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Science. 2018 Aug 17;361(6403). pii: eaar7191. doi: 10.1126/science.aar7191. Epub 2018 Aug 16.

Shifting the limits in wheat research and breeding using a fully annotated reference genome.

International Wheat Genome Sequencing Consortium (IWGSC); IWGSC RefSeq principal investigators:, Appels R1,2, Eversole K3,4, Feuillet C5, Keller B6, Rogers J7, Stein N8,9; IWGSC whole-genome assembly principal investigators:, Pozniak CJ10, Stein N8,9, Choulet F11, Distelfeld A12, Eversole K3,4, Poland J13, Rogers J7, Ronen G14, Sharpe AG15; Whole-genome sequencing and assembly:, Pozniak C10, Ronen G14, Stein N8,9, Barad O14, Baruch K14, Choulet F11, Keeble-Gagnère G16, Mascher M17,18, Sharpe AG15, Ben-Zvi G14, Josselin AA11; Hi-C data-based scaffolding:, Stein N8,9, Mascher M17,18, Himmelbach A17; Whole-genome assembly quality control and analyses:, Choulet F11, Keeble-Gagnère G16, Mascher M17,18, Rogers J7, Balfourier F11, Gutierrez-Gonzalez J19, Hayden M16, Josselin AA11, Koh C15, Muehlbauer G19, Pasam RK16, Paux E11, Pozniak CJ10, Rigault P20, Sharpe AG15, Tibbits J16, Tiwari V21; Pseudomolecule assembly:, Choulet F11, Keeble-Gagnère G16, Mascher M17,18, Josselin AA11, Rogers J7; RefSeq genome structure and gene analyses:, Spannagl M22, Choulet F11, Lang D22, Gundlach H22, Haberer G22, Keeble-Gagnère G16, Mayer KFX22,23, Ormanbekova D22,24, Paux E11, Prade V22, Šimková H25, Wicker T6; Automated annotation:, Choulet F11, Spannagl M22, Swarbreck D26, Rimbert H11, Felder M22, Guilhot N11, Gundlach H22, Haberer G22, Kaithakottil G26, Keilwagen J27, Lang D22, Leroy P11, Lux T22, Mayer KFX22,23, Twardziok S22, Venturini L26; Manual gene curation:, Appels R1,2, Rimbert H11, Choulet F11, Juhász A2,28, Keeble-Gagnère G16; Subgenome comparative analyses:, Choulet F11, Spannagl M22, Lang D22, Abrouk M25,29, Haberer G22, Keeble-Gagnère G16, Mayer KFX22,23, Wicker T6; Transposable elements:, Choulet F11, Wicker T6, Gundlach H22, Lang D22, Spannagl M22; Phylogenomic analyses:, Lang D22, Spannagl M22, Appels R1,2, Fischer I22; Transcriptome analyses and RNA-seq data:, Uauy C30, Borrill P30, Ramirez-Gonzalez RH30, Appels R1,2, Arnaud D31, Chalabi S31, Chalhoub B32,31, Choulet F11, Cory A10, Datla R33, Davey MW34, Hayden M16, Jacobs J34, Lang D22, Robinson SJ35, Spannagl M22, Steuernagel B30, Tibbits J16, Tiwari V21, van Ex F34, Wulff BBH30; Whole-genome methylome:, Pozniak CJ10, Robinson SJ35, Sharpe AG15, Cory A10; Histone mark analyses:, Benhamed M36, Paux E11, Bendahmane A36, Concia L36, Latrasse D36; BAC chromosome MTP IWGSC–Bayer Whole-Genome Profiling (WGP) tags:, Rogers J7, Jacobs J34, Alaux M37, Appels R1,2, Bartoš J25, Bellec A38, Berges H38, Doležel J25, Feuillet C5, Frenkel Z39, Gill B13, Korol A39, Letellier T37, Olsen OA40, Šimková H25, Singh K41, Valárik M25, van der Vossen E42, Vautrin S38, Weining S43; Chromosome LTC mapping and physical mapping quality control:, Korol A39, Frenkel Z39, Fahima T39, Glikson V44, Raats D26, Rogers J7; RH mapping:, Tiwari V21, Gill B13, Paux E11, Poland J13; Optical mapping:, Doležel J25, Číhalíková J25, Šimková H25, Toegelová H25, Vrána J25; Recombination analyses:, Sourdille P, Darrier B11; Gene family analyses:, Appels R1,2, Spannagl M22, Lang D22, Fischer I22, Ormanbekova D22,24, Prade V22; CBF gene family:, Barabaschi D45, Cattivelli L45; Dehydrin gene family:, Hernandez P46, Galvez S47, Budak H48; NLR gene family:, Steuernagel B30, Jones JDG49, Witek K49, Wulff BBH30, Yu G30; PPR gene family:, Small I50, Melonek J50, Zhou