Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment
Background Structural variations (SVs) in individual genomes are major determinants of complex traits, including adaptability to environmental variables. The Mongolian and Hainan cattle breeds in East Asia are of taurine and indicine origins that have evolved to adapt to cold and hot environments, r...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2023
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/132029 |
| _version_ | 1855538281576398848 |
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| author | Xiaoting Xia Fengwei Zhang Shuang Li Xiaoyu Luo Lixin Peng Zheng Dong Pausch, H. Leonard, A.S. Crysnanto, D. Shikang Wang Bin Tong Lenstra, J.A. Han Jianlin Fuyong Li Tieshan Xu Lihong Gu Liangliang Jin Ruihua Dang Yongzhen Huang Xianyong Lan Gang Ren Yu Wang Yuanpeng Gao Zhijie Ma Haijian Cheng Yun Ma Hong Chen Weijun Pang Chuzhao Lei Ningbo Chen |
| author_browse | Bin Tong Chuzhao Lei Crysnanto, D. Fengwei Zhang Fuyong Li Gang Ren Haijian Cheng Han Jianlin Hong Chen Lenstra, J.A. Leonard, A.S. Liangliang Jin Lihong Gu Lixin Peng Ningbo Chen Pausch, H. Ruihua Dang Shikang Wang Shuang Li Tieshan Xu Weijun Pang Xianyong Lan Xiaoting Xia Xiaoyu Luo Yongzhen Huang Yu Wang Yuanpeng Gao Yun Ma Zheng Dong Zhijie Ma |
| author_facet | Xiaoting Xia Fengwei Zhang Shuang Li Xiaoyu Luo Lixin Peng Zheng Dong Pausch, H. Leonard, A.S. Crysnanto, D. Shikang Wang Bin Tong Lenstra, J.A. Han Jianlin Fuyong Li Tieshan Xu Lihong Gu Liangliang Jin Ruihua Dang Yongzhen Huang Xianyong Lan Gang Ren Yu Wang Yuanpeng Gao Zhijie Ma Haijian Cheng Yun Ma Hong Chen Weijun Pang Chuzhao Lei Ningbo Chen |
| author_sort | Xiaoting Xia |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Background
Structural variations (SVs) in individual genomes are major determinants of complex traits, including adaptability to environmental variables. The Mongolian and Hainan cattle breeds in East Asia are of taurine and indicine origins that have evolved to adapt to cold and hot environments, respectively. However, few studies have investigated SVs in East Asian cattle genomes and their roles in environmental adaptation, and little is known about adaptively introgressed SVs in East Asian cattle.
Results
In this study, we examine the roles of SVs in the climate adaptation of these two cattle lineages by generating highly contiguous chromosome-scale genome assemblies. Comparison of the two assemblies along with 18 Mongolian and Hainan cattle genomes obtained by long-read sequencing data provides a catalog of 123,898 nonredundant SVs. Several SVs detected from long reads are in exons of genes associated with epidermal differentiation, skin barrier, and bovine tuberculosis resistance. Functional investigations show that a 108-bp exonic insertion in SPN may affect the uptake of Mycobacterium tuberculosis by macrophages, which might contribute to the low susceptibility of Hainan cattle to bovine tuberculosis. Genotyping of 373 whole genomes from 39 breeds identifies 2610 SVs that are differentiated along a “north–south” gradient in China and overlap with 862 related genes that are enriched in pathways related to environmental adaptation. We identify 1457 Chinese indicine-stratified SVs that possibly originate from banteng and are frequent in Chinese indicine cattle.
