Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing
Indicine cattle, also referred to as zebu (Bos taurus indicus), play a central role in pastoral communities across a wide range of agro-ecosystems, from extremely hot semiarid regions to hot humid tropical regions. However, their adaptive genetic changes following their dispersal into East Asia from...
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Springer
2023
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/135197 |
| _version_ | 1855542752613236736 |
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| author | Ningbo Chen Xiaoting Xia Quratulain Hanif Fengwei Zhang Ruihua Dang Bizhi Huang Yang Lyu Xiaoyu Luo Hucai Zhang Huixuan Yan Shikang Wang Fuwen Wang Jialei Chen Xiwen Guan Yangkai Liu Shuang Li Liangliang Jin Pengfei Wang Luyang Sun Jicai Zhang Jianyong Liu Kaixing Qu Yanhong Cao Junli Sun Yuying Liao Zhengzhong Xiao Ming Cai Lan Mu Amam Zonaed Siddiki Zonaed Siddiki, Amam Asif, Muhammad Mansoor, Shahid Babar, M.E. Hussain, Tanveer Silva, Gamamada Liyanage Lalanie Pradeepa Gorkhali, N.A. Terefe, E. Belay, G. Tijjani, Abdulfatai Zegeye, T. Gebre, M. Yun Ma Yu Wang Yongzhen Huang Xianyong Lan Hong Chen Migliore, N.R. Colombo, G. Semino, O. Achilli, A. Sinding, M.-H.S. Lenstra, J.A. Haijian Cheng Wenfa Lu Hanotte, Olivier H. Jianlin Han Yu Jiang Chuzhao Lei |
| author_browse | Achilli, A. Amam Zonaed Siddiki Asif, Muhammad Babar, M.E. Belay, G. Bizhi Huang Chuzhao Lei Colombo, G. Fengwei Zhang Fuwen Wang Gebre, M. Gorkhali, N.A. Haijian Cheng Hanotte, Olivier H. Hong Chen Hucai Zhang Huixuan Yan Hussain, Tanveer Jialei Chen Jianlin Han Jianyong Liu Jicai Zhang Junli Sun Kaixing Qu Lan Mu Lenstra, J.A. Liangliang Jin Luyang Sun Mansoor, Shahid Migliore, N.R. Ming Cai Ningbo Chen Pengfei Wang Quratulain Hanif Ruihua Dang Semino, O. Shikang Wang Shuang Li Silva, Gamamada Liyanage Lalanie Pradeepa Sinding, M.-H.S. Terefe, E. Tijjani, Abdulfatai Wenfa Lu Xianyong Lan Xiaoting Xia Xiaoyu Luo Xiwen Guan Yang Lyu Yangkai Liu Yanhong Cao Yongzhen Huang Yu Jiang Yu Wang Yun Ma Yuying Liao Zegeye, T. Zhengzhong Xiao Zonaed Siddiki, Amam |
| author_facet | Ningbo Chen Xiaoting Xia Quratulain Hanif Fengwei Zhang Ruihua Dang Bizhi Huang Yang Lyu Xiaoyu Luo Hucai Zhang Huixuan Yan Shikang Wang Fuwen Wang Jialei Chen Xiwen Guan Yangkai Liu Shuang Li Liangliang Jin Pengfei Wang Luyang Sun Jicai Zhang Jianyong Liu Kaixing Qu Yanhong Cao Junli Sun Yuying Liao Zhengzhong Xiao Ming Cai Lan Mu Amam Zonaed Siddiki Zonaed Siddiki, Amam Asif, Muhammad Mansoor, Shahid Babar, M.E. Hussain, Tanveer Silva, Gamamada Liyanage Lalanie Pradeepa Gorkhali, N.A. Terefe, E. Belay, G. Tijjani, Abdulfatai Zegeye, T. Gebre, M. Yun Ma Yu Wang Yongzhen Huang Xianyong Lan Hong Chen Migliore, N.R. Colombo, G. Semino, O. Achilli, A. Sinding, M.-H.S. Lenstra, J.A. Haijian Cheng Wenfa Lu Hanotte, Olivier H. Jianlin Han Yu Jiang Chuzhao Lei |
| author_sort | Ningbo Chen |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Indicine cattle, also referred to as zebu (Bos taurus indicus), play a central role in pastoral communities across a wide range of agro-ecosystems, from extremely hot semiarid regions to hot humid tropical regions. However, their adaptive genetic changes following their dispersal into East Asia from the Indian subcontinent have remained poorly documented. Here, we characterize their global genetic diversity using high-quality whole-genome sequencing data from 354 indicine cattle of 57 breeds/populations, including major indicine phylogeographic groups worldwide. We reveal their probable migration into East Asia was along a coastal route rather than inland routes and we detected introgression from other bovine species. Genomic regions carrying morphology-, immune-, and heat-tolerance-related genes underwent divergent selection according to Asian agro-ecologies. We identify distinct sets of loci that contain promising candidate variants for adaptation to hot semi-arid and hot humid tropical ecosystems. Our results indicate that the rapid and successful adaptation of East Asian indicine cattle to hot humid environments was promoted by localized introgression from banteng and/or gaur. Our findings provide insights into the history and environmental adaptation of indicine cattle. |
| format | Journal Article |
