Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation

Lin Zeng; He-Qun Liu; Xiao-Long Tu; Chang-Mian Ji; Xiao Gou; Ali Esmailizadeh; Sheng Wang; Ming-Shan Wang; Ming-Cheng Wang; Xiao-Long Li; Hadi Charati; Adeniyi C. Adeola; Rahamon Akinyele Moshood Adedokun; Olatunbosun Oladipo; Sunday Charles Olaogun; Oscar J. Sanke; Mangbon Godwin F.; Sheila Cecily Ommeh; Bernard Agwanda; Jacqueline Kasiiti Lichoti; Jian-Lin Han; Hong-Kun Zheng; Chang-Fa Wang; Ya-Ping Zhang; Laurent A. F. Frantz; Dong-Dong Wu

doi:10.24272/j.issn.2095-8137.2021.095

Volume 42 Issue 4

Jul. 2021

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Article Navigation > Zoological Research > 2021 > 42(4): 450-460

Lin Zeng, He-Qun Liu, Xiao-Long Tu, Chang-Mian Ji, Xiao Gou, Ali Esmailizadeh, Sheng Wang, Ming-Shan Wang, Ming-Cheng Wang, Xiao-Long Li, Hadi Charati, Adeniyi C. Adeola, Rahamon Akinyele Moshood Adedokun, Olatunbosun Oladipo, Sunday Charles Olaogun, Oscar J. Sanke, Mangbon Godwin F., Sheila Cecily Ommeh, Bernard Agwanda, Jacqueline Kasiiti Lichoti, Jian-Lin Han, Hong-Kun Zheng, Chang-Fa Wang, Ya-Ping Zhang, Laurent A. F. Frantz, Dong-Dong Wu. Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation. Zoological Research, 2021, 42(4): 450-460. doi: 10.24272/j.issn.2095-8137.2021.095

Citation:

Lin Zeng, He-Qun Liu, Xiao-Long Tu, Chang-Mian Ji, Xiao Gou, Ali Esmailizadeh, Sheng Wang, Ming-Shan Wang, Ming-Cheng Wang, Xiao-Long Li, Hadi Charati, Adeniyi C. Adeola, Rahamon Akinyele Moshood Adedokun, Olatunbosun Oladipo, Sunday Charles Olaogun, Oscar J. Sanke, Mangbon Godwin F., Sheila Cecily Ommeh, Bernard Agwanda, Jacqueline Kasiiti Lichoti, Jian-Lin Han, Hong-Kun Zheng, Chang-Fa Wang, Ya-Ping Zhang, Laurent A. F. Frantz, Dong-Dong Wu. Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation. Zoological Research, 2021, 42(4): 450-460. doi: 10.24272/j.issn.2095-8137.2021.095

Citation:

Lin Zeng, He-Qun Liu, Xiao-Long Tu, Chang-Mian Ji, Xiao Gou, Ali Esmailizadeh, Sheng Wang, Ming-Shan Wang, Ming-Cheng Wang, Xiao-Long Li, Hadi Charati, Adeniyi C. Adeola, Rahamon Akinyele Moshood Adedokun, Olatunbosun Oladipo, Sunday Charles Olaogun, Oscar J. Sanke, Mangbon Godwin F., Sheila Cecily Ommeh, Bernard Agwanda, Jacqueline Kasiiti Lichoti, Jian-Lin Han, Hong-Kun Zheng, Chang-Fa Wang, Ya-Ping Zhang, Laurent A. F. Frantz, Dong-Dong Wu. Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation. Zoological Research, 2021, 42(4): 450-460. doi: 10.24272/j.issn.2095-8137.2021.095

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Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation

doi: 10.24272/j.issn.2095-8137.2021.095

1.
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
2.
Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
3.
College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan 650201, China
4.
Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran
5.
Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
6.
Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
7.
Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
8.
Institute of Three-River-Source National Park, Chinese Academy of Sciences, Xining, Qinghai 810008, China
9.
School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
10.
Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
11.
Annoroad Gene Tech. (Beijing) Co., Ltd., Beijing 100176, China
12.
State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
13.
Department of Veterinary Medicine, University of Ibadan, Ibadan 200284, Nigeria
14.
Federal College of Animal Health and Production Technology, Moor-Plantation, Ibadan 234102, Nigeria
15.
Taraba State Ministry of Agriculture and Natural Resources, Jalingo 660221, Nigeria
16.
Division of Veterinary Office, Serti 663101, Nigeria
17.
Institute For Biotechnology Research Jomo Kenyatta University of Agriculture and Technology, Nairobi 62000-00200, Kenya
18.
Department of Zoology, National Museums of Kenya, Nairobi 40658-00100, Kenya
19.
State Department of Livestock, Ministry of Agriculture, Livestock, Fisheries and Irrigation, Nairobi 00625, Kenya
20.
Equus Laboratory, Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Ji’nan, Shandong 250131, China
21.
Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, Shandong 252059, China
22.
CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
23.
Biomarker Technologies Corporation, Beijing 101300, China
24.
Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich 80539, Germany

#Authors contributed equally to this work

Funds: This work was supported by the National Natural Science Foundation of China (31621062), Strategic Priority Research Program of the Chinese Academy of Sciences (XDA2004010302), and Second Tibetan Plateau Scientific Expedition and Research (STEP) Program (2019QZKK05010703). D.D.W. was supported by the National Natural Science Foundation of China (91731304, 31822048), Strategic Priority Research Program of the Chinese Academy of Sciences (XDB13020600), Qinghai Department of Science and Technology Major Project, and State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University (2018KF001). Sampling of this work was also supported by the Animal Branch of the Germplasm Bank of Wild Species, Chinese Academy of Sciences (Large Research Infrastructure Funding)

More Information

Corresponding author: E-mail: wangcf1967@163.com; zhangyp@mail.kiz.ac.cn; laurent.frantz@qmul.ac.uk; wudongdong@mail.kiz.ac.cn
Received Date: 2021-03-25
Accepted Date: 2021-06-21

Published Online: 2021-06-22

Publish Date: 2021-07-18

Abstract

Abstract

Over the last several hundred years, donkeys have adapted to high-altitude conditions on the Tibetan Plateau. Interestingly, the kiang, a closely related equid species, also inhabits this region. Previous reports have demonstrated the importance of specific genes and adaptive introgression in divergent lineages for adaptation to hypoxic conditions on the Tibetan Plateau. Here, we assessed whether donkeys and kiangs adapted to the Tibetan Plateau via the same or different biological pathways and whether adaptive introgression has occurred. We assembled a de novo genome from a kiang individual and analyzed the genomes of five kiangs and 93 donkeys (including 24 from the Tibetan Plateau). Our analyses suggested the existence of a strong hard selective sweep at the EPAS1 locus in kiangs. In Tibetan donkeys, however, another gene, i.e., EGLN1, was likely involved in their adaptation to high altitude. In addition, admixture analysis found no evidence for interspecific gene flow between kiangs and Tibetan donkeys. Our findings indicate that despite the short evolutionary time scale since the arrival of donkeys on the Tibetan Plateau, as well as the existence of a closely related species already adapted to hypoxia, Tibetan donkeys did not acquire adaptation via admixture but instead evolved adaptations via a different biological pathway.
- Kiang,
- Donkey,
- High altitude,
- Adaptation,
- Selection

#Authors contributed equally to this work

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References(60)

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