Integrated environmental and genomic analysis reveals the drivers of local adaptation in African indigenous chickens
Breeding for climate resilience is currently an important goal for sustainable livestock production. Local adaptations exhibited by indigenous livestock allow investigating the genetic control of this resilience. Ecological niche modeling (ENM) provides a powerful avenue to identify the main environ...
| Main Authors: | , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
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Oxford University Press
2021
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/109530 |
| _version_ | 1855541021232857088 |
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| author | Gheyas, Almas A. Vallejo Trujillo, Adriana Kebede, Adebabay Lozano Jaramillo, Maria Dessie, Tadelle Smith, Jacqueline Hanotte, Olivier H. |
| author_browse | Dessie, Tadelle Gheyas, Almas A. Hanotte, Olivier H. Kebede, Adebabay Lozano Jaramillo, Maria Smith, Jacqueline Vallejo Trujillo, Adriana |
| author_facet | Gheyas, Almas A. Vallejo Trujillo, Adriana Kebede, Adebabay Lozano Jaramillo, Maria Dessie, Tadelle Smith, Jacqueline Hanotte, Olivier H. |
| author_sort | Gheyas, Almas A. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Breeding for climate resilience is currently an important goal for sustainable livestock production. Local adaptations exhibited by indigenous livestock allow investigating the genetic control of this resilience. Ecological niche modeling (ENM) provides a powerful avenue to identify the main environmental drivers of selection. Here, we applied an integrative approach combining ENM with genome-wide selection signature analyses (XPEHH and Fst) and genotype−environment association (redundancy analysis), with the aim of identifying the genomic signatures of adaptation in African village chickens. By dissecting 34 agro-climatic variables from the ecosystems of 25 Ethiopian village chicken populations, ENM identified six key drivers of environmental challenges: One temperature variable—strongly correlated with elevation, three precipitation variables as proxies for water availability, and two soil/land cover variables as proxies of food availability for foraging chickens. Genome analyses based on whole-genome sequencing (n = 245), identified a few strongly supported genomic regions under selection for environmental challenges related to altitude, temperature, water scarcity, and food availability. These regions harbor several gene clusters including regulatory genes, suggesting a predominantly oligogenic control of environmental adaptation. Few candidate genes detected in relation to heat-stress, indicates likely epigenetic regulation of thermo-tolerance for a domestic species originating from a tropical Asian wild ancestor. These results provide possible explanations for the rapid past adaptation of chickens to diverse African agro-ecologies, while also representing new landmarks for sustainable breeding improvement for climate resilience. We show that the pre-identification of key environmental drivers, followed by genomic investigation, provides a powerful new approach for elucidating adaptation in domestic animals. |
| format | Journal Article |
| id | CGSpace109530 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace1095302024-08-27T10:37:17Z Integrated environmental and genomic analysis reveals the drivers of local adaptation in African indigenous chickens Gheyas, Almas A. Vallejo Trujillo, Adriana Kebede, Adebabay Lozano Jaramillo, Maria Dessie, Tadelle Smith, Jacqueline Hanotte, Olivier H. indigenous breeds environment genomes poultry chickens research animal breeding breeds Breeding for climate resilience is currently an important goal for sustainable livestock production. Local adaptations exhibited by indigenous livestock allow investigating the genetic control of this resilience. Ecological niche modeling (ENM) provides a powerful avenue to identify the main environmental drivers of selection. Here, we applied an integrative approach combining ENM with genome-wide selection signature analyses (XPEHH and Fst) and genotype−environment association (redundancy analysis), with the aim of identifying the genomic signatures of adaptation in African village chickens. By dissecting 34 agro-climatic variables from the ecosystems of 25 Ethiopian village chicken populations, ENM identified six key drivers of environmental challenges: One temperature variable—strongly correlated with elevation, three precipitation variables as proxies for water availability, and two soil/land cover variables as proxies of food availability for foraging chickens. Genome analyses based on whole-genome sequencing (n = 245), identified a few strongly supported genomic regions under selection for environmental challenges related to altitude, temperature, water scarcity, and food availability. These regions harbor several gene clusters including regulatory genes, suggesting a predominantly oligogenic control of environmental adaptation. Few candidate genes detected in relation to heat-stress, indicates likely epigenetic regulation of thermo-tolerance for a domestic species originating from a tropical Asian wild ancestor. These results provide possible explanations for the rapid past adaptation of chickens to diverse African agro-ecologies, while also representing new landmarks for sustainable breeding improvement for climate resilience. We show that the pre-identification of key environmental drivers, followed by genomic investigation, provides a powerful new approach for elucidating adaptation in domestic animals. 2021-10-21 2020-09-17T11:07:27Z 2020-09-17T11:07:27Z Journal Article https://hdl.handle.net/10568/109530 en Open Access Oxford University Press Gheyas, A.A., Trujillo, A.V., Kebede, A., Lozano-Jaramillo, M., Dessie, T., Smith, J. and Hanotte, O. 2021. Integrated environmental and genomic analysis reveals the drivers of local adaptation in African indigenous chickens. Molecular Biology and Evolution 38(10):4268–4285. |
| spellingShingle | indigenous breeds environment genomes poultry chickens research animal breeding breeds Gheyas, Almas A. Vallejo Trujillo, Adriana Kebede, Adebabay Lozano Jaramillo, Maria Dessie, Tadelle Smith, Jacqueline Hanotte, Olivier H. Integrated environmental and genomic analysis reveals the drivers of local adaptation in African indigenous chickens |
| title | Integrated environmental and genomic analysis reveals the drivers of local adaptation in African indigenous chickens |
| title_full | Integrated environmental and genomic analysis reveals the drivers of local adaptation in African indigenous chickens |
| title_fullStr | Integrated environmental and genomic analysis reveals the drivers of local adaptation in African indigenous chickens |
| title_full_unstemmed | Integrated environmental and genomic analysis reveals the drivers of local adaptation in African indigenous chickens |
| title_short | Integrated environmental and genomic analysis reveals the drivers of local adaptation in African indigenous chickens |
| title_sort | integrated environmental and genomic analysis reveals the drivers of local adaptation in african indigenous chickens |
| topic | indigenous breeds environment genomes poultry chickens research animal breeding breeds |
| url | https://hdl.handle.net/10568/109530 |
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