Molecular Analysis Using Mitochondrial DNA and Microsatellites to Infer the Formation Process of Japanese Native Horse Populations
- 342 Downloads
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 coancestry-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.
KEY WORDSJapanese native horses mitochondrial DNA D-loop microsatellite DNA genetic diversity phylogeny
We wish to thank Drs. N. Oguri and T. Oyunsuren for collecting blood samples of Asian and Japanese horses. We are grateful to the Japan Racing Association, and we also thank the staff of the DNA analysis section of the Laboratory of Racing Chemistry for collecting and providing samples of Japanese and European horses and for their kind encouragement.
- Hayashida, S. (1958). Ancestry of the native horses of Japan. Jpn. J. Zootech. Sci. 28:329 (In Japanese, with English summary).Google Scholar
- Kakoi, H., Nagata, S., and Kurosawa, M. (2001). DNA typing with 17 microsatellites for parentage verification of racehorses in Japan. Anim. Sci. J. 72:453.Google Scholar
- Nei, M. (1987). Molecular Evolutionary Genetics, Columbia University Press, New York.Google Scholar
- Nozawa, K. (1992). Origin and ancestry of native horses in Eastern Asia and Japan. Jpn. J. Equine Sci. 3:1 (In Japanese, with English summary).Google Scholar
- Nozawa, K. (2005). Horse. Rep. Soc. Res. Native Livestock 22:119.Google Scholar
- Ota, T. (1993). Dispan: Genetic Distance and Phylogenetic Analysis, Institute of Molecular Evolutionary Genetics, Pennsylvania State University, Pennsylvania.Google Scholar
- R Development Core Team (2006). R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Vienna, Austria.Google Scholar
- Royo, L. J., Pajares, G., Álvarez, I., Fernández, I., and Goyache, F. (2007). Genetic variability and differentiation in Spanish roe deer (Capreolus capreolus): A phylogeographic reassessment within the European framework. Mol. Phylogenet. Evol. 42:47.Google Scholar
- Schneider, S., Roessli, D., and Excoffier, L. (2000). Arlequin v .2.0: A Software for Population Genetics Data Analysis, Genetics and Biometry Laboratory, University of Geneva, Geneva, Switzerland.Google Scholar
- Solis, A., Jugo, B. M., Mériaux, J. C., Iriondo, M., Mazón, L. I., Aguirre A. I., Vicario, A., and Estomba, A. (2005). Genetic diversity within and among four south European native horse breeds based on microsatellite DNA analysis: Implications for conservation. J. Hered. 96:670.PubMedCrossRefGoogle Scholar