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Animal genetics2019; 50(5); 449-459; doi: 10.1111/age.12819

Genetic diversity and relationships among native Japanese horse breeds, the Japanese Thoroughbred and horses outside of Japan using genome-wide SNP data.

Abstract: Eight horse breeds-Hokkaido, Kiso, Misaki, Noma, Taishu, Tokara, Miyako and Yonaguni-are native to Japan. Although Japanese native breeds are believed to have originated from ancient Mongolian horses imported from the Korean Peninsula, the phylogenetic relationships among these breeds are not well elucidated. In the present study, we compared genetic diversity among 32 international horse breeds previously evaluated by the Equine Genetic Diversity Consortium, the eight Japanese native breeds and Japanese Thoroughbreds using genome-wide SNP genotype data. The proportion of polymorphic loci and expected heterozygosity showed that the native Japanese breeds, with the exception of the Hokkaido, have relatively low diversity compared to the other breeds sampled. Phylogenetic and cluster analyses demonstrated relationships among the breeds that largely reflect their geographic distribution in Japan. Based on these data, we suggest that Japanese horses originated from Mongolian horses migrating through the Korean Peninsula. The Japanese Thoroughbreds were distinct from the native breeds, and although they maintain similar overall diversity as Thoroughbreds from outside Japan, they also show evidence of uniqueness relative to the other Thoroughbred samples. This is the first study to place the eight native Japanese breeds and Japanese Thoroughbred in context with an international sample of diverse breeds.
© 2019 Stichting International Foundation for Animal Genetics.
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Publication Date: 2019-07-08 PubMed ID: 31282588DOI: 10.1111/age.12819Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research examines the genetic diversity and relationships between eight native Japanese horse breeds and Japanese Thoroughbreds, using genome-wide SNP (single nucleotide polymorphism) data. The study reveals that the Japanese native breeds may have originated from Mongolian horses that entered Japan via Korea. The Japanese Thoroughbreds were found to be distinct from native breeds and Thoroughbreds from other regions, although similar in overall diversity.

Research Objectives and Overview

  • The study focuses mainly on understanding the genetic diversity and relationships among eight native Japanese horse breeds, Japanese Thoroughbreds and various international horse breeds. It employs genome-wide SNP data collected from horses across different breeds and geographic regions.
  • The researchers hypothesize that the Japanese native breeds originated from ancient Mongolian horses that were imported through the Korean Peninsula.
  • The targeted Japanese horse breeds include Hokkaido, Kiso, Misaki, Noma, Taishu, Tokara, Miyako and Yonaguni. Additionally, the Japanese Thoroughbred was also investigated.

Findings and Conclusions

  • The proportion of polymorphic loci and expected heterozygosity levels indicate that, with the exception of Hokkaido, the native Japanese horse breeds have relatively lower genetic diversity compared to the other international breeds. This suggests limited genetic variation within these native breeds, which could be indicative of selective breeding or a small founder population.
  • Phylogenetic and cluster analyses reveal strong correlations between geographic distribution and genetic relationships among the studied breeds. These findings largely support the researchers’ original hypothesis regarding the origins of Japanese horses.
  • Interestingly, the Japanese Thoroughbreds demonstrate distinct genetic characteristics compared to both other Japanese native breeds and international Thoroughbreds. They maintain similar overall levels of genetic diversity as Thoroughbreds from other regions while also showing unique attributes not found in other Thoroughbred samples.
  • The study concludes by reaffirming the proposed origin of Japanese horses from ancient Mongolian horses, and draws attention to the distinct genetic characteristics of Japanese Thoroughbreds.

Implications and Future Research

  • This research provides the first comprehensive genetic comparison between native Japanese horse breeds, Japanese Thoroughbreds and a broad international sample of diverse breeds. It emphasizes the unique genetic profiles of native Japanese breeds and their potential origins.
  • The results can aid in future breeding programs and conservation efforts for these horse breeds. However, further research is needed to explore the specific unique attributes of Japanese Thoroughbreds and to fully understand their genetic diversity. Trends of inbreeding and other potential issues in managing genetic diversity in these native horse populations also warrant further exploration.

Cite This Article

APA
Tozaki T, Kikuchi M, Kakoi H, Hirota K, Nagata S, Yamashita D, Ohnuma T, Takasu M, Kobayashi I, Hobo S, Manglai D, Petersen JL. (2019). Genetic diversity and relationships among native Japanese horse breeds, the Japanese Thoroughbred and horses outside of Japan using genome-wide SNP data. Anim Genet, 50(5), 449-459. https://doi.org/10.1111/age.12819

Publication

Animal genetics
ISSN: 1365-2052
NlmUniqueID: 8605704
Country: England
Language: English
Volume: 50
Issue: 5
Pages: 449-459

Researcher Affiliations

Tozaki, T
  • Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Tochigi, 320-851, Japan.
  • Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan.
  • College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China.
Kikuchi, M
  • Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Tochigi, 320-851, Japan.
Kakoi, H
  • Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Tochigi, 320-851, Japan.
Hirota, K
  • Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Tochigi, 320-851, Japan.
Nagata, S
  • Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Tochigi, 320-851, Japan.
Yamashita, D
  • Japan Equine Affairs Association, Chuo-ku, Tokyo, 104-0033, Japan.
Ohnuma, T
  • Japan Equine Affairs Association, Chuo-ku, Tokyo, 104-0033, Japan.
Takasu, M
  • Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu, 501-1193, Japan.
Kobayashi, I
  • Sumiyoshi Livestock Science Station, Field Science Center, University of Miyazaki, Miyazaki, 880-0121, Japan.
Hobo, S
  • Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, 890-0065, Japan.
Manglai, D
  • College of Animal Science, Inner Mongolia Agricultural University, Hohhot, 010018, China.
Petersen, J L
  • Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, 68583-0908, USA.

MeSH Terms

  • Animals
  • Breeding
  • Cluster Analysis
  • Genetic Variation
  • Genome-Wide Association Study
  • Horses / classification
  • Horses / genetics
  • Japan
  • Phylogeny
  • Polymorphism, Single Nucleotide
  • Principal Component Analysis

Grant Funding

  • Kiso town

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Citations

This article has been cited 9 times.
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