Ecological niche modelling for delineating livestock ecotypes and exploring environmental genomic adaptation: The example of Ethiopian village chicken
In evolutionary ecology, an “ecotype” is a population that is genetically adapted to specific environmental conditions. Environmental and genetic characterisation of livestock ecotypes can play a crucial role in conservation and breeding improvement, particularly to achieve climate resilience. Howev...
| Autores principales: | , , , , , , |
|---|---|
| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Frontiers Media
2022
|
| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/121087 |
| _version_ | 1855517502419763200 |
|---|---|
| author | Vallejo Trujillo, Adriana Kebede, Adebabay Lozano Jaramillo, M. Dessie, Tadelle Smith, Jacqueline Hanotte, Olivier H. Gheyas, Almas A. |
| author_browse | Dessie, Tadelle Gheyas, Almas A. Hanotte, Olivier H. Kebede, Adebabay Lozano Jaramillo, M. Smith, Jacqueline Vallejo Trujillo, Adriana |
| author_facet | Vallejo Trujillo, Adriana Kebede, Adebabay Lozano Jaramillo, M. Dessie, Tadelle Smith, Jacqueline Hanotte, Olivier H. Gheyas, Almas A. |
| author_sort | Vallejo Trujillo, Adriana |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | In evolutionary ecology, an “ecotype” is a population that is genetically adapted to specific environmental conditions. Environmental and genetic characterisation of livestock ecotypes can play a crucial role in conservation and breeding improvement, particularly to achieve climate resilience. However, livestock ecotypes are often arbitrarily defined without a detailed characterisation of their agro-ecologies. In this study, we employ a novel integrated approach, combining ecological niche modelling (ENM) with genomics, to delineate ecotypes based on environmental characterisation of population habitats and unravel the signatures of adaptive selection in the ecotype genomes. The method was applied on 25 Ethiopian village chicken populations representing diverse agro-climatic conditions. ENM identified six key environmental drivers of adaptation and delineated 12 ecotypes. Within-ecotype selection signature analyses (using Hp and iHS methods) identified 1,056 candidate sweep regions (SRs) associated with diverse biological processes. While most SRs are ecotype-specific, the biological pathways perturbed by overlapping genes are largely shared among ecotypes. A few biological pathways were shared amongst most ecotypes and the genes involved showed functions important for scavenging chickens, e.g., neuronal development/processes, immune response, vision development, and learning. Genotype-environment association using redundancy analysis (RDA) allowed for correlating ∼33% of the SRs with major environmental drivers. Inspection of some strong candidate genes from selection signature analysis and RDA showed highly relevant functions in relation to the major environmental drivers of corresponding ecotypes. This integrated approach offers a powerful tool to gain insight into the complex processes of adaptive evolution including the genotype × environment (G × E) interactions. |
| format | Journal Article |
| id | CGSpace121087 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | CGSpace1210872025-12-08T10:29:22Z Ecological niche modelling for delineating livestock ecotypes and exploring environmental genomic adaptation: The example of Ethiopian village chicken Vallejo Trujillo, Adriana Kebede, Adebabay Lozano Jaramillo, M. Dessie, Tadelle Smith, Jacqueline Hanotte, Olivier H. Gheyas, Almas A. chickens livestock animal breeding genetics ecology In evolutionary ecology, an “ecotype” is a population that is genetically adapted to specific environmental conditions. Environmental and genetic characterisation of livestock ecotypes can play a crucial role in conservation and breeding improvement, particularly to achieve climate resilience. However, livestock ecotypes are often arbitrarily defined without a detailed characterisation of their agro-ecologies. In this study, we employ a novel integrated approach, combining ecological niche modelling (ENM) with genomics, to delineate ecotypes based on environmental characterisation of population habitats and unravel the signatures of adaptive