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

• Published in: Science (American Association for the Advancement of Science) 2018-08, Vol.361 (6403)
• Main Authors: Appels, Rudi, Eversole, Kellye, Stein, Nils, Feuillet, Catherine, Keller, Beat, Rogers, Jane, Pozniak, Curtis J., Choulet, Frédéric, Distelfeld, Assaf, Poland, Jesse, Ronen, Gil, Sharpe, Andrew G., Barad, Omer, Baruch, Kobi, Keeble-Gagnère, Gabriel, Mascher, Martin, Ben-Zvi, Gil, Josselin, Ambre-Aurore, Himmelbach, Axel, Balfourier, François, Gutierrez-Gonzalez, Juan, Hayden, Matthew, Koh, ChuShin, Muehlbauer, Gary, Pasam, Raj K., Paux, Etienne, Rigault, Philippe, Tibbits, Josquin, Tiwari, Vijay, Spannagl, Manuel, Lang, Daniel, Gundlach, Heidrun, Haberer, Georg, Mayer, Klaus F. X., Ormanbekova, Danara, Prade, Verena, Šimková, Hana, Wicker, Thomas, Swarbreck, David, Rimbert, Hélène, Felder, Marius, Guilhot, Nicolas, Kaithakottil, Gemy, Keilwagen, Jens, Leroy, Philippe, Lux, Thomas, Twardziok, Sven, Venturini, Luca, Juhász, Angéla, Abrouk, Michael, Fischer, Iris, Uauy, Cristobal, Borrill, Philippa, Ramirez-Gonzalez, Ricardo H., Arnaud, Dominique, Chalabi, Smahane, Chalhoub, Boulos, Cory, Aron, Datla, Raju, Davey, Mark W., Jacobs, John, Robinson, Stephen J., Steuernagel, Burkhard, van Ex, Fred, Wulff, Brande B. H., Benhamed, Moussa, Bendahmane, Abdelhafid, Concia, Lorenzo, Latrasse, David, Bartoš, Jan, Bellec, Arnaud, Berges, Hélène, Doležel, Jaroslav, Frenkel, Zeev, Gill, Bikram, Korol, Abraham, Letellier, Thomas, Olsen, Odd-Arne, Singh, Kuldeep, Valárik, Miroslav, van der Vossen, Edwin, Vautrin, Sonia, Weining, Song, Fahima, Tzion, Glikson, Vladimir, Raats, Dina, Číhalíková, Jarmila, Toegelová, Helena, Vrána, Jan, Sourdille, Pierre, Darrier, Benoit, Barabaschi, Delfina, Cattivelli, Luigi, Hernandez, Pilar, Galvez, Sergio, Budak, Hikmet, Jones, Jonathan D. G., Witek, Kamil, Yu, Guotai, Small, Ian
• Format: Article
• Language: English
• Subjects: Adaptation; Agricultural production; Agricultural research; Agronomy; Animal species; Annotations; Assembling; Assembly; Atlases as Topic; Bioinformatics; Biology; Biotechnology; Bread; Breeding; Calories; Chromosomes; Coding; Communities; Community Resources; Consortia; CRISPR; Crop yield; Crops; Deoxyribonucleic acid; Developmental stages; DNA; Editing; Flowering; Food sources; Gene expression; Gene Expression Regulation, Developmental; Gene Expression Regulation, Plant; Gene families; Gene mapping; Gene sequencing; Genetics; Genome editing; Genome, Plant; Genomes; Genomics; Global economy; Human populations; Innovations; Insects; Life Sciences; Molecular Sequence Annotation; Multigene Family; Networks; Nucleotide sequence; Phylogeny; Plant breeding; Plant protection; Polyploidy; Population growth; Quality; Quantitative Trait Loci; Reference Standards; Regulatory sequences; Transcriptome; Triticum - anatomy & histology; Triticum - classification; Triticum - genetics; Triticum - growth & development; Triticum aestivum; Wheat
• ISSN: 0036-8075; 1095-9203
• DOI: 10.1126/science.aar7191

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.