Shifting the limits in wheat research and breeding using a fully annotated reference genome
R. Appels(Murdoch University), Kellye Eversole(National Human Genome Research Institute), Nils Stein(The University of Western Australia), Catherine Feuillet(Institute of Crop Science), Beat Keller(University of Zurich), Jane Rogers(International Union for Conservation of Nature (United Kingdom)), Curtis Pozniak(University of Saskatchewan), Frédéric Choulet(Génétique, Diversité, Écophysiologie des Céréales), Assaf Distelfeld(Tel Aviv University), Jesse Poland(Kansas State University), Gil Ronen(Israel Institute for Biological Research), Andrew Sharpe(Global Institute for Water Security), Omer Barad(Israel Institute for Biological Research), Kobi Baruch(Israel Institute for Biological Research), Gabriel Keeble‐Gagnère(La Trobe University), Martin Mascher(German Centre for Integrative Biodiversity Research), Gil Ben-Zvi(Israel Institute for Biological Research), Ambre-Aurore Josselin(Génétique, Diversité, Écophysiologie des Céréales), Axel Himmelbach(Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)), François Balfourier(Génétique, Diversité, Écophysiologie des Céréales), Juan J. Gutiérrez-González(University of Minnesota), Matthew Hayden(La Trobe University), ChuShin Koh(Global Institute for Water Security), Gary J. Muehlbauer(University of Minnesota), Raj Pasam(La Trobe University), Etienne Paux(Génétique, Diversité, Écophysiologie des Céréales), Philippe Rigault(Defence Research and Development Canada), Josquin Tibbits(La Trobe University), Vijay Tiwari(Carnegie Department of Plant Biology), M. Spannagl(Helmholtz Zentrum München), Daniel Lang(Helmholtz Zentrum München), Heidrun Gundlach(Helmholtz Zentrum München), Georg Haberer(Helmholtz Zentrum München), Klaus Mayer(Helmholtz Zentrum München), Danara Ormanbekova(Helmholtz Zentrum München), Verena M. Prade(Helmholtz Zentrum München), Hana Šimková(Czech Academy of Sciences, Institute of Experimental Botany), Thomas Wicker(University of Zurich), David Swarbreck(Earlham Institute), Hélène Rimbert(Génétique, Diversité, Écophysiologie des Céréales), Marius Felder(Helmholtz Zentrum München), Nicolas Guilhot(Génétique, Diversité, Écophysiologie des Céréales), Gemy Kaithakottil(Earlham Institute), Jens Keilwagen(Julius Kühn-Institut), Philippe Leroy(Génétique, Diversité, Écophysiologie des Céréales), Thomas Lux(Helmholtz Zentrum München), Sven Twardziok(Helmholtz Zentrum München), Luca Venturini(Earlham Institute), Angéla Juhász(Murdoch University), Michaël Abrouk(Czech Academy of Sciences, Institute of Experimental Botany), Iris Fischer(Helmholtz Zentrum München), Cristóbal Uauy(Norwich Research Park), Philippa Borrill(Norwich Research Park), Ricardo H. Ramírez-González(Norwich Research Park), Dominique Arnaud(Institut National de la Recherche Agronomique du Niger), Smahane Chalabi(Institut National de la Recherche Agronomique du Niger), Boulos Chalhoub(Monsanto (United States)), Aron T. Cory(University of Saskatchewan), Raju Datla(Plant Biotechnology Institute), Mark W. Davey(Bayer (Belgium)), John Jacobs(Bayer (Belgium)), Stephen J. Robinson(Agriculture and Agri-Food Canada), Burkhard Steuernagel(Norwich Research Park), Fred van Ex(Bayer (Belgium)), Brande B. H. Wulff(Norwich Research Park), Moussa Benhamed(Institut des Sciences des Plantes de Paris Saclay), Abdelhafid Bendahmane(Institut des Sciences des Plantes de Paris Saclay), Lorenzo Concia(Institut des Sciences des Plantes de Paris Saclay), David Latrasse(Institut des Sciences des Plantes de Paris Saclay), Jan Bartoš(Czech Academy of