Genomic insights into the genetic diversity, lateral gaits and high-altitude adaptation of Chakouyi (CKY) horses.
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 (FROH 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.
Copyright © 2024 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved.
Publication Date: 2024-11-19 PubMed ID: 39571791DOI: 10.1016/j.jgg.2024.11.008Google Scholar: Lookup
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Summary
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The research article presents a detailed genetic analysis of Chakouyi (CKY) horses, highlighting their unique lateral gaits and ability to adapt to high altitudes. The study explores these defining characteristics using genomic sequencing from a wide range of horse breeds for comparison.
Genomic Comparison and Population Structure
- The researchers compared the genomes of 60 gaited CKY horses with 139 genomes from 19 other horse breeds. This comparison was made to understand the genetic differences and similarities between CKY horses and other breeds.
- Investigations using admixture, PCA, and neighbor-joining tree analyses helped establish a close genetic relationship between the CKY horses and other highland horse breeds, namely Tibetan and Chaidamu horses.
- The CKY horses were found to exhibit a decrease in nucleotide diversity (θπ) and a lower level of inbreeding (represented by the F coefficient) compared to other Chinese breeds. These patterns suggest that selective pressures may be at work in shaping the gene pool of the CKY breed.
Genetic Basis for Unique Traits
- A specific region of chromosome 23 in CKY horses was discovered to be associated with their unique lateral gaits. This region contains a prevalent nonsense mutation in the DMRT3 gene. This mutation has an 88% homozygosity rate, indicating that a large majority of CKY horses carry two copies of the altered gene, thereby suggesting a strong link to the unique gait of these horses.
- Beyond the distinctive gait, the study also identified genes associated with the high-altitude resilience of CKY horses. The presence of selection signals in the EPAS1 gene and the CAT gene seem to contribute to the high-altitude adaptation observed in these horses.
Conservation Implications
- The outcomes of this research underscore the importance of genetic diversity in maintaining the unique characteristics of CKY horses, particularly regarding their special lateral gaits and the ability to adapt to high-altitude environments.
- Thus, preserving genetic diversity is seen as crucial to sustain these unique traits within the CKY horse population.
Cite This Article
APA
Liu YK, Fu WW, Wang ZY, Pei SW, Li KH, Wu WW, Le MZ, Yue XP.
(2024).
Genomic insights into the genetic diversity, lateral gaits and high-altitude adaptation of Chakouyi (CKY) horses.
J Genet Genomics, 52(8), 1001-1010.
https://doi.org/10.1016/j.jgg.2024.11.008 Publication
Researcher Affiliations
- 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.
- 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.
- 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.
- 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.
- Extending Station for Animal Husbandry and Veterinary Technology of Tianzhu Xizang Autonomous County, Tianzhu, Gansu 733299, China.
- Xinjiang Uyghur Autonomous Region Academy of Animal Science, Urumqi, Xinjiang 830011, China.
- 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.
- 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. Electronic address: lexp@lzu.edu.cn.
MeSH Terms
- Animals
- Horses / genetics
- Horses / physiology
- Altitude
- Genetic Variation
- Genomics
- Adaptation, Physiological / genetics
- Polymorphism, Single Nucleotide
- Genome
- Basic Helix-Loop-Helix Transcription Factors / genetics
- Phylogeny
- Selection, Genetic
- Phenotype
Conflict of Interest Statement
Conflict of interest All of the authors declare that this research was conducted in the absence of any commercial or financial relationships that could be construed as potential conflicts of interest.
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