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The Journal of veterinary medical science2014; 76(11); 1451-1456; doi: 10.1292/jvms.14-0231

Genetic diversity of maternal lineage in the endangered Kiso horse based on polymorphism of the mitochondrial DNA D-loop region.

Abstract: To determine genetic characteristics of the maternal lineage of the Kiso horse based on polymorphisms of the mitochondrial DNA D-loop region, we collected blood samples from 136 Kiso horses, 91% of the entire population, and sequenced 411 bp from 15,437 to 15,847 in the region. First of all, we estimated the demographic history; by searching homology between the obtained and known sequences using Basic Local Alignment Search Tool, by mismatch analysis to evaluate the mutation processes using Arlequin, and by building a phylogenetic tree showing the relationship of the mtDNA haplotypes for 24 horse breeds around the world using Molecular Evolutionary Genetics Analysis softwear. The results suggested that various horses that came to Japan stayed at Kiso region and became ancestors of Kiso horse and also genetically supported the theory that the Kiso horse was historically improved by other Japanese native horse breeds. Next, we analyzed the diversity of current maternal lineage by classifying the resulting sequences, and by calculating the haplotype diversity and nucleotide diversity using Arlequin. Then, we visualized the relationship among haplotypes by a median-joining network using NETWORK 4.6.0.0. The results suggested the diversity of maternal lineage in the Kiso horse was reasonably maintained. Lastly, we predicted future change of the diversity of maternal lineage in Kiso horse by assessing the regional distribution of the acquired haplotypes. The distribution suggested that diversity of maternal lineage would possibly be reducing.
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Publication Date: 2014-07-24 PubMed ID: 25056676PubMed Central: PMC4272977DOI: 10.1292/jvms.14-0231Google Scholar: Lookup
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  • Non-U.S. Gov't

Summary

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This research studied the genetic diversity of the maternal lineage in Kiso horses, an endangered breed, by analyzing polymorphisms in the mitochondrial DNA D-loop region. Analyzing blood samples from 91% of the entire population, they found the horses have reasonable genetic diversity, although the future indication suggests potential reduction in diversity.

Genetic Characteristics and Historical Estimation

  • The researchers started by determining genetic attributes of the Kiso horse’s maternal lineage. This was done using polymorphisms from the mitochondrial DNA D-loop region.
  • Blood samples were collected from 136 Kiso horses, which represented 91% of the entire population. They then sequenced 411 bp within the region.
  • The team estimated the demographic history by comparing the obtained sequences with known sequences, using the Basic Local Alignment Search Tool. They also analyzed mutation processes using mismatch analysis in Arlequin, and created a phylogenetic tree to understand the relationship of mtDNA haplotypes for 24 different horse breeds using Molecular Evolutionary Genetics Analysis software.
  • The results suggested that various horses came to the Kiso region in Japan and became the ancestors of modern Kiso horses. This lends genetic support to the theory that the Kiso horse breed was improved historically by local Japanese breeds.

Diversity Analysis and Network Visualization

  • The researchers analyzed the current diversity of the maternal lineage by classifying the resultant sequences, and calculating haplotype and nucleotide diversity using Arlequin.
  • The relationship among haplotypes was illustrated through a median-joining network using NETWORK 4.6.0.0 software.
  • Their analysis showed that the diversity of the maternal lineage of the Kiso horse has been reasonably maintained thus far.

Predicting Future Diversity

  • Lastly, the team forecasted potential changes in the diversity of the Kiso horse’s maternal lineage by observing the regional distribution of the acquired haplotypes.
  • From this information, the researchers propose that there may be a possible reduction in the diversity of the maternal lineage of the Kiso horse in the future.

Cite This Article

APA
Takasu M, Ishihara N, Tozaki T, Kakoi H, Maeda M, Mukoyama H. (2014). Genetic diversity of maternal lineage in the endangered Kiso horse based on polymorphism of the mitochondrial DNA D-loop region. J Vet Med Sci, 76(11), 1451-1456. https://doi.org/10.1292/jvms.14-0231

Publication

The Journal of veterinary medical science
ISSN: 1347-7439
NlmUniqueID: 9105360
Country: Japan
Language: English
Volume: 76
Issue: 11
Pages: 1451-1456

Researcher Affiliations

Takasu, Masaki
  • Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
Ishihara, Namiko
    Tozaki, Teruaki
      Kakoi, Hironaga
        Maeda, Masami
          Mukoyama, Harutaka

            MeSH Terms

            • Animal Distribution
            • Animals
            • Base Sequence
            • Cluster Analysis
            • Computational Biology
            • DNA Primers / genetics
            • DNA, Mitochondrial / genetics
            • Endangered Species
            • Genetic Variation
            • Haplotypes / genetics
            • Horses / genetics
            • Molecular Sequence Data
            • Phylogeny
            • Sequence Analysis, DNA / veterinary
            • Sequence Homology

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            Citations

            This article has been cited 9 times.
            1. Nakamura M, Tozaki T, Kakoi H, Nakamura K, Rajabi-Toustani R, Ohba Y, Matsubara T, Takasu M. Decreased genetic diversity in Kiso horses revealed through annual microsatellite genotyping. J Vet Med Sci 2020 Apr 15;82(4):503-540.
              doi: 10.1292/jvms.19-0535pubmed: 32147602google scholar: lookup
            2. Kobayashi I, Akita M, Takasu M, Tozaki T, Kakoi H, Nakamura K, Senju N, Matsuyama R, Horii Y. Genetic characteristics of feral Misaki horses based on polymorphisms of microsatellites and mitochondrial DNA. J Vet Med Sci 2019 May 11;81(5):707-711.
              doi: 10.1292/jvms.18-0565pubmed: 30867351google scholar: lookup
            3. Nakamura K, Tozaki T, Kakoi H, Owada S, Takasu M. Variation in the MC1R, ASIP, and MATP genes responsible for coat color in Kiso horse as determined by SNaPshot™ genotyping. J Vet Med Sci 2019 Jan 8;81(1):100-102.
              doi: 10.1292/jvms.18-0458pubmed: 30464090google scholar: lookup
            4. Kakoi H, Kikuchi M, Tozaki T, Hirota KI, Nagata SI, Hobo S, Takasu M. Distribution of Y chromosomal haplotypes in Japanese native horse populations. J Equine Sci 2018;29(2):39-42.
              doi: 10.1294/jes.29.39pubmed: 29991921google scholar: lookup
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            7. Senju N, Tozaki T, Kakoi H, Almunia J, Maeda M, Matsuyama R, Takasu M. Genetic characterization of the Miyako horse based on polymorphisms of microsatellites and mitochondrial DNA. J Vet Med Sci 2017 Jan 24;79(1):218-223.
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            9. Agbani A, Aminou O, Machmoum M, Germot A, Badaoui B, Petit D, Piro M. A Systematic Literature Review of Mitochondrial DNA Analysis for Horse Genetic Diversity. Animals (Basel) 2025 Mar 20;15(6).
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