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

Kumar Gaurav; Sanu Arora; Paula Silva; Javier Sánchez-Martín; Richard Horsnell; Liangliang Gao; Gurcharn S. Brar; Victoria Widrig; W. John Raupp; Narinder Singh; Shuangye Wu; Sandip M. Kale; Catherine Chinoy; Paul Nicholson; Jesús Quiroz-Chávez; James Simmonds; Sadiye Hayta; Mark A. Smedley; Wendy Harwood; Suzannah Pearce; David Gilbert; Ngonidzashe Kangara; Catherine Gardener; Macarena Forner-Martínez; Jiaqian Liu; Guotai Yu; Scott A. Boden; Attilio Pascucci; Sreya Ghosh; Amber N. Hafeez; Tom O’Hara; Joshua Waites; Jitender Cheema; Burkhard Steuernagel; Mehran Patpour; Annemarie Fejer Justesen; Shuyu Liu; Jackie C. Rudd; Raz Avni; Amir Sharon; Barbara Steiner; Rizky Pasthika Kirana; Hermann Buerstmayr; Ali A. Mehrabi; Firuza Y. Nasyrova; Noam Chayut; Oadi Matny; Brian J. Steffenson; Nitika Sandhu; Parveen Chhuneja; Evans Lagudah; Ahmed F. Elkot; Simon Tyrrell; Xingdong Bian; Robert P. Davey; Martin Simonsen; Leif Schauser; Vijay K. Tiwari; H. Randy Kutcher; Pierre Hucl; Aili Li; Deng Cai Liu; Long Mao; Steven Xu; Gina Brown-Guedira; Justin Faris; Jan Dvorak; Ming Cheng Luo; Ksenia Krasileva; Thomas Lux; Susanne Artmeier; Klaus F.X. Mayer; Cristobal Uauy; Martin Mascher; Alison R. Bentley; Beat Keller; Jesse Poland; Brande B.H. Wulff

doi:10.1038/s41587-021-01058-4

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

Kumar Gaurav, Sanu Arora, Paula Silva, Javier Sánchez-Martín, Richard Horsnell, Liangliang Gao, Gurcharn S. Brar, Victoria Widrig, W. John Raupp, Narinder Singh, Shuangye Wu, Sandip M. Kale, Catherine Chinoy, Paul Nicholson, Jesús Quiroz-Chávez, James Simmonds, Sadiye Hayta, Mark A. Smedley, Wendy Harwood, Suzannah PearceDavid Gilbert, Ngonidzashe Kangara, Catherine Gardener, Macarena Forner-Martínez, Jiaqian Liu, Guotai Yu, Scott A. Boden, Attilio Pascucci, Sreya Ghosh, Amber N. Hafeez, Tom O’Hara, Joshua Waites, Jitender Cheema, Burkhard Steuernagel, Mehran Patpour, Annemarie Fejer Justesen, Shuyu Liu, Jackie C. Rudd, Raz Avni, Amir Sharon, Barbara Steiner, Rizky Pasthika Kirana, Hermann Buerstmayr, Ali A. Mehrabi, Firuza Y. Nasyrova, Noam Chayut, Oadi Matny, Brian J. Steffenson, Nitika Sandhu, Parveen Chhuneja, Evans Lagudah, Ahmed F. Elkot, Simon Tyrrell, Xingdong Bian, Robert P. Davey, Martin Simonsen, Leif Schauser, Vijay K. Tiwari, H. Randy Kutcher, Pierre Hucl, Aili Li, Deng Cai Liu, Long Mao, Steven Xu, Gina Brown-Guedira, Justin Faris, Jan Dvorak, Ming Cheng Luo, Ksenia Krasileva, Thomas Lux, Susanne Artmeier, Klaus F.X. Mayer, Cristobal Uauy, Martin Mascher, Alison R. Bentley, Beat Keller, Jesse Poland, Brande B.H. Wulff

Plant Pathology

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Abstract

Aegilops tauschii, the diploid wild progenitor of the D subgenome of bread wheat, is a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. Here we sequenced 242 Ae. tauschii accessions and compared them to the wheat D subgenome to characterize genomic diversity. We found that a rare lineage of Ae. tauschii geographically restricted to present-day Georgia contributed to the wheat D subgenome in the independent hybridizations that gave rise to modern bread wheat. Through k-mer-based association mapping, we identified 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 hexaploids incorporating diverse Ae. tauschii genomes. Exploiting the genomic diversity of the Ae. tauschii ancestral diploid genome permits rapid trait discovery and functional genetic validation in a hexaploid background amenable to breeding.

