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The Journal of veterinary medical science2016; 79(2); 425-431; doi: 10.1292/jvms.16-0040

Genetic diversity of the Yonaguni horse based on polymorphisms in microsatellites and mitochondrial DNA.

Abstract: Thirty-two microsatellites and a mitochondrial DNA haplotypes of endangered Yonaguni horses were analyzed to establish a pedigree registration system and to understand their genetic diversity for planning effective conservation. Blood samples were collected from 78 of the 130 horses in existence, and DNA was extracted and genotyped. There were two major findings. One is that it is possible to use microsatellites for Yonaguni horse pedigree registration in the future because the power of exclusion of parentage testing is reliable at 0.999998. The second is the clarification of the current genetic diversity of Yonaguni horses. The average number of alleles, observed heterozygosity, expected heterozygosity and fixation index were 4.4, 0.591, 0.601 and 0.016, respectively, for the analyzed horses. The probability of a genetic bottleneck, under the assumptions of the stepwise mutation model, was 0.432, suggesting that the genetic structure of the horses was not influenced by a recent bottleneck. Genetic distance between individuals was visualized by a phylogenetic tree based on the proportion of shared alleles. Structure analysis based on Bayesian clustering revealed the possibility that Yonaguni horses comprise four or five subpopulations. Consequently, although only two haplotypes were identified in the mitochondrial analysis, genetic diversity of Yonaguni horses was not particularly low in comparison with that of other breeds that are at risk of extinction.
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Publication Date: 2016-12-31 PubMed ID: 28049866PubMed Central: PMC5326952DOI: 10.1292/jvms.16-0040Google 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 study examined the genetic diversity of endangered Yonaguni horses using analysis of microsatellites and mitochondrial DNA. A potential pedigree registration system for the breed was established and the findings suggest that genetic diversity within the breed is higher than expected.

Methodology

  • The researchers collected blood samples from 78 out of the 130 known Yonaguni horses.
  • They isolated DNA from these samples and genotyped it using thirty-two different microsatellites.
  • They also analysed the DNA for mitochondrial haplotypes.

Findings

  • The study demonstrated the viability of using microsatellites for pedigree registration of Yonaguni horses. The exclusion power of parentage testing was proven to be highly reliable, with a value of 0.999998.
  • This genetic analysis helped clarify the current genetic diversity of the Yonaguni horses. Key metrics were as follows. The average number of alleles was 4.4; the observed heterozygosity was 0.591; the expected heterozygosity was 0.601; and the fixation index was 0.016. These figures suggested a healthy level of genetic variation within the population.
  • The probability of the genetic structure of the horses being influenced by a recent bottleneck was evaluated, under the assumptions of the stepwise mutation model. This probability was calculated to be 0.432, indicating that the population’s genetic composition had not been significantly shaped by a recent decrease in numbers.
  • The genetic distance between individual horses was visualised using a phylogenetic tree, based on shared allele proportions. This tree displayed the relationships between the horses at a genetic level.
  • A structure analysis based on Bayesian clustering suggested that the Yonaguni horses might be divided into four or five subpopulations.

Conclusion

  • Despite identifying only two haplotypes in the mitochondrial DNA analysis, the genetic diversity of Yonaguni horses was not notably low, particularly when compared with other breeds that are at risk of extinction.
  • This indicates that the breed, although endangered, has maintained a diverse genetic pool, which is a positive sign for the sustainability of the breed.
  • The findings of this research will help inform conservation measures for this breed, as maintaining genetic diversity is vital for its long-term survival.

Cite This Article

APA
Senju N, Tozaki T, Kakoi H, Shinjo A, Matsuyama R, Almunia J, Takasu M. (2016). Genetic diversity of the Yonaguni horse based on polymorphisms in microsatellites and mitochondrial DNA. J Vet Med Sci, 79(2), 425-431. https://doi.org/10.1292/jvms.16-0040

Publication

The Journal of veterinary medical science
ISSN: 1347-7439
NlmUniqueID: 9105360
Country: Japan
Language: English
Volume: 79
Issue: 2
Pages: 425-431

Researcher Affiliations

Senju, Natsuko
  • Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University,1-1 Yanagido, Gifu 501-1193, Japan.
Tozaki, Teruaki
    Kakoi, Hironaga
      Shinjo, Akihisa
        Matsuyama, Ryota
          Almunia, Julio
            Takasu, Masaki

              MeSH Terms

              • Animals
              • DNA, Mitochondrial
              • Female
              • Genetic Variation
              • Horses / classification
              • Horses / genetics
              • Japan
              • Male
              • Microsatellite Repeats
              • Pedigree
              • Phylogeny
              • Polymorphism, Genetic
              • Species Specificity

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              Citations

              This article has been cited 12 times.
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