Whole-Genome Sequence Analysis Reveals the Origin of the Chakouyi Horse.
Abstract: The Chakouyi horse is an ancient Chinese indigenous horse breed distributed in Gansu Province in northwestern China, and is also one of the key breeds protected by the government. However, the origin of the Chakouyi horse remains unclear. As it is distributed in a key region of the Silk Road, it was speculated that the origin of the Chakouyi horse might involve the foreign horse breeds found along this ancient commercial artery. In this study, whole-genome resequencing data of 12 horse breeds, including both indigenous and foreign horses, were applied to reveal the genetic relationships between the Chakouyi horse and other breeds, as well as the ancestry of this ancient breed. An analysis of the population structure and admixture showed that there is no close genetic affinity between the Chakouyi horse and the foreign horses while Chinese indigenous horse populations were grouped together in accordance with their geographic locations, and the Chakouyi horse showed a closer relationship with Kazak horses, Mongolian horses, and Tibetan horses. The results from the ancestral composition prediction indicated that the Kazak horse and the Mongolian horse might be two ancestors of the Chakouyi horse. Furthermore, the genome-wide selection signature analysis revealed that the DMRT3 gene was positively selected in the Chakouyi horse and related to the gait trait of the breed. Our results provide insights into the native origin of the Chakouyi horse and indicate that Kazak and Mongolian horses played important roles in the formation of the Chakouyi horse. Genetic communication between the Chakouyi horse and other horse populations could be attributed, at least partially, to population migrations and trade activities along the ancient commercial routes.
Publication Date: 2022-12-19 PubMed ID: 36553682PubMed Central: PMC9778315DOI: 10.3390/genes13122411Google Scholar: Lookup
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- Journal Article
- Research Support
- Non-U.S. Gov't
Summary
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This research paper investigates the genetic origins of the Chakouyi horse, a protected breed in China. By using whole-genome sequencing data from several horse breeds, the study determined that Kazak and Mongolian horses likely influenced the Chakouyi horse’s formation and identified a gene linked to this breed’s distinctive gait.
Understanding the Origin of the Chakouyi Horse
- The Chakouyi horse is a notable Chinese breed preserved in the northwestern province of Gansu. The study sets out to investigate the breed’s genetic origins, given its location along the Silk Road, an ancient trade route that could have facilitated genetic mixing with foreign horse breeds.
- The researchers utilized a technique called whole-genome resequencing, which provides a detailed look at the genetic composition of an organism. They sequenced the genomes of 12 horse breeds, including both indigenous and foreign varieties.
Identifying Genetic Relationships and Ancestors
- The researchers sought to identify any genetic relationships between the Chakouyi and other horse breeds. Using population structure and admixture analysis, they discovered no significant genetic affinity between the Chakouyi and foreign horses.
- Instead, they found that Chinese indigenous horse populations were grouped together according to their geographic locations. The Chakouyi horse exhibited a closer relationship with Kazak horses, Mongolian horses, and Tibetan horses.
- This indicated that the Kazak horse and Mongolian horse might be two ancestors of the Chakouyi horse, illustrating a potential lineage.
Identifying a Selected Gene and its Implications
- Beyond tracing lineage, the study also aimed to identify any specific genes that might be unique or particularly prominent in the Chakouyi horse. A genome-wide selection signature analysis was conducted, revealing that the DMRT3 gene was positively selected in the Chakouyi horse.
- The DMRT3 gene is associated with the gait trait of horses. This suggests that the specific gait of the Chakouyi horse could be attributed to the positive selection of this gene throughout the breed’s evolution.
Conclusions and Implications
- The study provides new insights into the native origin of the Chakouyi horse, suggesting that Kazak and Mongolian horses played key roles in the formation of this breed.
- Additionally, while no strong genetic links were found between the Chakouyi and foreign breeds, the study postulates that any genetic communication could have occurred due to population migrations and trade activities along historical commercial routes like the Silk Road.
Cite This Article
APA
Li Y, Liu Y, Wang M, Lin X, Li Y, Yang T, Feng M, Ling Y, Zhao C.
(2022).
Whole-Genome Sequence Analysis Reveals the Origin of the Chakouyi Horse.
Genes (Basel), 13(12).
https://doi.org/10.3390/genes13122411 Publication
Researcher Affiliations
- Equine Center, China Agricultural University, Beijing 100193, China.
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
- Equine Center, China Agricultural University, Beijing 100193, China.
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
- Equine Center, China Agricultural University, Beijing 100193, China.
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
- Equine Center, China Agricultural University, Beijing 100193, China.
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
- Equine Center, China Agricultural University, Beijing 100193, China.
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
- Equine Center, China Agricultural University, Beijing 100193, China.
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
- Equine Center, China Agricultural University, Beijing 100193, China.
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
- Equine Center, China Agricultural University, Beijing 100193, China.
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
- National Engineering Laboratory for Animal Breeding, Beijing 100193, China.
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing 100193, China.
- Beijing Key Laboratory of Animal Genetic Improvement, Beijing 100193, China.
MeSH Terms
- Animals
- Horses / genetics
- Polymorphism, Single Nucleotide / genetics
- Genome / genetics
- China
- Phenotype
- Sequence Analysis, DNA
Conflict of Interest Statement
The authors declare no conflict of interest.
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