenta
Arvind Bharti: Syngenta
Peter Langridge: University of Adelaide
Anthony Hall: Earlham Institute, Norwich Research Park
Cristobal Uauy: John Innes Centre
Martin Mascher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Simon G. Krattinger: University of Zurich
Hirokazu Handa: Institute of Crop Science, NARO
Kentaro K. Shimizu: University of Zurich
Assaf Distelfeld: University of Haifa
Ken Chalmers: University of Adelaide
Beat Keller: University of Zurich
Klaus F. X. Mayer: Helmholtz Zentrum München—German Research Center for Environmental Health
Jesse Poland: Kansas State University
Nils Stein: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Curt A. McCartney: Agriculture and Agri-Food Canada
Manuel Spannagl: Helmholtz Zentrum München—German Research Center for Environmental Health
Thomas Wicker: University of Zurich
Curtis J. Pozniak: University of Saskatchewan

Nature, 2020, vol. 588, issue 7837, 277-283

Abstract: Abstract Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome1, and the lack of genome-assembly data for multiple wheat lines2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses4,5. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm16, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.

Date: 2020
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DOI: 10.1038/s41586-020-2961-x

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