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; Curtis J. Pozniak

doi:10.1038/s41586-020-2961-x

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 BanLuca 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, Curtis J. Pozniak^*

^*Corresponding author for this work

School of Plant Sciences and Food Security

Research output: Contribution to journal › Article › peer-review

527 Scopus citations

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 lines^2,3. 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 stresses^4,5. 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.

Original language	English
Pages (from-to)	277-283
Number of pages	7
Journal	Nature
Volume	588
Issue number	7837
DOIs	https://doi.org/10.1038/s41586-020-2961-x
State	Published - 10 Dec 2020

Funding

Funders	Funder number
AMED NBRP	JP17km0210142
Bioplatforms Australia
ETH Zurich Institute of Agricultural Sciences
Fenaco Co-operative
NAP-PGREL
Swiss Federal Office of Agriculture
WHEATSeq	2819103915, FKZ 031A536A, 2819104015, 031A536B
Western Grains Research Foundation, Government of Saskatchewan
National Science Foundation	1339389
Kansas State University
Genome Canada
Kansas Wheat Commission
Biotechnology and Biological Sciences Research Council	BB/P016855/1, BB/P010733/1, BB/ J003557/1, BB/P010741/1, BB/P010768/1
Australian Research Council	CE140100008
Grains Research and Development Corporation
Ministry of Education, Culture, Sports, Science and Technology	JP16H06466, JP16H06469, JP16K21727, JP16H06464
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung	31003A_182318, CRSII5_183578
Bundesministerium für Bildung und Forschung	FKZ 031B0190
Core Research for Evolutional Science and Technology	JPMJCR16O3
Israel Science Foundation	1137/17
King Abdullah University of Science and Technology
Bundesministerium für Ernährung und Landwirtschaft	BMEL FKZ 2819103915
Universität Zürich
National Agriculture and Food Research Organization
Genome Prairie
Alberta Wheat Commission
Saskatchewan Wheat Development Commission

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1038/s41586-020-2961-x

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Walkowiak, S., Gao, L., Monat, C., Haberer, G., Kassa, M. T., Brinton, J., Ramirez-Gonzalez, R. H., Kolodziej, M. C., Delorean, E., Thambugala, D., Klymiuk, V., Byrns, B., Gundlach, H., Bandi, V., Siri, J. N., Nilsen, K., Aquino, C., Himmelbach, A., Copetti, D., ... Pozniak, C. J. (2020). Multiple wheat genomes reveal global variation in modern breeding. Nature, 588(7837), 277-283. https://doi.org/10.1038/s41586-020-2961-x