Original language	English (US)
Pages (from-to)	422-431
Number of pages	10
Journal	Nature biotechnology
Volume	40
Issue number	3
DOIs	https://doi.org/10.1038/s41587-021-01058-4
State	Published - Mar 2022

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© 2021, The Author(s).

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Gaurav, K., Arora, S., Silva, P., Sánchez-Martín, J., Horsnell, R., Gao, L., Brar, G. S., Widrig, V., John Raupp, W., Singh, N., Wu, S., Kale, S. M., Chinoy, C., Nicholson, P., Quiroz-Chávez, J., Simmonds, J., Hayta, S., Smedley, M. A., Harwood, W., ... Wulff, B. B. H. (2022). Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement. Nature biotechnology, 40(3), 422-431. https://doi.org/10.1038/s41587-021-01058-4

Gaurav, K, Arora, S, Silva, P, Sánchez-Martín, J, Horsnell, R, Gao, L, Brar, GS, Widrig, V, John Raupp, W, Singh, N, Wu, S, Kale, SM, Chinoy, C, Nicholson, P, Quiroz-Chávez, J, Simmonds, J, Hayta, S, Smedley, MA, Harwood, W, Pearce, S, Gilbert, D, Kangara, N, Gardener, C, Forner-Martínez, M, Liu, J, Yu, G, Boden, SA, Pascucci, A, Ghosh, S, Hafeez, AN, O’Hara, T, Waites, J, Cheema, J, Steuernagel, B, Patpour, M, Justesen, AF, Liu, S, Rudd, JC, Avni, R, Sharon, A, Steiner, B, Kirana, RP, Buerstmayr, H, Mehrabi, AA, Nasyrova, FY, Chayut, N, Matny, O, Steffenson, BJ, Sandhu, N, Chhuneja, P, Lagudah, E, Elkot, AF, Tyrrell, S, Bian, X, Davey, RP, Simonsen, M, Schauser, L, Tiwari, VK, Randy Kutcher, H, Hucl, P, Li, A, Liu, DC, Mao, L, Xu, S, Brown-Guedira, G, Faris, J, Dvorak, J, Luo, MC, Krasileva, K, Lux, T, Artmeier, S, Mayer, KFX, Uauy, C, Mascher, M, Bentley, AR, Keller, B, Poland, J & Wulff, BBH 2022, 'Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement', Nature biotechnology, vol. 40, no. 3, pp. 422-431. https://doi.org/10.1038/s41587-021-01058-4

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abstract = "Aegilops tauschii, the diploid wild progenitor of the D subgenome of bread wheat, is a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. Here we sequenced 242 Ae. tauschii accessions and compared them to the wheat D subgenome to characterize genomic diversity. We found that a rare lineage of Ae. tauschii geographically restricted to present-day Georgia contributed to the wheat D subgenome in the independent hybridizations that gave rise to modern bread wheat. Through k-mer-based association mapping, we identified 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 hexaploids incorporating diverse Ae. tauschii genomes. Exploiting the genomic diversity of the Ae. tauschii ancestral diploid genome permits rapid trait discovery and functional genetic validation in a hexaploid background amenable to breeding.",

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AU - Silva, Paula

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AU - Horsnell, Richard

AU - Gao, Liangliang

AU - Brar, Gurcharn S.

AU - Widrig, Victoria

AU - John Raupp, W.

AU - Singh, Narinder

AU - Wu, Shuangye

AU - Kale, Sandip M.

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AU - Liu, Deng Cai

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AU - Mayer, Klaus F.X.

AU - Uauy, Cristobal

AU - Mascher, Martin

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

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