Journal of Heredity 2003:94(5)
© 2003 The American Genetic Association 94:374-380
Microsatellite Variation in Japanese and Asian Horses and Their Phylogenetic Relationship Using a European Horse Outgroup
From the Department of Molecular Genetics, Laboratory of Racing Chemistry, 1731-2 Tsurutamachi, Utsunomiya, Tochigi 320-0851, Japan (Tozaki and Kurosawa); Max-Planck Institut für Biologie, Abteilung Immungenetik, Corrensstrasse 42, Tuebingen 72076, Germany (Takezaki); Equine Research Institute, Japan Racing Association, 321-4 Tokami, Utsunomiya, Tochigi 320-0856, Japan (Hasegawa and Ishida); Department of Physiological Chemistry, School of Pharmaceutical Sciences, Showa University, 1-5-8 Hatanodai, Shinagawa, Tokyo 142-8555, Japan (Tozaki and Tomita); Division of Population Genetics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan (Saitou); and Department of Animal Science, Faculty of Applied Life Science, Nippon Veterinary and Animal Science University, 1-7-1 Kyonacho, Musashino, Tokyo 180-8602, Japan (Mukoyama).
Address correspondence to Teruaki Tozaki, Department of Molecular Genetics, Laboratory of Racing Chemistry, 1731-2 Tsurutamachi, Utsunomiya, Tochigi 320-0851, Japan, or e-mail: ttozaki{at}nyc.odn.ne.jp (ttozaki{at}lrc.or.jp).
| Abstract |
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The genetic relationships of seven Japanese and four mainland-Asian horse populations, as well as two European horse populations, were estimated using data for 20 microsatellite loci. Mongolian horses showed the highest average heterozygosities (0.750.77) in all populations. Phylogenetic analysis showed the existence of three distinct clusters supported by high bootstrap values: the European cluster (Anglo-Arab and thoroughbreds), the Hokkaido-Kiso cluster, and the Mongolian cluster. The relationships of these clusters were consistent with their geographical distributions. Basing our assumptions on the phylogenetic tree and the genetic variation of horse populations, we suggest that Japanese horses originated from Mongolian horses migrating through the Korean Peninsula. The genetic relationship of Japanese horses corresponded to their geographical distribution. Microsatellite polymorphism data were shown to be useful for estimating the genetic relationships between Japanese horses and Asian horses.
In the domestic livestock species of Japan, the populations of native horses (Equus caballus) have been insulated from other horse populations and relatively free of artificial selection. Currently there are eight local populations of Japanese horses: Hokkaido, Kiso, Misaki, Noma, Taishu, Tokara, Miyako, and Yonaguni. The phylogenetic relationships among these Japanese horse populations is not well elucidated. Horses native to Japan have been kept in their local areas to avoid extinction, although there was previously some gene flow between the Japanese horse populations. The population sizes of these Japanese horses range from 35 to 100 horses, except for the native horses from Hokkaido, which include more than 2,000 horses (Nozawa 1992).
Ishida et al. (1995) conducted a phylogenetic study of thoroughbreds, Japanese (Hokkaido) horses, Mongolian horses, and Przewalskii's wild horses using the mitochondrial DNA (mtDNA) D-loop region. The study suggested that the Asian horses were similar to each other and distinct from thoroughbreds.
Hayashida (1958) classified Japanese horses into two groups according to body size and location. Medium-size and small-size horses are 130140 cm and 110120 cm in withers height, respectively. The medium-size horsesHokkaido, Kiso, and Misaki horseslive mainly on the three main islands of Japan (Hokkaido, Honshu, and Kyushu). The small-size horsesNoma, Taishu, Tokara, Miyako, and Yonaguni horseslive on islets (Shikoku, Tsushima, Tokara, Miyako, and Yonaguni) south and west of the main islands. Based on this classification, Hayashida (1958) proposed a two-wave migration hypothesis for the evolution of Japanese horse populations.
However, a recent study using the protein polymorphisms of 22 loci from 2,415 horses belonging to 34 horse populations in Japan and Asia (Nozawa et al. 1998) was inconsistent with this two-wave migration. The phylogenetic relationships among Japanese horses could not correspond to the geographical distribution in Japan (Nozawa et al. 1998). The difference between the phylogenetic relationship and the geographical distribution might be a consequence of a small population size, a bottleneck effect, and low polymorphism for protein loci. The 22 loci examined had monomorphism or two to three alleles in Japanese horses and were less informative for the determination of a phylogenetic relationship, although useful for Asian horses.