Sciences, Institute of Experimental Botany), Arnaud Bellec(Genomics and Biotechnology of the Fruits Laboratory), Hélène Bergès(Genomics and Biotechnology of the Fruits Laboratory), Jaroslav Doležel(Czech Academy of Sciences, Institute of Experimental Botany), Zeev Frenkel(University of Haifa), Bikram Gill(Kansas State University), Abraham B. Korol(University of Haifa), Thomas Letellier(Université Paris-Saclay), Odd-Arne Olsen(Norwegian University of Life Sciences), Kuldeep Singh(ICAR-National Bureau Of Plant Genetic Resources), Miroslav Valárik(Czech Academy of Sciences, Institute of Experimental Botany), Edwin van der Vossen(Agro Business Park), Sonia Vautrin(Genomics and Biotechnology of the Fruits Laboratory), Song Weining(North West Agriculture and Forestry University), Tzion Fahima(University of Haifa), Vladimir Glikson(University of Haifa), Dina Raats(Earlham Institute), Jarmila Číhalíková(Czech Academy of Sciences, Institute of Experimental Botany), Helena Toegelová(Czech Academy of Sciences, Institute of Experimental Botany), Jan Vrána(Czech Academy of Sciences, Institute of Experimental Botany), Pierre Sourdille(Génétique, Diversité, Écophysiologie des Céréales), Benoît Darrier(Génétique, Diversité, Écophysiologie des Céréales), Delfina Barabaschi(Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria), Luigi Cattivelli(Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria), Pilar Hernández(Instituto de Agricultura Sostenible), Sergio Gálvez(Universidad de Málaga), Hikmet Budak(Montana State University), Jonathan D. G. Jones(Norwich Research Park), Kamil Witek(Norwich Research Park), Guotai Yu(Norwich Research Park), Ian Small(ARC Centre of Excellence in Plant Energy Biology), Joanna Melonek(ARC Centre of Excellence in Plant Energy Biology), Ruonan Zhou(Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)), Tatiana Belova(Norwegian University of Life Sciences), K. Kanyuka(Rothamsted Research), Robert C. King(Rothamsted Research), Kirby T. Nilsen(University of Saskatchewan), Sean Walkowiak(University of Saskatchewan), Richard D. Cuthbert(Agriculture and Agri-Food Canada), R. E. Knox(Agriculture and Agri-Food Canada), Krysta Wiebe(University of Saskatchewan), Daoquan Xiang(Plant Biotechnology Institute), Antje Rohde(Bayer (Belgium)), T. J. Golds(Bayer (Belgium)), Jana Čížková(Czech Academy of Sciences, Institute of Experimental Botany), Bala Anı Akpınar(Montana State University), Sezgi Biyiklioglu(Montana State University), Liangliang Gao(Kansas State University), Amidou N’Daiye(University of Saskatchewan), Marie Kubaláková(Czech Academy of Sciences, Institute of Experimental Botany), Jan Šafář(Czech Academy of Sciences, Institute of Experimental Botany), Françoise Alfama(Université Paris-Saclay), Anne‐Françoise Adam‐Blondon(Université Paris-Saclay), Raphaël Flores(Université Paris-Saclay), Claire Guerche(Université Paris-Saclay), Mikaël Loaec(Université Paris-Saclay), Hadi Quesneville(Université Paris-Saclay), Janet Condie(Plant Biotechnology Institute), Jennifer Ens(University of Saskatchewan), Ron MacLachlan(University of Saskatchewan), Yifang Tan(Plant Biotechnology Institute), Adriana Alberti(Commissariat à l'Énergie Atomique et aux Énergies Alternatives), Jean‐Marc Aury(Commissariat à l'Énergie Atomique et aux Énergies Alternatives), Valérie Barbe(Commissariat à l'Énergie Atomique et aux Énergies Alternatives), Arnaud Couloux(Commissariat à l'Énergie Atomique et aux Énergies Alternatives), Corinne Cruaud(Commissariat à l'Énergie Atomique et aux Énergies Alternatives), Karine Labadie(Commissariat à l'Énergie