Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome

Fei He; Raj Pasam; Fan Shi; Surya Kant; Gabriel Keeble-Gagnere; Pippa Kay; Kerrie Forrest; Allan Fritz; Pierre Hucl; Krystalee Wiebe; Ron Knox; Richard Cuthbert; Curtis Pozniak; Alina Akhunova; Peter L. Morrell; John P. Davies; Steve R. Webb; German Spangenberg; Ben Hayes; Hans Daetwyler; Josquin Tibbits; Matthew Hayden; Eduard Akhunov

doi:10.1038/s41588-019-0382-2

Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome

Fei He, Raj Pasam, Fan Shi, Surya Kant, Gabriel Keeble-Gagnere, Pippa Kay, Kerrie Forrest, Allan Fritz, Pierre Hucl, Krystalee Wiebe, Ron Knox, Richard Cuthbert, Curtis Pozniak, Alina Akhunova, Peter L. Morrell, John P. Davies, Steve R. Webb, German Spangenberg, Ben Hayes, Hans DaetwylerJosquin Tibbits, Matthew Hayden, Eduard Akhunov

Agronomy and Plant Genetics

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183 Scopus citations

Abstract

Introgression is a potential source of beneficial genetic diversity. The contribution of introgression to adaptive evolution and improvement of wheat as it was disseminated worldwide remains unknown. We used targeted re-sequencing of 890 diverse accessions of hexaploid and tetraploid wheat to identify wild-relative introgression. Introgression, and selection for improvement and environmental adaptation, each reduced deleterious allele burden. Introgression increased diversity genome wide and in regions harboring major agronomic genes, and contributed alleles explaining a substantial proportion of phenotypic variation. These results suggest that historic gene flow from wild relatives made a substantial contribution to the adaptive diversity of modern bread wheat.

Original language	English (US)
Pages (from-to)	896-904
Number of pages	9
Journal	Nature Genetics
Volume	51
Issue number	5
DOIs	https://doi.org/10.1038/s41588-019-0382-2
State	Published - May 1 2019

Bibliographical note

Funding Information:
This project was supported by the Agriculture and Food Research Initiative Competitive Grants 2017-67007-25939 (Wheat-CAP) and 2016-67013-24473 from the USDA National Institute of Food and Agriculture, and grants from the Bill and Melinda Gates Foundation and Kansas Wheat Commission. Exome sequencing of Canadian wheat cultivars was supported through the Canadian Triticum Applied Genomics grant funded by Genome Canada, Genome Prairie, Saskatchewan Ministry of Agriculture, and the Western Grains Research Foundation. P.L.M. was supported by grant IOS-1339393 from the US National Science Foundation. Corteva Agriscience, Agriculture Division of DowDuPont provided financial support through collaboration with Agriculture Victoria Services enabling the development of the SNP dataset and technologies used in this manuscript. The authors would like to thank International Wheat Genome Sequencing Consortium for providing access to wheat genome sequence under Toronto agreement, D. Andresen for assistance with the computing resources of the KSU Beocat cluster funded by NSF grant ACI-144054 and K. Jordan for valuable suggestions and editing the manuscript.

Publisher Copyright:
© 2019, The Author(s), under exclusive licence to Springer Nature America, Inc.

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He, F., Pasam, R., Shi, F., Kant, S., Keeble-Gagnere, G., Kay, P., Forrest, K., Fritz, A., Hucl, P., Wiebe, K., Knox, R., Cuthbert, R., Pozniak, C., Akhunova, A., Morrell, P. L., Davies, J. P., Webb, S. R., Spangenberg, G., Hayes, B., ... Akhunov, E. (2019). Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome. Nature Genetics, 51(5), 896-904. https://doi.org/10.1038/s41588-019-0382-2

He, F, Pasam, R, Shi, F, Kant, S, Keeble-Gagnere, G, Kay, P, Forrest, K, Fritz, A, Hucl, P, Wiebe, K, Knox, R, Cuthbert, R, Pozniak, C, Akhunova, A, Morrell, PL, Davies, JP, Webb, SR, Spangenberg, G, Hayes, B, Daetwyler, H, Tibbits, J, Hayden, M & Akhunov, E 2019, 'Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome', Nature Genetics, vol. 51, no. 5, pp. 896-904. https://doi.org/10.1038/s41588-019-0382-2

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abstract = "Introgression is a potential source of beneficial genetic diversity. The contribution of introgression to adaptive evolution and improvement of wheat as it was disseminated worldwide remains unknown. We used targeted re-sequencing of 890 diverse accessions of hexaploid and tetraploid wheat to identify wild-relative introgression. Introgression, and selection for improvement and environmental adaptation, each reduced deleterious allele burden. Introgression increased diversity genome wide and in regions harboring major agronomic genes, and contributed alleles explaining a substantial proportion of phenotypic variation. These results suggest that historic gene flow from wild relatives made a substantial contribution to the adaptive diversity of modern bread wheat.",

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Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome

Abstract

Bibliographical note

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