Large-scale genomic analysis reveals the genetic cost of chicken domestication
Species domestication is generally characterized by the exploitation of high-impact mutations through processes that involve complex shifting demographics of domesticated species. These include not only inbreeding and artificial selection that may lead to the emergence of evolutionary bottlenecks, b...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2021
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/114059 |
| _version_ | 1855543763954302976 |
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| author | Ming-Shan Wang Jin-Jin Zhang Xing Guo Ming Li Meyer, R. Ashari, H. Zhu-Qing Zheng Sheng Wang Min-Sheng Peng Yu Jiang Mukesh Thakur Chatmongkon Suwannapoom Esmailizadeh, A. Nalini Yasoda Hirimuthugoda Moch Syamsul Arifin Zein Kusza, S. Hamed Kharrati-Koopaee Lin Zeng Yun-Mei Wang Ting-Ting Yin Min-Min Yang Ming-Li Li Xue-Mei Lu Lasagna, E. Ceccobelli, S. Humpita Gamaralalage Thilini Nisanka Gunwardana Thilina Madusanka Senasig Shao-Hong Feng Hao Zhang Bhuiyan, A.K.F.H. Khan, M.S. Silva, Gamamada Liyanage Lalanie Pradeepa Le Thi Thuy Okeyo Mwai, Ally Ibrahim, M.N.M. Guojie Zhang Kai-Xing Qu Hanotte, Olivier H. Shapiro, B. Bosse, M. Dong-Dong Wu Han Jianlin Ya-Ping Zhang |
| author_browse | Ashari, H. Bhuiyan, A.K.F.H. Bosse, M. Ceccobelli, S. Chatmongkon Suwannapoom Dong-Dong Wu Esmailizadeh, A. Guojie Zhang Hamed Kharrati-Koopaee Han Jianlin Hanotte, Olivier H. Hao Zhang Humpita Gamaralalage Thilini Nisanka Gunwardana Ibrahim, M.N.M. Jin-Jin Zhang Kai-Xing Qu Khan, M.S. Kusza, S. Lasagna, E. Le Thi Thuy Lin Zeng Meyer, R. Min-Min Yang Min-Sheng Peng Ming Li Ming-Li Li Ming-Shan Wang Moch Syamsul Arifin Zein Mukesh Thakur Nalini Yasoda Hirimuthugoda Okeyo Mwai, Ally Shao-Hong Feng Shapiro, B. Sheng Wang Silva, Gamamada Liyanage Lalanie Pradeepa Thilina Madusanka Senasig Ting-Ting Yin Xing Guo Xue-Mei Lu Ya-Ping Zhang Yu Jiang Yun-Mei Wang Zhu-Qing Zheng |
| author_facet | Ming-Shan Wang Jin-Jin Zhang Xing Guo Ming Li Meyer, R. Ashari, H. Zhu-Qing Zheng Sheng Wang Min-Sheng Peng Yu Jiang Mukesh Thakur Chatmongkon Suwannapoom Esmailizadeh, A. Nalini Yasoda Hirimuthugoda Moch Syamsul Arifin Zein Kusza, S. Hamed Kharrati-Koopaee Lin Zeng Yun-Mei Wang Ting-Ting Yin Min-Min Yang Ming-Li Li Xue-Mei Lu Lasagna, E. Ceccobelli, S. Humpita Gamaralalage Thilini Nisanka Gunwardana Thilina Madusanka Senasig Shao-Hong Feng Hao Zhang Bhuiyan, A.K.F.H. Khan, M.S. Silva, Gamamada Liyanage Lalanie Pradeepa Le Thi Thuy Okeyo Mwai, Ally Ibrahim, M.N.M. Guojie Zhang Kai-Xing Qu Hanotte, Olivier H. Shapiro, B. Bosse, M. Dong-Dong Wu Han Jianlin Ya-Ping Zhang |
| author_sort | Ming-Shan Wang |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Species domestication is generally characterized by the exploitation of high-impact mutations through processes that involve complex shifting demographics of domesticated species. These include not only inbreeding and artificial selection that may lead to the emergence of evolutionary bottlenecks, but also post-divergence gene flow and introgression. Although domestication potentially affects the occurrence of both desired and undesired mutations, the way wild relatives of domesticated species evolve and how expensive the genetic cost underlying domestication is remain poorly understood. Here, we investigated the demographic history and genetic load of chicken domestication.We analyzed a dataset comprising over 800 whole genomes from both indigenous chickens and wild jungle fowls. We show that despite having a higher genetic diversity than their wild counterparts (average π, 0.00326 vs. 0.00316), the red jungle fowls, the present-day domestic chickens experienced a dramatic population size decline during their early domestication. Our analyses suggest that the concomitant bottleneck induced 2.95% more deleterious mutations across chicken genomes compared with red jungle fowls, supporting the “cost of domestication” hypothesis. Particularly, we find that 62.4% of deleterious SNPs in domestic chickens are maintained in heterozygous states and masked as recessive alleles, challenging the power of modern breeding programs to effectively eliminate these genetic loads. Finally, we suggest that positive selection decreases the incidence but increases the frequency of deleterious SNPs in domestic chicken genomes.This study reveals a new landscape of demographic history and genomic changes associated with chicken domestication and provides insight into the evolutionary genomic profiles of domesticated animals managed under modern human selection. |
| format | Journal Article |
