Whole-genome sequence data suggests environmental adaptation of Ethiopian sheep populations
Great progress has been made over recent years in the identification of selection signatures in the genomes of livestock species. This work has primarily been carried out in commercial breeds for which the dominant selection pressures are associated with artificial selection. As agriculture and food...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Oxford University Press
2021
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/111051 |
| _version_ | 1855514972900032512 |
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| author | Wiener, P. Robert, C. Ahbara, A. Salavati, M. Abebe, A. Kebede, Adebabay Wragg, D. Friedrich, J. Vasoya, D. Hume, D.A. Djikeng, Appolinaire Watson, M. Prendergast, James G.D. Hanotte, Olivier H. Mwacharo, Joram M. Clark, E.L. |
| author_browse | Abebe, A. Ahbara, A. Clark, E.L. Djikeng, Appolinaire Friedrich, J. Hanotte, Olivier H. Hume, D.A. Kebede, Adebabay Mwacharo, Joram M. Prendergast, James G.D. Robert, C. Salavati, M. Vasoya, D. Watson, M. Wiener, P. Wragg, D. |
| author_facet | Wiener, P. Robert, C. Ahbara, A. Salavati, M. Abebe, A. Kebede, Adebabay Wragg, D. Friedrich, J. Vasoya, D. Hume, D.A. Djikeng, Appolinaire Watson, M. Prendergast, James G.D. Hanotte, Olivier H. Mwacharo, Joram M. Clark, E.L. |
| author_sort | Wiener, P. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Great progress has been made over recent years in the identification of selection signatures in the genomes of livestock species. This work has primarily been carried out in commercial breeds for which the dominant selection pressures are associated with artificial selection. As agriculture and food security are likely to be strongly affected by climate change, a better understanding of environment-imposed selection on agricultural species is warranted. Ethiopia is an ideal setting to investigate environmental adaptation in livestock due to its wide variation in geo-climatic characteristics and the extensive genetic and phenotypic variation of its livestock. Here, we identified over three million single nucleotide variants across 12 Ethiopian sheep populations and applied landscape genomics approaches to investigate the association between these variants and environmental variables. Our results suggest that environmental adaptation for precipitation-related variables is stronger than that related to altitude or temperature, consistent with large-scale meta-analyses of selection pressure across species. The set of genes showing association with environmental variables was enriched for genes highly expressed in human blood and nerve tissues. There was also evidence of enrichment for genes associated with high-altitude adaptation although no strong association was identified with hypoxia-inducible-factor (HIF) genes. One of the strongest altitude-related signals was for a collagen gene, consistent with previous studies of high-altitude adaptation. Several altitude-associated genes also showed evidence of adaptation with temperature, suggesting a relationship between responses to these environmental factors. These results provide a foundation to investigate further the effects of climatic variables on small ruminant populations. |
| format | Journal Article |
| id | CGSpace111051 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace1110512025-02-19T13:41:57Z Whole-genome sequence data suggests environmental adaptation of Ethiopian sheep populations Wiener, P. Robert, C. Ahbara, A. Salavati, M. Abebe, A. Kebede, Adebabay Wragg, D. Friedrich, J. Vasoya, D. Hume, D.A. Djikeng, Appolinaire Watson, M. Prendergast, James G.D. Hanotte, Olivier H. Mwacharo, Joram M. Clark, E.L. animal genetics genetics animal breeding sheep small ruminants Great progress has been made over recent years in the identification of selection signatures in the genomes of livestock species. This work has primarily been carried out in commercial breeds for which the dominant selection pressures are associated with artificial selection. As agriculture and food security are likely to be strongly affected by climate change, a better understanding of environment-imposed selection on agricultural species is warranted. Ethiopia is an ideal setting to investigate environmental adaptation in livestock due to its wide variation in geo-climatic characteristics and the extensive genetic and phenotypic variation of its livestock. Here, we identified over three million single nucleotide variants across 12 Ethiopian sheep populations and applied landscape genomics approaches to investigate the association between these variants and environmental variables. Our results suggest that environmental adaptation for precipitation-related variables is stronger than that related to altitude or temperature, consistent with large-scale meta-analyses of selection pressure across species. The set of genes showing association with environmental variables was enriched for genes highly expressed in human blood and nerve tissues. There was also evidence of enrichment for genes associated with high-altitude adaptation although no strong association was identified with hypoxia-inducible-factor (HIF) genes. One of the strongest altitude-related signals was for a collagen gene, consistent with previous studies of high-altitude adaptation. Several altitude-associated genes also showed evidence of adaptation with temperature, suggesting a relationship between responses to these environmental factors. These results provide a foundation to investigate further the effects of climatic variables on small ruminant populations. 2021-03-01 2021-01-29T16:56:23Z 2021-01-29T16:56:23Z Journal Article https://hdl.handle.net/10568/111051 en Open Access Oxford University Press Wiener, P., Robert, C., Ahbara, A., Salavati, M., Abebe, A., Kebede, A., Wragg, D., Friedrich, J., Vasoya, D., Hume, D.A., Djikeng, A., Watson, M., Prendergast, J.G.D., Hanotte, O., Mwacharo, J.M. and Clark, E.L. 2021. Whole-genome sequence data suggests environmental adaptation of Ethiopian sheep populations. Genome Biology and Evolution 13(1):evaa232. |
| spellingShingle | animal genetics genetics animal breeding sheep small ruminants Wiener, P. Robert, C. Ahbara, A. Salavati, M. Abebe, A. Kebede, Adebabay Wragg, D. Friedrich, J. Vasoya, D. Hume, D.A. Djikeng, Appolinaire Watson, M. Prendergast, James G.D. Hanotte, Olivier H. Mwacharo, Joram M. Clark, E.L. Whole-genome sequence data suggests environmental adaptation of Ethiopian sheep populations |
| title | Whole-genome sequence data suggests environmental adaptation of Ethiopian sheep populations |
| title_full | Whole-genome sequence data suggests environmental adaptation of Ethiopian sheep populations |
| title_fullStr | Whole-genome sequence data suggests environmental adaptation of Ethiopian sheep populations |
| title_full_unstemmed | Whole-genome sequence data suggests environmental adaptation of Ethiopian sheep populations |
| title_short | Whole-genome sequence data suggests environmental adaptation of Ethiopian sheep populations |
| title_sort | whole genome sequence data suggests environmental adaptation of ethiopian sheep populations |
| topic | animal genetics genetics animal breeding sheep small ruminants |
| url | https://hdl.handle.net/10568/111051 |
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