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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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.
The authors declare no competing interests.
Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Figures 1–13, Supplementary Tables 2, 3, 14–16, 19 and 20, and Supplementary Note
List of hexaploid wheat accessions used in the study.
Genetic differentiation between wheat landraces and cultivars
Distribution of population-based fd statistic and frequency of introgression (FI) across genome.
Distribution of introgression statistics across the wheat genome
Ancestral allelic states inferred using multiple outgroup species
Locations of introgressed genomic regions (IGRs).
Climatic and bioclimatic data from WorldClim database used in Bayenv analyses
Genomic regions associated with environmental adaptation
The genomic regions showing the evidence of improvement selection
The genomic regions shared by all three scans for introgression, XP-CLR and Bayenv
GO terms enriched for genes located in the regions detected using the XP-CLR, Bayenv and fd – statistics analyses
Overlap of GWAS signals with introgression
Homoeolog-specific bias in gene expression between introgressed (I) and non-introgressed (NI) genomic regions
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He, F., Pasam, R., Shi, F. et al. Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome. Nat Genet 51, 896–904 (2019). https://doi.org/10.1038/s41588-019-0382-2
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