Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep
Sheep were domesticated in the Fertile Crescent and then spread globally, where they have been encountering various environmental conditions. The Tibetan sheep has adapted to high altitudes on the Qinghai-Tibet Plateau over the past 3000 years. To explore genomic variants associated with high-altitu...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Oxford University Press
2024
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| Acceso en línea: | https://hdl.handle.net/10568/151842 |
| _version_ | 1855528746752147456 |
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| author | Chao Li Bingchun Chen Suo Langda Peng Pu Xiaojia Zhu Shiwei Zhou Kalds, P. Awang Cuoji Xiran Wang Haolin Zhu Yujiang Wu Renqin Cuomu Ba Gui Ming Li Yutao Wang Yan Li Wenwen Fang Ting Jia Tianchun Pu Xiangyu Pan Yudong Cai Chong He Liming Wang Yu Jiang Han Jianlin Yulin Chen Ping Zhou Pausch, H. Xiaolong Wang |
| author_browse | Awang Cuoji Ba Gui Bingchun Chen Chao Li Chong He Han Jianlin Haolin Zhu Kalds, P. Liming Wang Ming Li Pausch, H. Peng Pu Ping Zhou Renqin Cuomu Shiwei Zhou Suo Langda Tianchun Pu Ting Jia Wenwen Fang Xiangyu Pan Xiaojia Zhu Xiaolong Wang Xiran Wang Yan Li Yu Jiang Yudong Cai Yujiang Wu Yulin Chen Yutao Wang |
| author_facet | Chao Li Bingchun Chen Suo Langda Peng Pu Xiaojia Zhu Shiwei Zhou Kalds, P. Awang Cuoji Xiran Wang Haolin Zhu Yujiang Wu Renqin Cuomu Ba Gui Ming Li Yutao Wang Yan Li Wenwen Fang Ting Jia Tianchun Pu Xiangyu Pan Yudong Cai Chong He Liming Wang Yu Jiang Han Jianlin Yulin Chen Ping Zhou Pausch, H. Xiaolong Wang |
| author_sort | Chao Li |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Sheep were domesticated in the Fertile Crescent and then spread globally, where they have been encountering various environmental conditions. The Tibetan sheep has adapted to high altitudes on the Qinghai-Tibet Plateau over the past 3000 years. To explore genomic variants associated with high-altitude adaptation in Tibetan sheep, we analyzed Illumina short-reads of 994 whole genomes representing ∼ 60 sheep breeds/populations at varied altitudes, PacBio High fidelity (HiFi) reads of 13 breeds, and 96 transcriptomes from 12 sheep organs. Association testing between the inhabited altitudes and 34,298,967 variants was conducted to investigate the genetic architecture of altitude adaptation. Highly accurate HiFi reads were used to complement the current ovine reference assembly at the most significantly associated β-globin locus and to validate the presence of two haplotypes A and B among 13 sheep breeds. The haplotype A carried two homologous gene clusters: (1) HBE1, HBE2, HBB-like, and HBBC, and (2) HBE1-like, HBE2-like, HBB-like, and HBB; while the haplotype B lacked the first cluster. The high-altitude sheep showed highly frequent or nearly fixed haplotype A, while the low-altitude sheep dominated by haplotype B. We further demonstrated that sheep with haplotype A had an increased hemoglobin–O2 affinity compared with those carrying haplotype B. Another highly associated genomic region contained the EGLN1 gene which showed varied expression between high-altitude and low-altitude sheep. Our results provide evidence that the rapid adaptive evolution of advantageous alleles play an important role in facilitating the environmental adaptation of Tibetan sheep. |
| format | Journal Article |