| id | CGSpace114059 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1140592025-01-27T15:00:52Z Large-scale genomic analysis reveals the genetic cost of chicken domestication Ming-Shan Wang Jin-Jin Zhang Xing Guo Ming Li Meyer, R. Ashari, H. Zhu-Qing Zheng Sheng Wang Min-Sheng Peng Yu Jiang Mukesh Thakur Chatmongkon Suwannapoom Esmailizadeh, A. Nalini Yasoda Hirimuthugoda Moch Syamsul Arifin Zein Kusza, S. Hamed Kharrati-Koopaee Lin Zeng Yun-Mei Wang Ting-Ting Yin Min-Min Yang Ming-Li Li Xue-Mei Lu Lasagna, E. Ceccobelli, S. Humpita Gamaralalage Thilini Nisanka Gunwardana Thilina Madusanka Senasig Shao-Hong Feng Hao Zhang Bhuiyan, A.K.F.H. Khan, M.S. Silva, Gamamada Liyanage Lalanie Pradeepa Le Thi Thuy Okeyo Mwai, Ally Ibrahim, M.N.M. Guojie Zhang Kai-Xing Qu Hanotte, Olivier H. Shapiro, B. Bosse, M. Dong-Dong Wu Han Jianlin Ya-Ping Zhang animal breeding genetics chickens poultry Species domestication is generally characterized by the exploitation of high-impact mutations through processes that involve complex shifting demographics of domesticated species. These include not only inbreeding and artificial selection that may lead to the emergence of evolutionary bottlenecks, but also post-divergence gene flow and introgression. Although domestication potentially affects the occurrence of both desired and undesired mutations, the way wild relatives of domesticated species evolve and how expensive the genetic cost underlying domestication is remain poorly understood. Here, we investigated the demographic history and genetic load of chicken domestication.We analyzed a dataset comprising over 800 whole genomes from both indigenous chickens and wild jungle fowls. We show that despite having a higher genetic diversity than their wild counterparts (average π, 0.00326 vs. 0.00316), the red jungle fowls, the present-day domestic chickens experienced a dramatic population size decline during their early domestication. Our analyses suggest that the concomitant bottleneck induced 2.95% more deleterious mutations across chicken genomes compared with red jungle fowls, supporting the “cost of domestication” hypothesis. Particularly, we find that 62.4% of deleterious SNPs in domestic chickens are maintained in heterozygous states and masked as recessive alleles, challenging the power of modern breeding programs to effectively eliminate these genetic loads. Finally, we suggest that positive selection decreases the incidence but increases the frequency of deleterious SNPs in domestic chicken genomes.This study reveals a new landscape of demographic history and genomic changes associated with chicken domestication and provides insight into the evolutionary genomic profiles of domesticated animals managed under modern human selection. 2021-12 2021-06-22T06:27:10Z 2021-06-22T06:27:10Z Journal Article https://hdl.handle.net/10568/114059 en Open Access Springer Ming-Shan Wang, Jin-Jin Zhang, Xing Guo, Ming Li, Meyer, R., Ashari, H., Zhu-Qing Zheng, Sheng Wang, Min-Sheng Peng, Yu Jiang, Mukesh Thakur, Chatmongkon Suwannapoom, Esmailizadeh, A., Nalini Yasoda Hirimuthugoda, Moch Syamsul Arifin Zein, Szilvia Kusza, Hamed Kharrati-Koopaee, Lin Zeng, Yun-Mei Wang, Ting-Ting Yin, Min-Min Yang, Ming-Li Li1, Xue-Mei Lu, Emiliano Lasagna, Ceccobelli, S., Humpita Gamaralalage Thilini Nisanka Gunwardana, Thilina Madusanka Senasig, Shao-Hong Feng, Hao Zhang, Bhuiyan, A.K.F.H., Khan, M.S., Gamamada Liyanage Lalanie Pradeepa Silva, Le Thi Thuy, Mwai, O.A., Ibrahim, M.N.M., Guojie Zhang, Kai-Xing Qu, Hanotte, O., Shapiro, B., Bosse, M., Dong-Dong Wu, Jian-Lin Han and Ya-Ping Zhang. 2021. Large-scale genomic analysis reveals the genetic cost of chicken domestication. BMC Biology 19:118. |
| spellingShingle | animal breeding genetics chickens poultry Ming-Shan Wang Jin-Jin Zhang Xing Guo Ming Li Meyer, R. Ashari, H. Zhu-Qing Zheng Sheng Wang Min-Sheng Peng Yu Jiang Mukesh Thakur Chatmongkon Suwannapoom Esmailizadeh, A. Nalini Yasoda Hirimuthugoda Moch Syamsul Arifin Zein Kusza, S. Hamed Kharrati-Koopaee Lin Zeng Yun-Mei Wang Ting-Ting Yin Min-Min Yang Ming-Li Li Xue-Mei Lu Lasagna, E. Ceccobelli, S. Humpita Gamaralalage Thilini Nisanka Gunwardana Thilina Madusanka Senasig Shao-Hong Feng Hao Zhang Bhuiyan, A.K.F.H. Khan, M.S. Silva, Gamamada Liyanage Lalanie Pradeepa Le Thi Thuy Okeyo Mwai, Ally Ibrahim, M.N.M. Guojie Zhang Kai-Xing Qu Hanotte, Olivier H. Shapiro, B. Bosse, M. Dong-Dong Wu Han Jianlin Ya-Ping Zhang Large-scale genomic analysis reveals the genetic cost of chicken domestication |
| title | Large-scale genomic analysis reveals the genetic cost of chicken domestication |
| title_full | Large-scale genomic analysis reveals the genetic cost of chicken domestication |
| title_fullStr | Large-scale genomic analysis reveals the genetic cost of chicken domestication |
| title_full_unstemmed | Large-scale genomic analysis reveals the genetic cost of chicken domestication |
| title_short | Large-scale genomic analysis reveals the genetic cost of chicken domestication |
| title_sort | large scale genomic analysis reveals the genetic cost of chicken domestication |
| topic | animal breeding genetics chickens poultry |
| url | https://hdl.handle.net/10568/114059 |
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