@article{730d37dd85b24d26b4f647128bc1da76,

title = "Multiple wheat genomes reveal global variation in modern breeding",

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.",

author = "Sean Walkowiak and Liangliang Gao and Cecile Monat and Georg Haberer and Kassa, {Mulualem T.} and Jemima Brinton and Ramirez-Gonzalez, {Ricardo H.} and Kolodziej, {Markus C.} and Emily Delorean and Dinushika Thambugala and Valentyna Klymiuk and Brook Byrns and Heidrun Gundlach and Venkat Bandi and Siri, {Jorge Nunez} and Kirby Nilsen and Catharine Aquino and Axel Himmelbach and Dario Copetti and Tomohiro Ban and Luca Venturini and Michael Bevan and Bernardo Clavijo and Koo, {Dal Hoe} and Jennifer Ens and Krystalee Wiebe and Amidou N{\textquoteright}Diaye and Fritz, {Allen K.} and Carl Gutwin and Anne Fiebig and Christine Fosker and Fu, {Bin Xiao} and Accinelli, {Gonzalo Garcia} and Gardner, {Keith A.} and Nick Fradgley and Juan Gutierrez-Gonzalez and Gwyneth Halstead-Nussloch and Masaomi Hatakeyama and Koh, {Chu Shin} and Jasline Deek and Costamagna, {Alejandro C.} and Pierre Fobert and Darren Heavens and Hiroyuki Kanamori and Kanako Kawaura and Fuminori Kobayashi and Ksenia Krasileva and Tony Kuo and Neil McKenzie and Kazuki Murata and Yusuke Nabeka and Timothy Paape and Sudharsan Padmarasu and Lawrence Percival-Alwyn and Sateesh Kagale and Uwe Scholz and Jun Sese and Philomin Juliana and Ravi Singh and Rie Shimizu-Inatsugi and David Swarbreck and James Cockram and Hikmet Budak and Toshiaki Tameshige and Tsuyoshi Tanaka and Hiroyuki Tsuji and Jonathan Wright and Jianzhong Wu and Burkhard Steuernagel and Ian Small and Sylvie Cloutier and Gabriel Keeble-Gagn{\`e}re and Gary Muehlbauer and Josquin Tibbets and Shuhei Nasuda and Joanna Melonek and Hucl, {Pierre J.} and Sharpe, {Andrew G.} and Matthew Clark and Erik Legg and Arvind Bharti and Peter Langridge and Anthony Hall and Cristobal Uauy and Martin Mascher and Krattinger, {Simon G.} and Hirokazu Handa and Shimizu, {Kentaro K.} and Assaf Distelfeld and Ken Chalmers and Beat Keller and Mayer, {Klaus F.X.} and Jesse Poland and Nils Stein and McCartney, {Curt A.} and Manuel Spannagl and Thomas Wicker and Pozniak, {Curtis J.}",

note = "Publisher Copyright: {\textcopyright} 2020, The Author(s).",

year = "2020",

month = dec,

day = "10",

doi = "10.1038/s41586-020-2961-x",

language = "אנגלית",

volume = "588",

pages = "277--283",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Research",

number = "7837",

}

Walkowiak, S, Gao, L, Monat, C, Haberer, G, Kassa, MT, Brinton, J, Ramirez-Gonzalez, RH, Kolodziej, MC, Delorean, E, Thambugala, D, Klymiuk, V, Byrns, B, Gundlach, H, Bandi, V, Siri, JN, Nilsen, K, Aquino, C, Himmelbach, A, Copetti, D, Ban, T, Venturini, L, Bevan, M, Clavijo, B, Koo, DH, Ens, J, Wiebe, K, N’Diaye, A, Fritz, AK, Gutwin, C, Fiebig, A, Fosker, C, Fu, BX, Accinelli, GG, Gardner, KA, Fradgley, N, Gutierrez-Gonzalez, J, Halstead-Nussloch, G, Hatakeyama, M, Koh, CS, Deek, J, Costamagna, AC, Fobert, P, Heavens, D, Kanamori, H, Kawaura, K, Kobayashi, F, Krasileva, K, Kuo, T, McKenzie, N, Murata, K, Nabeka, Y, Paape, T, Padmarasu, S, Percival-Alwyn, L, Kagale, S, Scholz, U, Sese, J, Juliana, P, Singh, R, Shimizu-Inatsugi, R, Swarbreck, D, Cockram, J, Budak, H, Tameshige, T, Tanaka, T, Tsuji, H, Wright, J, Wu, J, Steuernagel, B, Small, I, Cloutier, S, Keeble-Gagnère, G, Muehlbauer, G, Tibbets, J, Nasuda, S, Melonek, J, Hucl, PJ, Sharpe, AG, Clark, M, Legg, E, Bharti, A, Langridge, P, Hall, A, Uauy, C, Mascher, M, Krattinger, SG, Handa, H, Shimizu, KK, Distelfeld, A, Chalmers, K, Keller, B, Mayer, KFX, Poland, J, Stein, N, McCartney, CA, Spannagl, M, Wicker, T & Pozniak, CJ 2020, 'Multiple wheat genomes reveal global variation in modern breeding', Nature, vol. 588, no. 7837, pp. 277-283. https://doi.org/10.1038/s41586-020-2961-x

TY - JOUR

T1 - Multiple wheat genomes reveal global variation in modern breeding

AU - Walkowiak, Sean

AU - Gao, Liangliang

AU - Monat, Cecile

AU - Haberer, Georg

AU - Kassa, Mulualem T.