| id | CGSpace151842 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace1518422025-12-08T10:06:44Z Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep Chao Li Bingchun Chen Suo Langda Peng Pu Xiaojia Zhu Shiwei Zhou Kalds, P. Awang Cuoji Xiran Wang Haolin Zhu Yujiang Wu Renqin Cuomu Ba Gui Ming Li Yutao Wang Yan Li Wenwen Fang Ting Jia Tianchun Pu Xiangyu Pan Yudong Cai Chong He Liming Wang Yu Jiang Han Jianlin Yulin Chen Ping Zhou Pausch, H. Xiaolong Wang sheep genetics animal breeding adaptation breeds genomes testing evolution variants alleles gene altitude genetic haplotypes genetic control Sheep were domesticated in the Fertile Crescent and then spread globally, where they have been encountering various environmental conditions. The Tibetan sheep has adapted to high altitudes on the Qinghai-Tibet Plateau over the past 3000 years. To explore genomic variants associated with high-altitude adaptation in Tibetan sheep, we analyzed Illumina short-reads of 994 whole genomes representing ∼ 60 sheep breeds/populations at varied altitudes, PacBio High fidelity (HiFi) reads of 13 breeds, and 96 transcriptomes from 12 sheep organs. Association testing between the inhabited altitudes and 34,298,967 variants was conducted to investigate the genetic architecture of altitude adaptation. Highly accurate HiFi reads were used to complement the current ovine reference assembly at the most significantly associated β-globin locus and to validate the presence of two haplotypes A and B among 13 sheep breeds. The haplotype A carried two homologous gene clusters: (1) HBE1, HBE2, HBB-like, and HBBC, and (2) HBE1-like, HBE2-like, HBB-like, and HBB; while the haplotype B lacked the first cluster. The high-altitude sheep showed highly frequent or nearly fixed haplotype A, while the low-altitude sheep dominated by haplotype B. We further demonstrated that sheep with haplotype A had an increased hemoglobin–O2 affinity compared with those carrying haplotype B. Another highly associated genomic region contained the EGLN1 gene which showed varied expression between high-altitude and low-altitude sheep. Our results provide evidence that the rapid adaptive evolution of advantageous alleles play an important role in facilitating the environmental adaptation of Tibetan sheep. 2024-07-03 2024-08-25T18:18:32Z 2024-08-25T18:18:32Z Journal Article https://hdl.handle.net/10568/151842 en Open Access Oxford University Press Chao Li, Bingchun Chen, Suo Langda, Peng Pu, Xiaojia Zhu, Shiwei Zhou, Kalds, P., Ke Zhang, Bhati, M., Leonard, A., Shuhong Huang, Ran Li, Awang Cuoji, Xiran Wang, Haolin Zhu, Yujiang Wu, Renqin Cuomu, Ba Gui, Ming Li, Yutao Wang, Yan Li, Wenwen Fang, Ting Jia, Tianchun Pu, Xiangyu Pan, Yudong Cai, Chong He, Liming Wang, Yu Jiang, Jian-Lin Han, Yulin Chen, Ping Zhou, Pausch, H. and Xiaolong Wang. 2024. Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep. Genomics, Proteomics & Bioinformatics 22(2):qzae030. |
| spellingShingle | sheep genetics animal breeding adaptation breeds genomes testing evolution variants alleles gene altitude genetic haplotypes genetic control Chao Li Bingchun Chen Suo Langda Peng Pu Xiaojia Zhu Shiwei Zhou Kalds, P. Awang Cuoji Xiran Wang Haolin Zhu Yujiang Wu Renqin Cuomu Ba Gui Ming Li Yutao Wang Yan Li Wenwen Fang Ting Jia Tianchun Pu Xiangyu Pan Yudong Cai Chong He Liming Wang Yu Jiang Han Jianlin Yulin Chen Ping Zhou Pausch, H. Xiaolong Wang Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep |
| title | Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep |
| title_full | Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep |
| title_fullStr | Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep |
| title_full_unstemmed | Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep |
| title_short | Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep |
| title_sort | multi omic analyses shed light on the genetic control of high altitude adaptation in sheep |
| topic | sheep genetics animal breeding adaptation breeds genomes testing evolution variants alleles gene altitude genetic haplotypes genetic control |
| url | https://hdl.handle.net/10568/151842 |
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