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.
Bibliographical noteFunding Information:
The authors would like to thank the following for their financial support of research that enabled the completion of the IWGSC RefSeq v1.0 Project: Agence Nationale pour la Recherche (ANR), ANR-11-BSV5-0015-Ploid-Ploid Wheat-Unravelling bases of polyploidy success in wheat and ANR-16-TERC-0026-01- 3DWHEAT; Agriculture and Agri-Food Canada National Wheat Improvement Program and the AgriFlex Program; Alberta Wheat Development Commission through the Canadian Applied Tricticum Genomics (CTAG2); Australian Government, Department of Industry, Innovation, Climate Change, Science, Research, and Tertiary Education, Australia China Science and Research Fund Group Mission (Funding Agreement ACSRF00542); Australian Research Council Centre of Excellence in Plant Energy Biology (CE140100008); Australian Research Council Laureate Fellowship (FL140100179); Bayer CropScience; Biotechnology and Biological Sciences Research Council (BBSRC) 20:20 Wheat (project number BB/J00426X/1), Institute Strategic Programme grant (BB/ J004669/1), Designing Future Wheat (DFW) Institute Strategic Programme (BB/P016855/1), the Wheat Genomics for Sustainable Agriculture (BB/J003557/1), and the Anniversary Future Leader Fellowship (BB/M014045/1); Canada First Research Excellence Fund through the Designing Crops for Global Food Security initiative at the University of Saskatchewan; Council for Agricultural Research and Economics, Italy, through CREA-Interomics; Department of Biotechnology, Ministry of Science and Technology, Government of India File No. F grant no. BT/IWGSC/03/TF/2008; DFG (SFB924) for support of KFXM; European Commission through the TriticeaeGenome (FP7-212019); France Génomique (ANR-10-INBS-09) Genome Canada through the CTAG2 project; Genome Prairie through the CTAG2 project; German Academic Exchange Service (DAAD) PPP Australien 1j16; German Federal Ministry of Food and Agriculture grant 2819103915 WHEATSEQ; German Ministry of Education and Research grant 031A536 de.NBI; Global Institute for Food Security Genomics and Bioinformatics fund; Gordon and Betty Moore Foundation grant GBMF4725 to Two Blades Foundation; Grain Research Development Corporation (GRDC) Australia; Graminor AS NFR project 199387, Expanding the technology base for Norwegian wheat breeding; Sequencing wheat chromosome 7B; illumina; INRA, French National Institute for Agricultural Research; International Wheat Genome Sequencing Consortium and its sponsors; Israel Science Foundation grants 999/12, 1137/17, and 1824/12; Junta de Andalucía, Spain, project P12-AGR-0482; MINECO (Spanish Ministry of Economy, Industry, and Competitiveness) project BIO2011-15237-E; Ministry of Agriculture, Forestry, and Fisheries of Japan through Genomics for Agricultural Innovation, KGS-1003 and through Genomics-based Technology for Agricultural Improvement, NGB-1003; Ministry of Education and Science of Russian Federation project RFMEFI60414X0106 and project RFMEFI60414 X0107; Ministry of Education, Youth, and Sport of the Czech Republic award no. LO1204 (National Program of Sustainability I); Nisshin Flour Milling, Inc.; National Research Council of Canada Wheat Flagship program; Norwegian University of Life Sciences (NMBU) NFR project 199387, Expanding the technology base for Norwegian wheat breeding, Sequencing wheat chromosome 7B; National Science Foundation, United States, award (FAIN) 1339389, GPF-PG: Genome Structure and Diversity of Wheat and Its Wild Relatives, award DBI-0701916, and award IIP-1338897; Russian Science Foundation project 14-14- 00161; Saskatchewan Ministry of Agriculture through the CTAG2 project; Saskatchewan Wheat Development Commission through the CTAG2 project; The Czech Science Foundation award no. 521/ 06/1723 (Construction of BAC library and physical mapping of the wheat chromosome 3D), award no. 521-08-1629 (Construction of BAC DNA libraries specific for chromosome 4AL and positional cloning of gene for adult plant resistance to powdery mildew in wheat), award no. P501/10/1740 (Physical map of the wheat chromosome 4AL and positional cloning of a gene for yield), award no. P501/12/2554 (Physical map of wheat chromosome arm 7DS and its use to clone a Russian wheat aphid-resistance gene), award no. P501/12/G090 (Evolution and function of complex plant genomes), award no. 14-07164S (Cloning and molecular characterization of wheat QPm-tut-4A gene conferring seedling and adult plant race-nonspecific powdery-mildew resistance), and award no. 13-08786S (Chromosome arm 3DS of bread wheat: Its sequence and function in allopolyploid genome); The Research Council of Norway (NFR) project 199387, Expanding the technology base for Norwegian wheat breeding; Sequencing wheat chromosome 7B; U.S. Department of Agriculture NIFA 2008-35300-04588, the University of Zurich; Western Grains Research Foundation through the CTAG2 project; Western Grains Research Foundation National Wheat Improvement Program; and the Winifred-Asbjornson Plant Science Endowment Fund. The research leading to these results has also received funding from the French Government managed by the ANR under the Investment for the Future program (BreedWheat project ANR-10-BTBR-03), from FranceAgriMer (2011-0971 and 2013-0544), French Funds to support Plant Breeding (FSOV), and INRA. Axiom genotyping was conducted on the genotyping platform GENTYANE at INRA Clermont-Ferrand (gentyane.clermont.inra.fr). This research was supported in part by the NBI Computing infrastructure for Science (CiS) group through the HPC cluster.