Conclusions
Our findings highlight the unique contribution of SVs in East Asian cattle to environmental adaptation and disease resistance. |
| format | Journal Article |
| id | CGSpace132029 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1320292025-01-28T07:08:05Z Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment Xiaoting Xia Fengwei Zhang Shuang Li Xiaoyu Luo Lixin Peng Zheng Dong Pausch, H. Leonard, A.S. Crysnanto, D. Shikang Wang Bin Tong Lenstra, J.A. Han Jianlin Fuyong Li Tieshan Xu Lihong Gu Liangliang Jin Ruihua Dang Yongzhen Huang Xianyong Lan Gang Ren Yu Wang Yuanpeng Gao Zhijie Ma Haijian Cheng Yun Ma Hong Chen Weijun Pang Chuzhao Lei Ningbo Chen cattle genetics animal breeding genomes Background Structural variations (SVs) in individual genomes are major determinants of complex traits, including adaptability to environmental variables. The Mongolian and Hainan cattle breeds in East Asia are of taurine and indicine origins that have evolved to adapt to cold and hot environments, respectively. However, few studies have investigated SVs in East Asian cattle genomes and their roles in environmental adaptation, and little is known about adaptively introgressed SVs in East Asian cattle. Results In this study, we examine the roles of SVs in the climate adaptation of these two cattle lineages by generating highly contiguous chromosome-scale genome assemblies. Comparison of the two assemblies along with 18 Mongolian and Hainan cattle genomes obtained by long-read sequencing data provides a catalog of 123,898 nonredundant SVs. Several SVs detected from long reads are in exons of genes associated with epidermal differentiation, skin barrier, and bovine tuberculosis resistance. Functional investigations show that a 108-bp exonic insertion in SPN may affect the uptake of Mycobacterium tuberculosis by macrophages, which might contribute to the low susceptibility of Hainan cattle to bovine tuberculosis. Genotyping of 373 whole genomes from 39 breeds identifies 2610 SVs that are differentiated along a “north–south” gradient in China and overlap with 862 related genes that are enriched in pathways related to environmental adaptation. We identify 1457 Chinese indicine-stratified SVs that possibly originate from banteng and are frequent in Chinese indicine cattle. Conclusions Our findings highlight the unique contribution of SVs in East Asian cattle to environmental adaptation and disease resistance. 2023-09-18 2023-09-27T12:14:56Z 2023-09-27T12:14:56Z Journal Article https://hdl.handle.net/10568/132029 en Open Access Springer Xiaoting Xia, Fengwei Zhang, Shuang Li, Xiaoyu Luo, Lixin Peng, Zheng Dong, Pausch, H., Leonard, A.S., Crysnanto, D., Shikang Wang, Bin Tong, Lenstra, J.A., Jianlin Han, Fuyong Li, Tieshan Xu, Lihong Gu, Liangliang Jin, Ruihua Dang, Yongzhen Huang, Xianyong Lan, Gang Ren, Yu Wang, Yuanpeng Gao, Zhijie Ma, Haijian Cheng, Yun Ma, Hong Chen, Weijun Pang, Chuzhao Lei and Ningbo Chen. 2023. Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment. Genome Biology 24:211.c |
| spellingShingle | cattle genetics animal breeding genomes Xiaoting Xia Fengwei Zhang Shuang Li Xiaoyu Luo Lixin Peng Zheng Dong Pausch, H. Leonard, A.S. Crysnanto, D. Shikang Wang Bin Tong Lenstra, J.A. Han Jianlin Fuyong Li Tieshan Xu Lihong Gu Liangliang Jin Ruihua Dang Yongzhen Huang Xianyong Lan Gang Ren Yu Wang Yuanpeng Gao Zhijie Ma Haijian Cheng Yun Ma Hong Chen Weijun Pang Chuzhao Lei Ningbo Chen Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment |
| title | Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment |
| title_full | Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment |
| title_fullStr | Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment |
| title_full_unstemmed | Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment |
| title_short | Structural variation and introgression from wild populations in East Asian cattle genomes confer adaptation to local environment |
| title_sort | structural variation and introgression from wild populations in east asian cattle genomes confer adaptation to local environment |
| topic | cattle genetics animal breeding genomes |
| url | https://hdl.handle.net/10568/132029 |
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