Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement

Authors: GAURAV, KUMAR - John Innes Center; ARORA, SANU - John Innes Center; SILVA, PAULA - Kansas State University; SANCHEZ-MARTINEZ, JAVIER - University Of Zurich; HORSNELL, RICHARD - National Institute Of Agricultural Botany (NIAB); GAO, LIANGLIANG - Kansas State University; BRAR, GURCHARAN - University Of Saskatchewan; WIDRIG, VICTORIA - University Of Zurich; RAUPP, JON - Kansas State University; SINGH, NARINDER - Kansas State University; Xu, Steven; Brown-Guedira, Gina; Faris, Justin; WULFF, BRANDE - John Innes Center

Submitted to: Nature Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/16/2021
Publication Date: 11/1/2021
Citation: Gaurav, K., Arora, S., Silva, P., Sanchez-Martinez, J., Horsnell, R., Gao, L., Brar, G., Widrig, V., Raupp, J., Singh, N., Xu, S.S., Brown Guedira, G.L., Faris, J.D., Wulff, B.B., et al. 2021. Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement. Nature Biotechnology. 40:422-431. https://doi.org/10.1038/s41587-021-01058-4.
DOI: https://doi.org/10.1038/s41587-021-01058-4

Interpretive Summary: Modern day wheat evolved through the convergence of three different relative species and maintains the complete genetic makeup of all three species in the form of genomes A, B and D. A species of goatgrass contributed the D genome, and today goatgrass is often tapped as a genetic resource to improve traits in wheat such as yield, quality, and disease and pest resistance. To better understand the degree of genetic diversity in goatgrass, we determined the D genome DNA sequences of 242 goatgrass lines. Analysis of these DNA sequences led to the discovery of a geographically-restricted lineage of goatgrass directly involved in the formation of modern wheat thereby shedding light on the evolutionary events that shaped today’s wheat. Further genetic analysis was used to precisely identify segments of the goatgrass genome harboring genes governing resistance to diseases and pests, which were then transferred to wheat lines using cross hybridization and biotechnological methods. The genetic and genomic resources generated from this research provides wheat researchers an end-to-end pipeline for rapid and systematic exploration of the goatgrass gene pool for improving modern bread wheat.

Technical Abstract: Aegilops tauschii, the wild diploid progenitor of the D subgenome of bread wheat, constitutes a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. To better define and understand this diversity, we sequenced 242 Ae. tauschii accessions and compared them to the wheat D subgenome. We characterized a rare, geographically-restricted lineage of Ae. tauschii and discovered that it contributed to the wheat D subgenome, thereby elucidating the origin of bread wheat from at least two independent hybridizations. We then used k-mer—based association mapping to identify discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of ‘synthetic’ hexaploids incorporating diverse Ae. tauschii genomes. Thus, our end-to-end pipeline permits rapid trait discovery in the diploid ancestor through to functional genetic validation in a hexaploid background amenable to breeding.