Atomique et aux Énergies Alternatives), Sophie Mangenot(Commissariat à l'Énergie Atomique et aux Énergies Alternatives), Patrick Wincker(Centre National de la Recherche Scientifique), Gaganpreet Kaur(Kansas State University), Ming‐Cheng Luo(University of California, Davis), Sunish K. Sehgal(South Dakota State University), Parveen Chhuneja(ICAR-National Bureau Of Plant Genetic Resources), O. P. Gupta(ICAR-National Bureau Of Plant Genetic Resources), Suruchi Jindal(ICAR-National Bureau Of Plant Genetic Resources), Parampreet Kaur(ICAR-National Bureau Of Plant Genetic Resources), Palvi Malik(ICAR-National Bureau Of Plant Genetic Resources), Priti Sharma(ICAR-National Bureau Of Plant Genetic Resources), Bharat Yadav(ICAR-National Bureau Of Plant Genetic Resources), Nisha Singh(National Research Centre on Plant Biotechnology), Jitendra P. Khurana(University of Delhi), Chanderkant Chaudhary(University of Delhi), Paramjit Khurana(University of Delhi), Vinod Kumar(National Research Centre on Plant Biotechnology), Ajay Kumar Mahato(National Research Centre on Plant Biotechnology), Saloni Mathur(University of Delhi), Amitha Mithra Sevanthi(National Research Centre on Plant Biotechnology), Naveen Sharma(University of Delhi), R. S. Tomar(National Research Centre on Plant Biotechnology), Kateřina Holušová(Czech Academy of Sciences, Institute of Experimental Botany), Ondřej Plíhal(Centre of the Region Haná for Biotechnical and Agricultural Research), Matthew D. Clark(Natural History Museum), Darren Heavens(Earlham Institute), George Kettleborough(Earlham Institute), Jon Wright(Earlham Institute), Barbora Balcárková(Czech Academy of Sciences, Institute of Experimental Botany), Yuqin Hu(University of California, Davis), Е. А. Салина(Institute of Cytology and Genetics), Nikolai V. Ravin(Lomonosov Moscow State University), K. G. Skryabin(Lomonosov Moscow State University), Alexey V. Beletsky(Bioengineering Center), Vitaly V. Kadnikov(Bioengineering Center), Andrey V. Mardanov(Bioengineering Center), Michail Nesterov(Institute of Cytology and Genetics), Andrey L. Rakitin(Bioengineering Center), E. M. Sergeeva(Institute of Cytology and Genetics), Hirokazu Handa(Institute of Crop Science), Hiroyuki Kanamori(Institute of Crop Science), Satoshi Katagiri(Institute of Crop Science), Fuminori Kobayashi(Institute of Crop Science), Shuhei Nasuda(Kyoto University), Tsuyoshi Tanaka(Institute of Crop Science), Jianzhong Wu(Institute of Crop Science), Federica Cattonaro(Istituto di Genomica Applicata), Min Jiumeng(BGI Group (China)), Karl Kugler(Helmholtz Zentrum München), Matthias Pfeifer(Helmholtz Zentrum München), Simen R. Sandve(Norwegian University of Life Sciences), Xun Xu(BGI Group (China)), Bujie Zhan(Norwegian University of Life Sciences), Jacqueline Batley(The University of Western Australia), Philipp E. Bayer(The University of Western Australia), David Edwards(The University of Western Australia), Satomi Hayashi(Queensland University of Technology), Zuzana Tulpová(Czech Academy of Sciences, Institute of Experimental Botany), Paul Visendi(University of Greenwich), Licao Cui(North West Agriculture and Forestry University), Xianghong Du(North West Agriculture and Forestry University), Kewei Feng(North West Agriculture and Forestry University), Xiaojun Nie(North West Agriculture and Forestry University), Wei Tong(North West Agriculture and Forestry University), Le Wang(North West Agriculture and Forestry University)
Cited by 3,357Open Access
Abstract
An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.
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