Molecular analysis using mitochondrial DNA and microsatellites to infer the formation process of Japanese native horse populations.
Abstract: To assess the genetic diversity of Japanese native horse populations, we examined seven such populations using mitochondrial DNA (mtDNA) and microsatellite analyses. Four reference populations of Mongolian horses and European breeds were employed as other equids. In the mtDNA analysis, the control region (D-loop) of 411 bp was sequenced, and 12 haplotypes with 33 variable sites were identified in the Japanese native horses. The phylogenetic tree constructed by haplogrouping and using worldwide geographic references indicated that the haplotypes of the Japanese native horses were derived from six equid clusters. Compared with the foreign populations, the Japanese native populations showed lower within-population diversity and higher between-population differentiation. Microsatellite analysis, using 27 markers, found an average number of alleles per locus of 9.6 in 318 native and foreign horses. In most native populations, the within-population diversity was lower than that observed in foreign populations. The genetic distance matrix based on allelic frequency indicated that several native populations had notably high between-population differentiation. The molecular co-ancestry-based genetic distance matrix revealed that the European populations were differentiated from the Japanese and Mongolian populations, and no clear groups could be identified among the Japanese native horse populations. The genetic distance matrices had few correlations with the geographic distribution of the Japanese native populations. Based on the results of both mtDNA and microsatellite analyses, it could be speculated that each native population was formed by the founder populations derived from Mongolian horses. The genetic construction of each population appears to have been derived from independent breeding in each local area since the time of population fission, and this was accompanied by drastic genetic drift in recent times. This information will help to elucidate the ancestry of Japanese native horses.
Publication Date: 2007-02-01 PubMed ID: 17265183DOI: 10.1007/s10528-007-9083-0Google Scholar: Lookup
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Summary
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This research study investigated the genetic diversity of seven Japanese native horse populations using mitochondrial DNA and microsatellite analyses, revealing low within-population diversity and high between-population differentiation, suggesting that each population originated independently from Mongolian horses.
Mitochondrial DNA Analysis
- The team scrutinized a section of the mitochondrial DNA (mtDNA) known as the control region or D-loop. In the seven Japanese native horse populations examined, 12 different genetic configurations or haplotypes, with a total of 33 variable sites, were found.
- They constructed a phylogenetic tree, grouping the haplotypes and referencing other horses globally, to determine the ancestral lineage and genetic divergence of these horse populations.
- The haplotypes of the Japanese horses were traced back to six different equid clusters, showing a genetic diversity that suggests multiple direct ancestors.
Microsatellite Analysis
- Escalating the scope of their genetic investigation, the team also executed a microsatellite analysis using 27 marker points.
- They used these markers to examine the genetic diversity within and between populations. Each of the 318 horses, both native and foreign, carried approximately 9.6 unique genetic attributes per locus on average.
- Findings across most native Japanese populations demonstrated a lower within-population diversity compared to that observed in foreign populations. This suggests that the Japanese native horse populations have been fairly isolated genetically, maintaining a relatively distinct and homogenous genetic make-up within individual populations.
Genetic Distance and Geographical Distribution
- The study found that the genetic differences between populations were not correlated significantly with their geographical distribution. Irrespective of where the populations reside, their unique genetic structures do not follow a spatially aligned distribution.
- Genetic distance matrices revealed that the European populations were distinctly different from the Japanese and Mongolian populations, and no clear groups could be identified within the Japanese native horse populations. This again illustrates the high level of genetic differentiation between these populations.
Origins of Japanese Native Horses
- From the results observed, the researchers speculate that each native Japanese horse population descended from different founder populations that originated from Mongolian horses.
- The genetic makeup of each population indicates that there has been independent breeding in each geographical area since the populations initially diverged. This localized breeding is likely responsible for the high levels of within-population homogeneity and the drastic genetic changes or ‘genetic drift’ observed in modern times.
- This novel genetic information helps to shed light on the ancestry and evolution of Japanese native horses, offering a clearer understanding of their genetic journey over time.
Cite This Article
APA
Kakoi H, Tozaki T, Gawahara H.
(2007).
Molecular analysis using mitochondrial DNA and microsatellites to infer the formation process of Japanese native horse populations.
Biochem Genet, 45(3-4), 375-395.
https://doi.org/10.1007/s10528-007-9083-0 Publication
Researcher Affiliations
- Laboratory of Racing Chemistry, 1731-2 Tsuruta-machi, Utsunomiya, Tochigi 320-0851, Japan. h-kakoi@lrc.or.jp
MeSH Terms
- Animals
- Base Sequence
- DNA, Mitochondrial / genetics
- Genetic Heterogeneity
- Geography
- Haplotypes
- Horses / genetics
- Japan
- Microsatellite Repeats / genetics
- Molecular Sequence Data
- Phylogeny
- Sequence Analysis, DNA
Citations
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