Genomic insights into the genetic diversity, lateral gaits and high-altitude adaptation of Chakouyi (CKY) horses

Yang-Kai Liu; Wei-Wei Fu; Zhong-Yu Wang; Sheng-Wei Pei; Kai-Hui Li; Wei-Wei Wu; Meng-Zhen Le; Xiang-Peng Yue

doi:10.1016/j.jgg.2024.11.008

Volume 52 Issue 8

Aug. 2025

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Article Navigation > Journal of Genetics and Genomics > 2025 > 52(8): 1001-1010

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Genomic insights into the genetic diversity, lateral gaits and high-altitude adaptation of Chakouyi (CKY) horses

doi: 10.1016/j.jgg.2024.11.008

a. State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China;
b. Extending Station for Animal Husbandry and Veterinary Technology of Tianzhu Xizang Autonomous County, Tianzhu, Gansu 733299, China;
c. Xinjiang Uyghur Autonomous Region Academy of Animal Science, Urumqi, Xinjiang 830011, China

Funds:

We would like to express our gratitude to the members of the Extending Station for Animal Husbandry and Veterinary Technology of Tianzhu Xizang Autonomous County for their help in sample collection and data acquisition. This research was supported by the Supercomputing Center of Lanzhou University and the Chakouyi horse conservation project from the Tianzhu Xizang Autonomous County Government ([20]0097).

Received Date: 2024-05-10
Accepted Date: 2024-11-13
Rev Recd Date: 2024-11-12
Publish Date: 2024-11-19

Abstract

Abstract

Chakouyi (CKY) horses from the Qinghai‒Xizang Plateau are well known for their unique lateral gaits and high-altitude adaptation, but genetic mechanisms underlying these phenotypes remain unclear. This study presents a comparison of 60 newly resequenced genomes of gaited CKY horses with 139 public genomes from 19 horse breeds. Population structure analyses (admixture, PCA, and neighbor-joining tree) reveal a close genetic relationship between CKY and other highland breeds (Tibetan and Chaidamu horses). Compared with other Chinese breeds, CKY horses present reduced nucleotide diversity (θπ) and lower inbreeding (F_ROH coefficient), suggesting possible selective pressures. A key region on chromosome 23 (Chr23: 22.3–22.6 Mb) is associated with the lateral gaits and harbors a highly prevalent nonsense mutation (Chr 23:22,391,254 C>A, Ser301STOP) in the DMRT3 gene, with an 88% homozygosity rate, which is strongly correlated with the distinctive gait of CKY horses. Furthermore, selection signals reveal that the EPAS1 gene is related to high-altitude adaptation, and the CAT gene contributes to altitude resilience in CKY horses. These findings suggest that preserving genetic diversity is essential for maintaining the unique gaits and high-altitude adaptations of CKY horses.
- Chakouyi horse,
- Genetic diversity,
- Selection signatures,
- Lateral gait,
- High-altitude adaptation,
- DMRT3 gene

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References

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