Molecular analysis using mitochondrial DNA and microsatellites to infer the formation process of Japanese native horse populations.

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.