Shifting the limits in wheat research and breeding using a fully annotated reference genome
R. AppelsAgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, AustraliaKellye EversoleEversole Associates, 5207 Wyoming Road, Bethesda, MD 20816, USANils SteinLeibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, GermanyCatherine FeuilletBayer CropScience, Crop Science Division, Research and Development, Innovation Centre, 3500 Paramount Parkway, Morrisville, NC 27560, USABeat KellerDepartment of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, SwitzerlandJane RogersInternational Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge CB23 1HE, UKCurtis PozniakUniversity of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, CanadaFrédéric ChouletGDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, FranceAssaf DistelfeldSchool of Plant Sciences and Food Security, Tel Aviv University, Ramat Aviv 69978, IsraelJesse PolandPlant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USAGil RonenNRGene Ltd., 5 Golda Meir Street, Ness Ziona 7403648, IsraelAndrew SharpeUniversity of Saskatchewan, Global Institute for Food Security, 110 Gymnasium Place, Saskatoon, SK S7N 4J8, CanadaOmer BaradNRGene Ltd., 5 Golda Meir Street, Ness Ziona 7403648, IsraelKobi BaruchNRGene Ltd., 5 Golda Meir Street, Ness Ziona 7403648, IsraelGabriel Keeble‐GagnèreAgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, AustraliaMartin MascherGerman Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, GermanyGil Ben-ZviNRGene Ltd., 5 Golda Meir Street, Ness Ziona 7403648, IsraelAmbre-Aurore JosselinGDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, FranceAxel HimmelbachLeibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, GermanyFrançois BalfourierGDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, FranceJuan J. Gutiérrez-GonzálezDepartment of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, St. Paul, MN 55108, USAMatthew HaydenAgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, AustraliaChuShin KohUniversity of Saskatchewan, Global Institute for Food Security, 110 Gymnasium Place, Saskatoon, SK S7N 4J8, CanadaGary J. MuehlbauerDepartment of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, St. Paul, MN 55108, USARaj PasamAgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, AustraliaEtienne PauxGDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, FrancePhilippe RigaultGYDLE, Suite 220, 1135 Grande Allée, Ouest, Québec, QC G1S 1E7, CanadaJosquin TibbitsAgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, AustraliaVijay TiwariPlant Science and Landscape Architecture, University of Maryland, 4291 Fieldhouse Road, 2102 Plant Sciences Building, College Park, MD 20742, USAM. SpannaglHelmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, GermanyDaniel LangHelmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, GermanyHeidrun GundlachHelmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, GermanyGeorg HabererHelmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, GermanyKlaus MayerHelmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, GermanyDanara OrmanbekovaDepartment of Agricultural Sciences, University of Bologna, Viale Fanin, 44 40127 Bologna, ItalyVerena M. PradeHelmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, GermanyHana ŠimkováInstitute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech RepublicThomas WickerDepartment of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, SwitzerlandDavid SwarbreckEarlham Institute, Core Bioinformatics, Norwich NR4 7UZ, UKHélène RimbertGDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, FranceMarius FelderHelmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, GermanyNicolas GuilhotGDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, FranceGemy KaithakottilEarlham Institute, Core Bioinformatics, Norwich NR4 7UZ, UKJens KeilwagenJulius Kühn-Institut, Institute for Biosafety in Plant Biotechnology, Erwin-Baur-Str. 27, 06484 Quedlinburg, GermanyPhilippe LeroyGDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, FranceThomas LuxHelmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, GermanySven TwardziokHelmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, GermanyLuca VenturiniEarlham Institute, Core Bioinformatics, Norwich NR4 7UZ, UKAngéla JuhászAgricultural Institute, MTA Centre for Agricultural Research, Applied Genomics Department, 2 Brunszvik Street, Martonvásár H 2462, HungaryMichaël AbroukBiological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi ArabiaIris FischerHelmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, GermanyCristóbal UauyJohn Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UKPhilippa BorrillJohn Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UKRicardo H. Ramírez-GonzálezJohn Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UKDominique ArnaudInstitut National de la Recherche Agronomique (INRA), 2 rue Gaston Crémieux, 91057 Evry Cedex, FranceSmahane