Multiple wheat genomes reveal global variation in modern breeding

Citation

Walkowiak, S., Gao, L., Monat, C., Haberer, G., Kassa, M.T., Brinton, J., Ramirez-Gonzalez, R.H., Kolodziej, M.C., Delorean, E., Thambugala, D., Klymiuk, V., Byrns, B., Gundlach, H., Bandi, V., Siri, J.N., Nilsen, K., Aquino, C., Himmelbach, A., Copetti, D., Ban, T., Venturini, L., Bevan, M., Clavijo, B., Koo, D.H., Ens, J., Wiebe, K., N’Diaye, A., Fritz, A.K., Gutwin, C., Fiebig, A., Fosker, C., Fu, B.X., Accinelli, G.G., Gardner, K.A., Fradgley, N., Gutierrez-Gonzalez, J., Halstead-Nussloch, G., Hatakeyama, M., Koh, C.S., Deek, J., Costamagna, A.C., Fobert, P., Heavens, D., Kanamori, H., Kawaura, K., Kobayashi, F., Krasileva, K., Kuo, T., McKenzie, N., Murata, K., Nabeka, Y., Paape, T., Padmarasu, S., Percival-Alwyn, L., Kagale, S., Scholz, U., Sese, J., Juliana, P., Singh, R., Shimizu-Inatsugi, R., Swarbreck, D., Cockram, J., Budak, H., Tameshige, T., Tanaka, T., Tsuji, H., Wright, J., Wu, J., Steuernagel, B., Small, I., Cloutier, S., Keeble-Gagnère, G., Muehlbauer, G., Tibbets, J., Nasuda, S., Melonek, J., Hucl, P.J., Sharpe, A.G., Clark, M., Legg, E., Bharti, A., Langridge, P., Hall, A., Uauy, C., Mascher, M., Krattinger, S.G., Handa, H., Shimizu, K.K., Distelfeld, A., Chalmers, K., Keller, B., Mayer, K.F.X., Poland, J., Stein, N., McCartney, C.A., Spannagl, M., Wicker, T., Pozniak, C.J. (2020). Multiple wheat genomes reveal global variation in modern breeding. Nature, [online] 588(7837), 277-283. http://dx.doi.org/10.1038/s41586-020-2961-x

Plain language summary

Wheat provides 20% of the proteins and 20% of the calories necessary to feed the world’s population. Wheat is therefore a staple food to the same extent as rice. This may be where the similarity between these two cereals ends. Indeed, they are vastly different in their genome complexity. All the genes in rice are contained in a genome of 400 million nucleotides. While this seems big, it is in fact 40 times smaller than the bread wheat genome at 16000. In addition to its sheer size, the wheat genome comprises a lot of repetitive sequences, all of which contributing to the daunting task that is the decoding and understanding of its primary DNA sequence. While the rice genome sequence was released in 2002, the first wheat genome sequence, that of line Chinese Spring, only came in 2018. A reference sequence is a useful and necessary resource but it does not represent the genetic variability that exists within the species. DNA sequencing of other lines is often conducted to gain this understanding. The sequencing depth and its resulting assemblies will dictate the information potential that it can provide. Here, we produced high quality chromosome-level assemblies of ten additional wheat lines and five slightly lower-level assemblies. While it took 16 years longer than rice to publish the first wheat genome sequence, it only took two years beyond that to produce ten more. This comprehensive nature of this information allows not only to understand variation among genes but also to understand breeders have shaped the genetic make-up of this staple crop. For example, this information was crucial to identify and isolate the Sm1 gene which is broadly used in Western Canada to provide resistance against the orange blossom wheat midge, an insect pest that can wreak havoc to the wheat crop. Breeders regularly identify useful genes in wild relatives which they cross into wheat. The high level of resolution provided by the sequence of the 10+ Wheat Genome Project (http://www.10wheatgenomes.com/) featured here led to the identification of entire chromosomal regions that had been introgressed from such wild relatives and provided a comprehensive cataloguing of the segments and their origin. This was possible only through the high-level resolution and quality of the sequence assemblies provided. Many human diseases such as Alzheimer, autism, Crohn, Parkinson and many more have been associated with “copy number” and “presence-absence” variants. The same is true in plants; meaning that there are many traits that are the results of these types of genetic variations. To dissect such variation, a high-quality assembly is a prerequisite; hence the research presented here achieve this and provide the necessary resources to dissect the role of a wide variety of genetic variations and to associate them with important traits such as yield, grain quality and resistance to biotic and abiotic stresses.

Abstract

Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome1, and the lack of genome-assembly data for multiple wheat lines2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses4,5. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm16, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.

Publication date

2020-12-10

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