Multiple wheat genomes reveal global variation in modern breeding

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 genome, and the lack of genome-assembly data for multiple wheat lines. 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 stresses. 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 *Sm1*, 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.

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, 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, Curtis J. Pozniak