R17; Prolamin gene family:, Juhász A2,28, Belova T40, Appels R1,2, Olsen OA40; WAK gene family:, Kanyuka K51, King R52; Stem solidness (SSt1) QTL team:, Nilsen K10, Walkowiak S10, Pozniak CJ10, Cuthbert R53, Datla R33, Knox R53, Wiebe K10, Xiang D33; Flowering locus C (FLC) gene team:, Rohde A54, Golds T34; Genome size analysis:, Doležel J25, Čížková J25, Tibbits J16; MicroRNA and tRNA annotation:, Budak H48, Akpinar BA48, Biyiklioglu S48; Genetic maps and mapping:, Muehlbauer G19, Poland J13, Gao L13, Gutierrez-Gonzalez J19, N'Daiye A10; BAC libraries and chromosome sorting:, Doležel J25, Šimková H25, Číhalíková J25, Kubaláková M25, Šafář J25, Vrána J25; BAC pooling, BAC library repository, and access:, Berges H38, Bellec A38, Vautrin S38; IWGSC sequence and data repository and access:, Alaux M37, Alfama F37, Adam-Blondon AF37, Flores R37, Guerche C37, Letellier T37, Loaec M37, Quesneville H37; Physical maps and BAC-based sequences:; 1A BAC sequencing and assembly:, Pozniak CJ10, Sharpe AG33,15, Walkowiak S, Budak H48, Condie J33, Ens J10, Koh C15, Maclachlan R10, Tan Y33, Wicker T6; 1B BAC sequencing and assembly:, Choulet F11, Paux E11, Alberti A55, Aury JM55, Balfourier F11, Barbe V55, Couloux A55, Cruaud C55, Labadie K55, Mangenot S55, Wincker P55,56,57; 1D, 4D, and 6D physical mapping:, Gill B13, Kaur G13, Luo M58, Sehgal S59; 2AL physical mapping:, Singh K41, Chhuneja P41, Gupta OP41, Jindal S41, Kaur P41, Malik P41, Sharma P41, Yadav B41; 2AS physical mapping:, Singh NK60, Khurana J61, Chaudhary C61, Khurana P61, Kumar V60, Mahato A60, Mathur S61, Sevanthi A60, Sharma N61, Tomar RS60; 2B, 2D, 4B, 5BL, and 5DL IWGSC–Bayer Whole-Genome Profiling (WGP) physical maps:, Rogers J7, Jacobs J34, Alaux M37, Bellec A38, Berges H38, Doležel J25, Feuillet C5, Frenkel Z39, Gill B13, Korol A39, van der Vossen E42, Vautrin S38; 3AL physical mapping:, Gill B13, Kaur G13, Luo M58, Sehgal S59; 3DS physical mapping and BAC sequencing and assembly:, Bartoš J25, Holušová K25, Plíhal O62; 3DL BAC sequencing and assembly:, Clark MD26,63, Heavens D26, Kettleborough G26, Wright J26; 4A physical mapping, BAC sequencing, assembly, and annotation:, Valárik M25, Abrouk M25,29, Balcárková B25, Holušová K25, Hu Y58, Luo M58; 5BS BAC sequencing and assembly:, Salina E64, Ravin N65,66, Skryabin K65,66, Beletsky A65, Kadnikov V65, Mardanov A65, Nesterov M64, Rakitin A65, Sergeeva E64; 6B BAC sequencing and assembly:, Handa H67, Kanamori H67, Katagiri S67, Kobayashi F67, Nasuda S68, Tanaka T67, Wu J67; 7A physical mapping and BAC sequencing:, Appels R1,2, Hayden M16, Keeble-Gagnère G16, Rigault P20, Tibbits J16; 7B physical mapping, BAC sequencing, and assembly:, Olsen OA40, Belova T40, Cattonaro F69, Jiumeng M70, Kugler K22, Mayer KFX22,23, Pfeifer M22, Sandve S71, Xun X72, Zhan B40; 7DS BAC sequencing and assembly:, Šimková H25, Abrouk M25,29, Batley J73, Bayer PE73, Edwards D73, Hayashi S74, Toegelová H25, Tulpová Z25, Visendi P75; 7DL physical mapping and BAC sequencing:, Weining S43, Cui L43, Du X43, Feng K43, Nie X43, Tong W43, Wang L43; Figures:, Borrill P30, Gundlach H22, Galvez S47, Kaithakottil G26, Lang D22, Lux T22, Mascher M17,18, Ormanbekova D22,24, Prade V22, Ramirez-Gonzalez RH30, Spannagl M22, Stein N8,9, Uauy C30, Venturini L26; Manuscript writing team:, Stein N8,9, Appels R1,2, Eversole K3,4, Rogers J7, Borrill P30, Cattivelli L45, Choulet F11, Hernandez P46, Kanyuka K51, Lang D22, Mascher M17,18, Nilsen K10, Paux E11, Pozniak CJ10, Ramirez-Gonzalez RH30, Šimková H25, Small I50, Spannagl M22, Swarbreck D26, Uauy C30.