| id | CGSpace135197 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1351972025-12-08T09:54:28Z Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing Ningbo Chen Xiaoting Xia Quratulain Hanif Fengwei Zhang Ruihua Dang Bizhi Huang Yang Lyu Xiaoyu Luo Hucai Zhang Huixuan Yan Shikang Wang Fuwen Wang Jialei Chen Xiwen Guan Yangkai Liu Shuang Li Liangliang Jin Pengfei Wang Luyang Sun Jicai Zhang Jianyong Liu Kaixing Qu Yanhong Cao Junli Sun Yuying Liao Zhengzhong Xiao Ming Cai Lan Mu Amam Zonaed Siddiki Zonaed Siddiki, Amam Asif, Muhammad Mansoor, Shahid Babar, M.E. Hussain, Tanveer Silva, Gamamada Liyanage Lalanie Pradeepa Gorkhali, N.A. Terefe, E. Belay, G. Tijjani, Abdulfatai Zegeye, T. Gebre, M. Yun Ma Yu Wang Yongzhen Huang Xianyong Lan Hong Chen Migliore, N.R. Colombo, G. Semino, O. Achilli, A. Sinding, M.-H.S. Lenstra, J.A. Haijian Cheng Wenfa Lu Hanotte, Olivier H. Jianlin Han Yu Jiang Chuzhao Lei animal breeding genetics livestock Indicine cattle, also referred to as zebu (Bos taurus indicus), play a central role in pastoral communities across a wide range of agro-ecosystems, from extremely hot semiarid regions to hot humid tropical regions. However, their adaptive genetic changes following their dispersal into East Asia from the Indian subcontinent have remained poorly documented. Here, we characterize their global genetic diversity using high-quality whole-genome sequencing data from 354 indicine cattle of 57 breeds/populations, including major indicine phylogeographic groups worldwide. We reveal their probable migration into East Asia was along a coastal route rather than inland routes and we detected introgression from other bovine species. Genomic regions carrying morphology-, immune-, and heat-tolerance-related genes underwent divergent selection according to Asian agro-ecologies. We identify distinct sets of loci that contain promising candidate variants for adaptation to hot semi-arid and hot humid tropical ecosystems. Our results indicate that the rapid and successful adaptation of East Asian indicine cattle to hot humid environments was promoted by localized introgression from banteng and/or gaur. Our findings provide insights into the history and environmental adaptation of indicine cattle. 2023 2023-12-11T15:27:21Z 2023-12-11T15:27:21Z Journal Article https://hdl.handle.net/10568/135197 en Open Access Springer Ningbo Chen, Xiaoting Xia, Quratulain Hanif, Fengwei Zhang, Ruihua Dang, Bizhi Huang, Yang Lyu, Xiaoyu Luo, Hucai Zhang, Huixuan Yan, Shikang Wang, Fuwen Wang, Jialei Chen, Xiwen Guan, Yangkai Liu, Shuang Li, Liangliang Jin, Pengfei Wang, Luyang Sun, Jicai Zhang, Jianyong Liu, Kaixing Qu, Yanhong Cao, Junli Sun, Yuying Liao, Zhengzhong Xiao, Ming Cai, Lan Mu, Amam Zonaed Siddiki, Muhammad Asif, Shahid Mansoor, Masroor Ellahi Babar, Tanveer Hussain, Gamamada Liyanage Lalanie Pradeepa Silva, Neena Amatya Gorkhali, Terefe, E., Belay, G., Tijjani, A., Zegeye, T., Gebre, M., Yun Ma, Yu Wang, Yongzhen Huang, Xianyong Lan, Hong Chen, Migliore, N.R., Colombo, G., Semino, O., Achilli, A., Sinding, , M.-H.S., Lenstra, J.A., Haijian Cheng, Wenfa Lu, Hanotte, O., Jianlin Han, Yu Jiang and Chuzhao Lei. 2023. Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing. Nature Communications 14:7803. |
| spellingShingle | animal breeding genetics livestock Ningbo Chen Xiaoting Xia Quratulain Hanif Fengwei Zhang Ruihua Dang Bizhi Huang Yang Lyu Xiaoyu Luo Hucai Zhang Huixuan Yan Shikang Wang Fuwen Wang Jialei Chen Xiwen Guan Yangkai Liu Shuang Li Liangliang Jin Pengfei Wang Luyang Sun Jicai Zhang Jianyong Liu Kaixing Qu Yanhong Cao Junli Sun Yuying Liao Zhengzhong Xiao Ming Cai Lan Mu Amam Zonaed Siddiki Zonaed Siddiki, Amam Asif, Muhammad Mansoor, Shahid Babar, M.E. Hussain, Tanveer Silva, Gamamada Liyanage Lalanie Pradeepa Gorkhali, N.A. Terefe, E. Belay, G. Tijjani, Abdulfatai Zegeye, T. Gebre, M. Yun Ma Yu Wang Yongzhen Huang Xianyong Lan Hong Chen Migliore, N.R. Colombo, G. Semino, O. Achilli, A. Sinding, M.-H.S. Lenstra, J.A. Haijian Cheng Wenfa Lu Hanotte, Olivier H. Jianlin Han Yu Jiang Chuzhao Lei Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing |
| title | Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing |
| title_full | Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing |
| title_fullStr | Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing |
| title_full_unstemmed | Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing |
| title_short | Global genetic diversity, introgression, and evolutionary adaptation of indicine cattle revealed by whole genome sequencing |
| title_sort | global genetic diversity introgression and evolutionary adaptation of indicine cattle revealed by whole genome sequencing |
| topic | animal breeding genetics livestock |
| url | https://hdl.handle.net/10568/135197 |
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