Whole genome sequencing reveals signals of adaptive admixture in Creole cattle
Abstract The Creole cattle from Guadeloupe (GUA) are well adapted to the tropical environment. Its admixed genome likely played an important role in such adaptation. Here, we sought to detect genomic signatures of selection in the GUA genome. For this purpose, we sequenced 23 GUA individuals and com...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-07-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-38774-7 |
| _version_ | 1797769476122345472 |
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| author | Slim Ben-Jemaa Gabriele Adam Mekki Boussaha Philippe Bardou Christophe Klopp Nathalie Mandonnet Michel Naves |
| author_facet | Slim Ben-Jemaa Gabriele Adam Mekki Boussaha Philippe Bardou Christophe Klopp Nathalie Mandonnet Michel Naves |
| author_sort | Slim Ben-Jemaa |
| collection | DOAJ |
| description | Abstract The Creole cattle from Guadeloupe (GUA) are well adapted to the tropical environment. Its admixed genome likely played an important role in such adaptation. Here, we sought to detect genomic signatures of selection in the GUA genome. For this purpose, we sequenced 23 GUA individuals and combined our data with sequenced genomes of 99 animals representative of European, African and indicine groups. We detect 17,228,983 single nucleotide polymorphisms (SNPs) in the GUA genome, providing the most detailed exploration, to date, of patterns of genetic variation in this breed. We confirm the higher level of African and indicine ancestries, compared to the European ancestry and we highlight the African origin of indicine ancestry in the GUA genome. We identify five strong candidate regions showing an excess of indicine ancestry and consistently supported across the different detection methods. These regions encompass genes with adaptive roles in relation to immunity, thermotolerance and physical activity. We confirmed a previously identified horn-related gene, RXFP2, as a gene under strong selective pressure in the GUA population likely owing to human-driven (socio-cultural) pressure. Findings from this study provide insight into the genetic mechanisms associated with resilience traits in livestock. |
| first_indexed | 2024-03-12T21:09:36Z |
| format | Article |
| id | doaj.art-030dc42e94764fbea491adbb916ef60d |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-12T21:09:36Z |
| publishDate | 2023-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-030dc42e94764fbea491adbb916ef60d2023-07-30T11:15:18ZengNature PortfolioScientific Reports2045-23222023-07-0113111210.1038/s41598-023-38774-7Whole genome sequencing reveals signals of adaptive admixture in Creole cattleSlim Ben-Jemaa0Gabriele Adam1Mekki Boussaha2Philippe Bardou3Christophe Klopp4Nathalie Mandonnet5Michel Naves6INRAE, ASSETINRAE, ASSETAgroParisTech, GABI, INRAE, Université Paris-SaclayGenPhySE, Ecole Nationale Vétérinaire de Toulouse (ENVT), INRA, Université de ToulouseGenotoul Bioinfo, BioInfoMics, MIAT UR875, Sigenae, INRAEINRAE, ASSETINRAE, ASSETAbstract The Creole cattle from Guadeloupe (GUA) are well adapted to the tropical environment. Its admixed genome likely played an important role in such adaptation. Here, we sought to detect genomic signatures of selection in the GUA genome. For this purpose, we sequenced 23 GUA individuals and combined our data with sequenced genomes of 99 animals representative of European, African and indicine groups. We detect 17,228,983 single nucleotide polymorphisms (SNPs) in the GUA genome, providing the most detailed exploration, to date, of patterns of genetic variation in this breed. We confirm the higher level of African and indicine ancestries, compared to the European ancestry and we highlight the African origin of indicine ancestry in the GUA genome. We identify five strong candidate regions showing an excess of indicine ancestry and consistently supported across the different detection methods. These regions encompass genes with adaptive roles in relation to immunity, thermotolerance and physical activity. We confirmed a previously identified horn-related gene, RXFP2, as a gene under strong selective pressure in the GUA population likely owing to human-driven (socio-cultural) pressure. Findings from this study provide insight into the genetic mechanisms associated with resilience traits in livestock.https://doi.org/10.1038/s41598-023-38774-7 |
| spellingShingle | Slim Ben-Jemaa Gabriele Adam Mekki Boussaha Philippe Bardou Christophe Klopp Nathalie Mandonnet Michel Naves Whole genome sequencing reveals signals of adaptive admixture in Creole cattle Scientific Reports |
| title | Whole genome sequencing reveals signals of adaptive admixture in Creole cattle |
| title_full | Whole genome sequencing reveals signals of adaptive admixture in Creole cattle |
| title_fullStr | Whole genome sequencing reveals signals of adaptive admixture in Creole cattle |
| title_full_unstemmed | Whole genome sequencing reveals signals of adaptive admixture in Creole cattle |
| title_short | Whole genome sequencing reveals signals of adaptive admixture in Creole cattle |
| title_sort | whole genome sequencing reveals signals of adaptive admixture in creole cattle |
| url | https://doi.org/10.1038/s41598-023-38774-7 |
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