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Home / Equine Research Bank / J Equine Sci / Genetic analyses for conservation of the traditional Tokara ...
Journal of equine science2018; 29(4); 97-104; doi: 10.1294/jes.29.97

Genetic analyses for conservation of the traditional Tokara horse using 31 microsatellite markers.

Abstract: In order to promote conservation of the traditional Tokara horse in its remaining three breeding areas in Japan (Nakanoshima, Kaimondake, and Iriki), we genotyped 123 horses using 31 microsatellite markers and determined their genetic diversity. On average, the number of alleles (N), observed heterozygosity (H), expected heterozygosity (H), and inbreeding coefficient (F) among all horses were 3.0, 0.424, 0.481, and 0.108, respectively. Compared with other endangered horse breeds, we found that, even though the size of the Tokara horse population has recently increased, the N, H, and H of Tokara horses are still notably lower than those of other breeds. Neighbor-joining tree and STRUCTURE analysis showed that the current population of Tokara horses is divided into three subpopulations, corresponding to their respective feeding and breeding areas: Nakanoshima, Kaimondake, and Iriki. This subdivision was also reflected in the N of microsatellite DNAs, with four, three, and four different loci showing single alleles in Nakanoshima, Kaimondake, and Iriki horses, respectively. These alleles are considered to have become fixed as a consequence of breeding within the limited number of horses in each area. Since Tokara horses are currently strongly divided into subpopulations, it is vitally important to exchange several horses among their different breeding units in order to maintain the genetic diversity of the Tokara horse as a unique breed. The data obtained in this study contribute toward explaining the history of Tokara horses and also provide important information for future monitoring of population diversity and guiding conservation measures for this endangered breed.
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Publication Date: 2018-12-18 PubMed ID: 30607133PubMed Central: PMC6306296DOI: 10.1294/jes.29.97Google Scholar: Lookup
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Summary

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The study investigates the genetic diversity of the endangered traditional Tokara horse breed in Japan using microsatellite markers, finding that the population, divided into three subpopulations, shows lower genetic diversity than other endangered horse breeds and suggesting conservation measures such as inter-breeding.

Research Methodology

  • The researchers genotyped 123 horses from the three remaining Tokara horse breeding areas (Nakanoshima, Kaimondake, and Iriki) using 31 microsatellite markers, which are short, repetitive DNA sequences used in genetic research to measure the level of genetic variation within a species.
  • The team analyzed four key attributes: the number of alleles (N), observed heterozygosity (H – a measure of genetic variation), expected heterozygosity (also H, estimating genetic variability), and the inbreeding coefficient (F), which indicates the likelihood of obtaining two identical genes from an ancestor.

Investigative Findings

  • On average, among all sampled horses, the attributes were as follows: N=3.0, H=0.424 (observed), H=0.481 (expected), and F=0.108.
  • The genetic diversity of the Tokara horses, as indicated by their allele count and heterozygosity levels, is notably lower than other endangered horse breeds, suggesting a higher degree of inbreeding and genetic similarity.
  • Even though the size of the Tokara horse population has recently increased, this has not led to an equivalent increase in genetic diversity.

Population Structure

  • Neighbor-joining tree and STRUCTURE analysis (statistical techniques used to identify population subsets based on genetic data) revealed the Tokara horses are divided into three distinct subpopulations, mirroring their respective feeding and breeding locations in Nakanoshima, Kaimondake, and Iriki.
  • Each subpopulation displayed unique genetic traits, likely caused by inbreeding within small, isolated populations.
  • Four, three, and four different loci (specific spots on a chromosome) displayed single alleles in Nakanoshima, Kaimondake, and Iriki horses, respectively. This genetic fixation points to restricted breeding within each area.

Conservation Recommendations

  • To maintain genetic diversity and protect the Tokara horse as a distinct breed, the researchers recommend that several horses should be exchanged among different breeding units.
  • The study data inform the history of Tokara horses and provide crucial information for future population diversity monitoring and conservation efforts for this endangered breed.

Cite This Article

APA
Senokuchi A, Ishikawa S, Tozaki T, Takasu M, Kakoi H, Misumi K, Hobo S. (2018). Genetic analyses for conservation of the traditional Tokara horse using 31 microsatellite markers. J Equine Sci, 29(4), 97-104. https://doi.org/10.1294/jes.29.97

Publication

Journal of equine science
ISSN: 1340-3516
NlmUniqueID: 9503751
Country: Japan
Language: English
Volume: 29
Issue: 4
Pages: 97-104

Researcher Affiliations

Senokuchi, Akane
  • Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan.
Ishikawa, Shingo
  • Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan.
Tozaki, Teruaki
  • Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi 320-0851, Japan.
  • Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan.
Takasu, Masaki
  • Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan.
Kakoi, Hironaga
  • Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi 320-0851, Japan.
Misumi, Kazuhiro
  • Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan.
Hobo, Seiji
  • Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan.

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Citations

This article has been cited 7 times.
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  5. Yamashita N, Hatazoe T, Misumi K, Hobo S. Hematological and blood biochemical parameters of Tokara horses in Kaimon Foothills Nature Park. J Vet Med Sci 2025 Dec 1;87(12):1405-1407.
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