selection in the ecotype genomes. The method was applied on 25 Ethiopian village chicken populations representing diverse agro-climatic conditions. ENM identified six key environmental drivers of adaptation and delineated 12 ecotypes. Within-ecotype selection signature analyses (using Hp and iHS methods) identified 1,056 candidate sweep regions (SRs) associated with diverse biological processes. While most SRs are ecotype-specific, the biological pathways perturbed by overlapping genes are largely shared among ecotypes. A few biological pathways were shared amongst most ecotypes and the genes involved showed functions important for scavenging chickens, e.g., neuronal development/processes, immune response, vision development, and learning. Genotype-environment association using redundancy analysis (RDA) allowed for correlating ∼33% of the SRs with major environmental drivers. Inspection of some strong candidate genes from selection signature analysis and RDA showed highly relevant functions in relation to the major environmental drivers of corresponding ecotypes. This integrated approach offers a powerful tool to gain insight into the complex processes of adaptive evolution including the genotype × environment (G × E) interactions. 2022-08-04 2022-09-05T10:19:25Z 2022-09-05T10:19:25Z Journal Article https://hdl.handle.net/10568/121087 en Open Access Frontiers Media Vallejo-Trujillo, A., Kebede, A., Lozano-Jaramillo, M., Dessie, T., Smith, J., Hanotte, O. and Gheyas, A.A. 2022. Ecological niche modelling for delineating livestock ecotypes and exploring environmental genomic adaptation: The example of Ethiopian village chicken. Frontiers in ecology and evolution 10:866587. |
| spellingShingle | chickens livestock animal breeding genetics ecology Vallejo Trujillo, Adriana Kebede, Adebabay Lozano Jaramillo, M. Dessie, Tadelle Smith, Jacqueline Hanotte, Olivier H. Gheyas, Almas A. Ecological niche modelling for delineating livestock ecotypes and exploring environmental genomic adaptation: The example of Ethiopian village chicken |
| title | Ecological niche modelling for delineating livestock ecotypes and exploring environmental genomic adaptation: The example of Ethiopian village chicken |
| title_full | Ecological niche modelling for delineating livestock ecotypes and exploring environmental genomic adaptation: The example of Ethiopian village chicken |
| title_fullStr | Ecological niche modelling for delineating livestock ecotypes and exploring environmental genomic adaptation: The example of Ethiopian village chicken |
| title_full_unstemmed | Ecological niche modelling for delineating livestock ecotypes and exploring environmental genomic adaptation: The example of Ethiopian village chicken |
| title_short | Ecological niche modelling for delineating livestock ecotypes and exploring environmental genomic adaptation: The example of Ethiopian village chicken |
| title_sort | ecological niche modelling for delineating livestock ecotypes and exploring environmental genomic adaptation the example of ethiopian village chicken |
| topic | chickens livestock animal breeding genetics ecology |
| url | https://hdl.handle.net/10568/121087 |
| work_keys_str_mv | AT vallejotrujilloadriana ecologicalnichemodellingfordelineatinglivestockecotypesandexploringenvironmentalgenomicadaptationtheexampleofethiopianvillagechicken AT kebedeadebabay ecologicalnichemodellingfordelineatinglivestockecotypesandexploringenvironmentalgenomicadaptationtheexampleofethiopianvillagechicken AT lozanojaramillom ecologicalnichemodellingfordelineatinglivestockecotypesandexploringenvironmentalgenomicadaptationtheexampleofethiopianvillagechicken AT dessietadelle ecologicalnichemodellingfordelineatinglivestockecotypesandexploringenvironmentalgenomicadaptationtheexampleofethiopianvillagechicken AT smithjacqueline ecologicalnichemodellingfordelineatinglivestockecotypesandexploringenvironmentalgenomicadaptationtheexampleofethiopianvillagechicken AT hanotteolivierh ecologicalnichemodellingfordelineatinglivestockecotypesandexploringenvironmentalgenomicadaptationtheexampleofethiopianvillagechicken AT gheyasalmasa ecologicalnichemodellingfordelineatinglivestockecotypesandexploringenvironmentalgenomicadaptationtheexampleofethiopianvillagechicken |