The wild species genome ancestry of domestic chickens

Lawal, Raman Akinyanju; Martin, Simon H.; Vanmechelen, Koen; Vereijken, Addie; Silva, Pradeepa; Al-Atiyat, Raed Mahmoud; Aljumaah, Riyadh Salah; Mwacharo, Joram M.; Wu, Dong-Dong; Zhang, Ya-Ping; Hocking, Paul M.; Smith, Jacqueline; Wragg, David; Hanotte, Olivier

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 withbiological 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.

Citation

Lawal, R. A., Martin, S. H., Vanmechelen, K., Vereijken, A., Silva, P., Al-Atiyat, R. M., Aljumaah, R. S., Mwacharo, J. M., Wu, D.-D., Zhang, Y.-P., Hocking, P. M., Smith, J., Wragg, D., & Hanotte, O. (2020). The wild species genome ancestry of domestic chickens. BMC Biology, 18(1), Article 13 (2020). https://doi.org/10.1186/s12915-020-0738-1

• Journal Article Type: Article
• Acceptance Date: Jan 8, 2020
• Online Publication Date: Feb 12, 2020
• Publication Date: Feb 12, 2020
• Deposit Date: Jan 14, 2020
• Publicly Available Date: Feb 12, 2020
• Journal: BMC Biology
• Electronic ISSN: 1741-7007
• Publisher: Springer Verlag
• Peer Reviewed: Peer Reviewed
• Volume: 18
• Issue: 1
• Article Number: 13 (2020)
• DOI: https://doi.org/10.1186/s12915-020-0738-1
• Keywords: Biotechnology; Plant Science; General Biochemistry, Genetics and Molecular Biology; Developmental Biology; Cell Biology; Physiology; Ecology, Evolution, Behavior and Systematics; Structural Biology; General Agricultural and Biological Sciences
• Public URL: https://nottingham-repository.worktribe.com/output/3724012
• Publisher URL: https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-020-0738-1
• Additional Information: Received: 2 August 2019; Accepted: 8 January 2020; First Online: 12 February 2020; : Not applicable; : Appropriate credits in the legend of Fig.InternalRef removeda have been included for the photographers of the junglefowl pictures.; : The authors declare that they have no competing interests.