AU - Brinton, Jemima

AU - Ramirez-Gonzalez, Ricardo H.

AU - Kolodziej, Markus C.

AU - Delorean, Emily

AU - Thambugala, Dinushika

AU - Klymiuk, Valentyna

AU - Byrns, Brook

AU - Gundlach, Heidrun

AU - Bandi, Venkat

AU - Siri, Jorge Nunez

AU - Nilsen, Kirby

AU - Aquino, Catharine

AU - Himmelbach, Axel

AU - Copetti, Dario

AU - Ban, Tomohiro

AU - Venturini, Luca

AU - Bevan, Michael

AU - Clavijo, Bernardo

AU - Koo, Dal Hoe

AU - Ens, Jennifer

AU - Wiebe, Krystalee

AU - N’Diaye, Amidou

AU - Fritz, Allen K.

AU - Gutwin, Carl

AU - Fiebig, Anne

AU - Fosker, Christine

AU - Fu, Bin Xiao

AU - Accinelli, Gonzalo Garcia

AU - Gardner, Keith A.

AU - Fradgley, Nick

AU - Gutierrez-Gonzalez, Juan

AU - Halstead-Nussloch, Gwyneth

AU - Hatakeyama, Masaomi

AU - Koh, Chu Shin

AU - Deek, Jasline

AU - Costamagna, Alejandro C.

AU - Fobert, Pierre

AU - Heavens, Darren

AU - Kanamori, Hiroyuki

AU - Kawaura, Kanako

AU - Kobayashi, Fuminori

AU - Krasileva, Ksenia

AU - Kuo, Tony

AU - McKenzie, Neil

AU - Murata, Kazuki

AU - Nabeka, Yusuke

AU - Paape, Timothy

AU - Padmarasu, Sudharsan

AU - Percival-Alwyn, Lawrence

AU - Kagale, Sateesh

AU - Scholz, Uwe

AU - Sese, Jun

AU - Juliana, Philomin

AU - Singh, Ravi

AU - Shimizu-Inatsugi, Rie

AU - Swarbreck, David

AU - Cockram, James

AU - Budak, Hikmet

AU - Tameshige, Toshiaki

AU - Tanaka, Tsuyoshi

AU - Tsuji, Hiroyuki

AU - Wright, Jonathan

AU - Wu, Jianzhong

AU - Steuernagel, Burkhard

AU - Small, Ian

AU - Cloutier, Sylvie

AU - Keeble-Gagnère, Gabriel

AU - Muehlbauer, Gary

AU - Tibbets, Josquin

AU - Nasuda, Shuhei

AU - Melonek, Joanna

AU - Hucl, Pierre J.

AU - Sharpe, Andrew G.

AU - Clark, Matthew

AU - Legg, Erik

AU - Bharti, Arvind

AU - Langridge, Peter

AU - Hall, Anthony

AU - Uauy, Cristobal

AU - Mascher, Martin

AU - Krattinger, Simon G.

AU - Handa, Hirokazu

AU - Shimizu, Kentaro K.

AU - Distelfeld, Assaf

AU - Chalmers, Ken

AU - Keller, Beat

AU - Mayer, Klaus F.X.

AU - Poland, Jesse

AU - Stein, Nils

AU - McCartney, Curt A.

AU - Spannagl, Manuel

AU - Wicker, Thomas

AU - Pozniak, Curtis J.

PY - 2020/12/10

Y1 - 2020/12/10

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85095987683&partnerID=8YFLogxK

U2 - 10.1038/s41586-020-2961-x

DO - 10.1038/s41586-020-2961-x

M3 - ???researchoutput.researchoutputtypes.contributiontojournal.article???

C2 - 33239791

AN - SCOPUS:85095987683

SN - 0028-0836

VL - 588

SP - 277

EP - 283

JO - Nature

JF - Nature

IS - 7837

ER -

Multiple wheat genomes reveal global variation in modern breeding

Abstract

Funding

UN SDGs

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