The wild species genome ancestry of domestic chickens
Abstract Background Hybridisation and introgression play key roles in the evolutionary history of animal species. They are commonly observed within several orders in wild birds. The domestic chicken Gallus gallus domesticus is the most common livestock species. More than 65 billion chickens are rais...
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| Format: | Article |
| Language: | English |
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BMC
2020-02-01
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| Series: | BMC Biology |
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| Online Access: | https://doi.org/10.1186/s12915-020-0738-1 |
| _version_ | 1818946094506180608 |
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| author | Raman Akinyanju Lawal Simon H. Martin Koen Vanmechelen Addie Vereijken Pradeepa Silva Raed Mahmoud Al-Atiyat Riyadh Salah Aljumaah Joram M. Mwacharo Dong-Dong Wu Ya-Ping Zhang Paul M. Hocking Jacqueline Smith David Wragg Olivier Hanotte |
| author_facet | Raman Akinyanju Lawal Simon H. Martin Koen Vanmechelen Addie Vereijken Pradeepa Silva Raed Mahmoud Al-Atiyat Riyadh Salah Aljumaah Joram M. Mwacharo Dong-Dong Wu Ya-Ping Zhang Paul M. Hocking Jacqueline Smith David Wragg Olivier Hanotte |
| author_sort | Raman Akinyanju Lawal |
| collection | DOAJ |
| description | Abstract Background Hybridisation and introgression play key roles in the evolutionary history of animal species. They are commonly observed within several orders in wild birds. The domestic chicken Gallus gallus domesticus is the most common livestock species. More than 65 billion chickens are raised annually to produce meat and 80 million metric tons of egg for global human consumption by the commercial sector. Unravelling the origin of its genetic diversity has major application for sustainable breeding improvement programmes. Results In this study, we report genome-wide analyses for signatures of introgression between indigenous domestic village chicken and the four wild Gallus species. We first assess the genome-wide phylogeny and divergence time across the genus Gallus. Genome-wide sequence divergence analysis supports a sister relationship between the Grey junglefowl G. sonneratii and Ceylon junglefowl G. lafayettii. Both species form a clade that is sister to the Red junglefowl G. gallus, with the Green junglefowl G. varius the most ancient lineage within the genus. We reveal extensive bidirectional introgression between the Grey junglefowl and the domestic chicken and to a much lesser extent with the Ceylon junglefowl. We identify a single case of Green junglefowl introgression. These introgressed regions include genes with biological functions related to development and immune system. Conclusions Our study shows that while the Red junglefowl is the main ancestral species, introgressive hybridisation episodes have impacted the genome and contributed to the diversity of the domestic chicken, although likely at different levels across its geographic range. |
| first_indexed | 2024-12-20T08:09:33Z |
| format | Article |
| id | doaj.art-dd711d0b7cbb49de9f17f37b59e83755 |
| institution | Directory Open Access Journal |
| issn | 1741-7007 |
| language | English |
| last_indexed | 2024-12-20T08:09:33Z |
| publishDate | 2020-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Biology |
| spelling | doaj.art-dd711d0b7cbb49de9f17f37b59e837552022-12-21T19:47:19ZengBMCBMC Biology1741-70072020-02-0118111810.1186/s12915-020-0738-1The wild species genome ancestry of domestic chickensRaman Akinyanju Lawal0Simon H. Martin1Koen Vanmechelen2Addie Vereijken3Pradeepa Silva4Raed Mahmoud Al-Atiyat5Riyadh Salah Aljumaah6Joram M. Mwacharo7Dong-Dong Wu8Ya-Ping Zhang9Paul M. Hocking10Jacqueline Smith11David Wragg12Olivier Hanotte13Cells, Organisms and Molecular Genetics, School of Life Sciences, University of NottinghamPresent Address: Institute of Evolutionary Biology, University of EdinburghOpen University of Diversity - Mouth FoundationTechnology and Service B.V., Hendrix GeneticsDepartment of Animal Science, Faculty of Agriculture, University of PeradeniyaGenetics and Biotechnology, Animal Science Department, Agriculture Faculty, Mutah UniversityDepartment of Animal Production, King Saud UniversitySmall Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA)Center for Excellence in Animal Evolution and Genetics, Chinese Academy of SciencesCenter for Excellence in Animal Evolution and Genetics, Chinese Academy of SciencesThe Roslin Institute and Royal (Dick) School of Veterinary Studies, University of EdinburghThe Roslin Institute and Royal (Dick) School of Veterinary Studies, University of EdinburghCentre for Tropical Livestock Genetics and Health, The Roslin InstituteCells, Organisms and Molecular Genetics, School of Life Sciences, University of NottinghamAbstract Background Hybridisation and introgression play key roles in the evolutionary history of animal species. They are commonly observed within several orders in wild birds. The domestic chicken Gallus gallus domesticus is the most common livestock species. More than 65 billion chickens are raised annually to produce meat and 80 million metric tons of egg for global human consumption by the commercial sector. Unravelling the origin of its genetic diversity has major application for sustainable breeding improvement programmes. Results In this study, we report genome-wide analyses for signatures of introgression between indigenous domestic village chicken and the four wild Gallus species. We first assess the genome-wide phylogeny and divergence time across the genus Gallus. Genome-wide sequence divergence analysis supports a sister relationship between the Grey junglefowl G. sonneratii and Ceylon junglefowl G. lafayettii. Both species form a clade that is sister to the Red junglefowl G. gallus, with the Green junglefowl G. varius the most ancient lineage within the genus. We reveal extensive bidirectional introgression between the Grey junglefowl and the domestic chicken and to a much lesser extent with the Ceylon junglefowl. We identify a single case of Green junglefowl introgression. These introgressed regions include genes with biological functions related to development and immune system. Conclusions Our study shows that while the Red junglefowl is the main ancestral species, introgressive hybridisation episodes have impacted the genome and contributed to the diversity of the domestic chicken, although likely at different levels across its geographic range.https://doi.org/10.1186/s12915-020-0738-1Chicken introgressionGenetic diversityChicken domesticationLivestock speciesDivergence timeGallus species |
| spellingShingle | Raman Akinyanju Lawal Simon H. Martin Koen Vanmechelen Addie Vereijken Pradeepa Silva Raed Mahmoud Al-Atiyat Riyadh Salah Aljumaah Joram M. Mwacharo Dong-Dong Wu Ya-Ping Zhang Paul M. Hocking Jacqueline Smith David Wragg Olivier Hanotte The wild species genome ancestry of domestic chickens BMC Biology Chicken introgression Genetic diversity Chicken domestication Livestock species Divergence time Gallus species |
| title | The wild species genome ancestry of domestic chickens |
| title_full | The wild species genome ancestry of domestic chickens |
| title_fullStr | The wild species genome ancestry of domestic chickens |
| title_full_unstemmed | The wild species genome ancestry of domestic chickens |
| title_short | The wild species genome ancestry of domestic chickens |
| title_sort | wild species genome ancestry of domestic chickens |
| topic | Chicken introgression Genetic diversity Chicken domestication Livestock species Divergence time Gallus species |
| url | https://doi.org/10.1186/s12915-020-0738-1 |
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