ChalabiInstitut National de la Recherche Agronomique (INRA), 2 rue Gaston Crémieux, 91057 Evry Cedex, FranceBoulos ChalhoubInstitut National de la Recherche Agronomique (INRA), 2 rue Gaston Crémieux, 91057 Evry Cedex, FranceAron T. CoryUniversity of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, CanadaRaju DatlaNational Research Council Canada, Aquatic and Crop Resource Development, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, CanadaMark W. DaveyBayer CropScience, Trait Research, Innovation Center, Technologiepark 38, 9052 Gent, BelgiumJohn JacobsBayer CropScience, Trait Research, Innovation Center, Technologiepark 38, 9052 Gent, BelgiumStephen J. RobinsonAgriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N 0X2, CanadaBurkhard SteuernagelJohn Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UKFred van ExBayer CropScience, Trait Research, Innovation Center, Technologiepark 38, 9052 Gent, BelgiumBrande B. H. WulffJohn Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UKMoussa BenhamedBiology Department, Institute of Plant Sciences–Paris-Saclay, Bâtiment 630, rue de Noetzlin, Plateau du Moulon, CS80004, 91192 Gif-sur-Yvette Cedex, FranceAbdelhafid BendahmaneBiology Department, Institute of Plant Sciences–Paris-Saclay, Bâtiment 630, rue de Noetzlin, Plateau du Moulon, CS80004, 91192 Gif-sur-Yvette Cedex, FranceLorenzo ConciaBiology Department, Institute of Plant Sciences–Paris-Saclay, Bâtiment 630, rue de Noetzlin, Plateau du Moulon, CS80004, 91192 Gif-sur-Yvette Cedex, FranceDavid LatrasseBiology Department, Institute of Plant Sciences–Paris-Saclay, Bâtiment 630, rue de Noetzlin, Plateau du Moulon, CS80004, 91192 Gif-sur-Yvette Cedex, FranceJan BartošInstitute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech RepublicArnaud BellecINRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, FranceHélène BergèsINRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, FranceJaroslav DoleželInstitute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech RepublicZeev FrenkelUniversity of Haifa, Institute of Evolution and the Department of Evolutionary and Environmental Biology, 199 Abba-Hushi Avenue, Mount Carmel, Haifa 3498838, IsraelBikram GillPlant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USAAbraham B. KorolUniversity of Haifa, Institute of Evolution and the Department of Evolutionary and Environmental Biology, 199 Abba-Hushi Avenue, Mount Carmel, Haifa 3498838, IsraelThomas LetellierURGI, INRA, Université Paris-Saclay, 78026 Versailles, FranceOdd-Arne OlsenFaculty of Bioscience, Department of Plant Science, Norwegian University of Life Sciences, Arboretveien 6, 1433 Ås, NorwayKuldeep SinghPunjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR–National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, IndiaMiroslav ValárikInstitute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech RepublicEdwin van der VossenKeygene, N.V., Agro Business Park 90, 6708 PW Wageningen, NetherlandsSonia VautrinINRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, FranceSong WeiningState Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712101, ChinaTzion FahimaUniversity of Haifa, Institute of Evolution and the Department of Evolutionary and Environmental Biology, 199 Abba-Hushi Avenue, Mount Carmel, Haifa 3498838, IsraelVladimir GliksonMultiQTL Ltd., University of Haifa, Haifa 3498838, IsraelDina RaatsEarlham Institute, Core Bioinformatics, Norwich NR4 7UZ, UKJarmila ČíhalíkováInstitute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech RepublicHelena ToegelováInstitute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech RepublicJan VránaInstitute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech RepublicPierre SourdilleGDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, FranceBenoît DarrierGDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, FranceDelfina BarabaschiCouncil for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, via S. Protaso, 302, I -29017 Fiorenzuola d’Arda, ItalyLuigi CattivelliCouncil for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, via S. Protaso, 302, I -29017 Fiorenzuola d’Arda, ItalyPilar HernándezInstituto de Agricultura Sostenible (IAS-CSIC), Consejo Superior de Investigaciones Científicas, Alameda del Obispo s/n, 14004 Córdoba, SpainSergio GálvezUniversidad de Málaga, Lenguajes y Ciencias de la Computación, Campus de Teatinos, 29071 Málaga, SpainHikmet BudakPlant Sciences and Plant Pathology, Cereal Genomics Lab, Montana State University, 412 Leon Johnson Hall, Bozeman, MT 59717, USAJonathan D. G. JonesThe Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UKKamil WitekThe Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UKGuotai YuJohn Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UKIan SmallSchool of Molecular Sciences, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
2018en
ABI
Annotatsiya
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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