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.
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REFERENCES
Álvarez, I., Gutiérrez, J. P., Royo, L. J., Fernández, I., Gómez, E., Arranz, J. J., and Goyache, F. (2005). Testing the usefulness of the molecular coancestry information to assess genetic relationships in livestock using a set of Spanish sheep breeds. J. Anim. Sci. 83:737.
Caballero, A., and Toro, M. A. (2002). Analysis of genetic diversity for the management of conserved subdivided populations. Conserv. Genet. 3:289.
Cañon, J., Checa, M. L., Carleos, C., Vega-Pla, J. L., Vallejo, M., and Dunner, S. (2000). The genetic structure of Spanish Celtic horse breeds inferred from microsatellite data. Anim. Genet. 31:39.
Eding, H., and Meuwissen, T. H. E. (2001). Marker-based estimates of between and within population kinships for the conservation of genetic diversity. J. Anim. Breed. Genet. 118:141.
Gutiérrez, J. P., Royo, L. J., Álvarez, I., and Goyache, F. (2005). MolKin v 2.0: A computer program for genetic analysis of populations using molecular coancestry information. J. Hered. 96:718.
Hayashida, S. (1958). Ancestry of the native horses of Japan. Jpn. J. Zootech. Sci. 28:329 (In Japanese, with English summary).
Hill, E. W., Bradley, D. G., Al-Barody, M., Ertugrul, O., Splan, R. K., Zakharov, I., and Cunningham, E. P. (2002). History and integrity of thoroughbred dam lines revealed in equine mtDNA variation. Anim. Genet. 33:287.
Jansen, T., Forster, P., Levine, M. A., Oelke, H., Hurles, M., Renfrew, C., Weber, J., and Olek, K. (2002). Mitochondrial DNA and the origins of the domestic horse. Proc. Natl. Acad. Sci. U.S.A. 99:10905.
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.
Keyser-Tracqui, C., Blandin-Frappin, P., Francfort, H.-P., Ricaut, F.-X., Lepetz, S., Crubézy, E., Samashev, Z., and Ludes, B. (2005). Mitochondrial DNA analysis of horses recovered from a frozen tomb (Berel site, Kazakhstan, third century BC). Anim. Genet. 36:203.
Mantel, N. (1967). The detection of disease clustering and a generalized regression approach. Cancer Res. 27:209.
Nei, M. (1987). Molecular Evolutionary Genetics, Columbia University Press, New York.
Nei, M., Tajima, F., and Tateno, Y. (1983). Accuracy of estimated phylogenetic trees from molecular data. J. Mol. Evol. 19:153.
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).
Nozawa, K. (2005). Horse. Rep. Soc. Res. Native Livestock 22:119.
Nozawa, K., Shotake, T., Ito, S., and Kawamoto, Y. (1998). Phylogenetic relationships among Japanese native and alien horses estimated by protein polymorphisms. J. Equine Sci. 9:53.
Ota, T. (1993). Dispan: Genetic Distance and Phylogenetic Analysis, Institute of Molecular Evolutionary Genetics, Pennsylvania State University, Pennsylvania.
Randi, E., Alves, P. C., Carranza, J., Milošević-Zlatanović, S., Sfougaris, A., and Mucci, N. (2004). Phylogeography of roe deer (Capreolus capreolus) populations: The effects of historical genetic subdivisions and recent nonequilibrium dynamics. Mol. Ecol. 13:3071.
R Development Core Team (2006). R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Vienna, Austria.
Reynolds, J., Weir, B. S., and Cockerham, C. C. (1983). Estimation of the coancestry coefficient: Basis for a short-term genetic distance. Genetics 105:767.
Royo, L. J., Álvarez, I., Beja-Pereira, A., Molina, A., Fernández, I., Jordana, J., Gómez, E., Gutiérrez, J. P., and Goyache, F. (2005). The origins of Iberian horses assessed via mitochondrial DNA. J. Hered. 96:663.
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.
Saitou, N., and Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406.
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.
Slatkin, M. (1995). A measure of population subdivision based on microsatellite allele frequencies. Genetics 139:457.
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.
Tamura, K., and Nei, M. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10:512.
Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994). Clustal W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673.
Tozaki, T., Kakoi, H., Mashima, S., Hirota, K., Hasegawa, T., Ishida, N., Miura, N., Choi-Miura, N. H., and Tomita, M. (2001). Population study and validation of paternity testing for thoroughbred horses by 15 microsatellite loci. J. Vet. Med. Sci. 63:1191.
Tozaki, T., Takezaki, N., Hasegawa, T., Ishida, N., Kurosawa, M., Tomita, M., Saitou, N., and Mukoyama, H. (2003). Microsatellite variation in Japanese and Asian horses and their phylogenetic relationship using a European horse outgroup. J. Hered. 94:374.
Vilà, C., Leonard, J. A., Götherström, A., Marklund, S., Sandberg, K., Lidén, K., Wayne, R. K., and Ellegren, H. (2001). Widespread origins of domestic horse lineages. Science 291:474.
Xu, X., and Árnason, U. (1994). The complete mitochondrial DNA sequence of the horse, Equus caballus: Extensive heteroplasmy of the control region. Gene 148:357.
ACKNOWLEDGMENTS
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.
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An erratum to this article can be found at http://dx.doi.org/10.1007/s10528-007-9112-z
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Kakoi, H., Tozaki, T. & Gawahara, H. Molecular Analysis Using Mitochondrial DNA and Microsatellites to Infer the Formation Process of Japanese Native Horse Populations. Biochem Genet 45, 375–395 (2007). https://doi.org/10.1007/s10528-007-9083-0
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DOI: https://doi.org/10.1007/s10528-007-9083-0