Author information

1
AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia. rudi.appels@unimelb.edu.au eversole@eversoleassociates.com stein@ipk-gatersleben.de.
2
Murdoch University, Australia-China Centre for Wheat Improvement, School of Veterinary and Life Sciences, 90 South Street, Murdoch, WA 6150, Australia.
3
International Wheat Genome Sequencing Consortium (IWGSC), 5207 Wyoming Road, Bethesda, MD 20816, USA. rudi.appels@unimelb.edu.au eversole@eversoleassociates.com stein@ipk-gatersleben.de.
4
Eversole Associates, 5207 Wyoming Road, Bethesda, MD 20816, USA.
5
Bayer CropScience, Crop Science Division, Research and Development, Innovation Centre, 3500 Paramount Parkway, Morrisville, NC 27560, USA.
6
Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland.
7
International Wheat Genome Sequencing Consortium (IWGSC), 18 High Street, Little Eversden, Cambridge CB23 1HE, UK.
8
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany. rudi.appels@unimelb.edu.au eversole@eversoleassociates.com stein@ipk-gatersleben.de.
9
The University of Western Australia (UWA), School of Agriculture and Environment, 35 Stirling Highway, Crawley, WA 6009, Australia.
10
University of Saskatchewan, Crop Development Centre, Agriculture Building, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada.
11
GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France.
12
School of Plant Sciences and Food Security, Tel Aviv University, Ramat Aviv 69978, Israel.
13
Plant Pathology, Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA.
14
NRGene Ltd., 5 Golda Meir Street, Ness Ziona 7403648, Israel.
15
University of Saskatchewan, Global Institute for Food Security, 110 Gymnasium Place, Saskatoon, SK S7N 4J8, Canada.
16
AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport, and Resources, 5 Ring Road, La Trobe University, Bundoora, VIC 3083, Australia.
17
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank, Corrensstr. 3, 06466 Stadt Seeland, Germany.
18
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
19
Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, St. Paul, MN 55108, USA.
20
GYDLE, Suite 220, 1135 Grande Allée, Ouest, Québec, QC G1S 1E7, Canada.
21
Plant Science and Landscape Architecture, University of Maryland, 4291 Fieldhouse Road, 2102 Plant Sciences Building, College Park, MD 20742, USA.
22
Helmholtz Center Munich, Plant Genome and Systems Biology (PGSB), Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.
23
School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany.
24
Department of Agricultural Sciences, University of Bologna, Viale Fanin, 44 40127 Bologna, Italy.
25
Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, CZ-78371 Olomouc, Czech Republic.
26
Earlham Institute, Core Bioinformatics, Norwich NR4 7UZ, UK.
27
Julius Kühn-Institut, Institute for Biosafety in Plant Biotechnology, Erwin-Baur-Str. 27, 06484 Quedlinburg, Germany.
28
Agricultural Institute, MTA Centre for Agricultural Research, Applied Genomics Department, 2 Brunszvik Street, Martonvásár H 2462, Hungary.
29
Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia.
30
John Innes Centre, Crop Genetics, Norwich Research Park, Norwich NR4 7UH, UK.
31
Institut National de la Recherche Agronomique (INRA), 2 rue Gaston Crémieux, 91057 Evry Cedex, France.
32
Monsanto SAS, 28000 Boissay, France.
33
National Research Council Canada, Aquatic and Crop Resource Development, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada.
34
Bayer CropScience, Trait Research, Innovation Center, Technologiepark 38, 9052 Gent, Belgium.
35
Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N 0X2, Canada.
36
Biology Department, Institute of Plant Sciences-Paris-Saclay, Bâtiment 630, rue de Noetzlin, Plateau du Moulon, CS80004, 91192 Gif-sur-Yvette Cedex, France.
37
URGI, INRA, Université Paris-Saclay, 78026 Versailles, France.
38
INRA, CNRGV, chemin de Borde Rouge, CS 52627, 31326 Castanet-Tolosan Cedex, France.
39
University of Haifa, Institute of Evolution and the Department of Evolutionary and Environmental Biology, 199 Abba-Hushi Avenue, Mount Carmel, Haifa 3498838, Israel.
40
Faculty of Bioscience, Department of Plant Science, Norwegian University of Life Sciences, Arboretveien 6, 1433 Ås, Norway.
41
Punjab Agricultural University, Ludhiana, School of Agricultural Biotechnology, ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, New Delhi 110012, India.
42
Keygene, N.V., Agro Business Park 90, 6708 PW Wageningen, Netherlands.
43
State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712101, China.
44
MultiQTL Ltd., University of Haifa, Haifa 3498838, Israel.
45
Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics, via S. Protaso, 302, I -29017 Fiorenzuola d'Arda, Italy.
46
Instituto de Agricultura Sostenible (IAS-CSIC), Consejo Superior de Investigaciones Científicas, Alameda del Obispo s/n, 14004 Córdoba, Spain.
47
Universidad de Málaga, Lenguajes y Ciencias de la Computación, Campus de Teatinos, 29071 Málaga, Spain.
48
Plant Sciences and Plant Pathology, Cereal Genomics Lab, Montana State University, 412 Leon Johnson Hall, Bozeman, MT 59717, USA.
49
The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK.
50
School of Molecular Sciences, ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.
51
Rothamsted Research, Biointeractions and Crop Protection, West Common, Harpenden AL5 2JQ, UK.
52
Rothamsted Research, Computational and Analytical Sciences, West Common, Harpenden AL5 2JQ, UK.
53
Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, Box 1030, Swift Current, SK S9H 3X2, Canada.
54
Bayer CropScience, Breeding and Trait Development, Technologiepark 38, 9052 Gent, Belgium.
55
CEA-Institut de Biologie François-Jacob, Genoscope, 2 rue Gaston Crémieux, 91057 Evry Cedex, France.
56
CNRS, UMR 8030, CP5706, 91057 Evry, France.
57
Université d'Evry, UMR 8030, CP5706, 91057 Evry, France.
58
Department of Plant Sciences, University of California, Davis, One Shield Avenue, Davis, CA 95617, USA.
59
Agronomy Horticulture and Plant Science, South Dakota State University, 2108 Jackrabbit Drive, Brookings, SD 57006, USA.
60
ICAR-National Research Centre on Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India.
61
University of Delhi South Campus, Interdisciplinary Center for Plant Genomics and Department of Plant Molecular Biology, Benito Juarez Road, New Delhi 110021, India.
62
Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic.
63
Department of Lifesciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.
64
The Federal Research Center Institute of Cytology and Genetics, SB RAS, pr. Lavrentyeva 10, Novosibirsk 630090, Russia.
65
Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, Leninsky Avenue 33, Building 2, Moscow 119071, Russia.
66
Faculty of Biology, Moscow State University, Leninskie Gory, 1, Moscow 119991, Russia.
67
Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan.
68
Graduate School of Agriculture, Kyoto University, Kitashirakawaoiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan.
69
Instituto di Genomica Applicata, Via J. Linussio 51, Udine 33100, Italy.
70
BGI-Shenzhen, BGI Genomics, Building No. 7, BGI Park, No. 21 Hongan 3rd Street, Yantian District, Shenzhen 518083, China.
71
Faculty of Bioscience, Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Arboretveien 6, 1433 Ås, Norway.
72
BGI-Shenzhen, BGI Genomics, Yantian District, Shenzhen 518083, Guangdong, China.
73
School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia.
74
Queensland University of Technology, Earth, Environmental and Biological Sciences, Brisbane, QLD 4001, Australia.
75
University of Greenwich, Natural Resources Institute, Central Avenue, Chatham, Kent ME4 4TB, UK.

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.

PMID:
30115783
DOI:
10.1126/science.aar7191
[Indexed for MEDLINE]

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