Recently many microsatellites were isolated from horse genome DNA (Tozaki et al. 2000a,b,c, 2001b). Microsatellites, in particular the (CA/TG)n repeats, which were constructed with tandemly repeated DNA sequences consisting of poly(dC-dA)/(dG-dT) repeats, have been found to be common in all eukaryotic genomes, occurring once for every 3060 kb (Litt and Luty 1989; Stallings et al. 1991; Weber and May 1989). As microsatellites are also frequently polymorphic and evolutionarily conserved in the eukaryotic genome, they provide useful markers for comparative studies of genetic variation, parentage testing, and studies of gene flow (Bjørnstad and Røed 2001; Cunningham et al. 2001; Tozaki et al. 2001a) and have recently been the markers of choice for analyses of population structure in wild and domesticated species (Bowcock et al. 1994; Kim et al. 2001; Takahashi et al. 1998).
The genetic relationships of many horse populations in Europe have been investigated recently using microsatellites (Canon et al. 2000; Vila et al. 2001). However, the genetic relationships of horse populations in Japan have not been investigated using microsatellites.
In the present study, we analyzed 20 microsatellite loci, which were originally characterized in thoroughbred horses to infer the phylogenetic relationships among Japanese and Asian horses. In addition, we compared the levels of polymorphism between Japanese and Asian horses.
| Materials and Methods |
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Animals
Sampling localities are shown in Figure 1. We collected blood samples from 60 Mongolian horses: Dzaamar (n = 22), Bajandzargalan (n = 18), and Garshar (n = 20). In addition, we collected blood samples from a total of 135 Japanese horses: Hokkaido (n = 24), Kiso (n = 21), Misaki (n = 16), Noma (n = 16), Taishu (n = 10), Tokara (n = 24), and Yonaguni (n = 24). We also collected blood samples from Korean horses (n = 21), thoroughbred horses (n = 25), and Anglo-Arab horses (n = 18). No horses were injured in any way during the collecting of samples. Genomic DNAs were prepared from whole blood samples. Genomic DNAs from thoroughbred horses were extracted using the MagExtractor System MFX-2000 (Toyobo, Osaka, Japan) according to the manufacturer's protocols. Following digestion with proteinase K (2 mg/ml) in extraction buffer (10 mM Tris, 10 mM EDTA, 0.1 M NaCl, 2% SDS), genomic DNAs from Asian horses were extracted by phenol/chloroform, precipitated with ethanol, washed, and resuspended in a sterile TE buffer (10 mM Tris-HCl, 0.1 mM EDTA, pH 8.0).
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Microsatellites
In this study we used the following 20 microsatellite loci: TKY2 (Sakagami et al. 1995); TKY3 (Tozaki et al. 1995); HTG3, HTG4, HTG5, HTG6 (Ellegren et al. 1992); HTG7, HTG10, HTG15 (Marklund et al. 1994); HMS1, HMS2, HMS3, HMS5, HMS7, HMS8 (Guérin et al. 1994); VHL20 (van Haeringen et al. 1994); and AHT4, ASB1, ASB2, and ASB3 (Swinburne et al. 2000).
Genotyping
Forward primers of all the microsatellites were labeled with Cy-5 (Amersham Biosciences, Piscataway, NJ). Each polymerase chain reaction (PCR) amplification was performed in a total volume of 20 µl of the following mixture: 2050 ng of equine genomic DNA, 5 pmol of a Cy-5-labeled forward primer, 5 pmol of reverse primer, 200 µM of dNTP, 2 µl of 10x reaction buffer; and 0.1 U of rTaq polymerase (Takara Bio, Shiga, Japan). PCR amplification entailed initial denaturation (94°C, 4 min); 30 cycles of 1 min each at 94°C, 5560°C, and 72°C; and then 60 min at 72°C for final extension in a GeneAmp PCR System 9600 (Applied Biosystems, Foster City, CA). The final extension step at 72°C for 60 min promoted a complete nontemplated 3'-nucleotide addition. The amplified fragments were analyzed through electrophoresis with an ALF express DNA sequencer (Amersham Biosciences) using an 8% polyacrylamide gel containing 7 M urea (Biomate, Tokyo, Japan). Finally, the raw data obtained were converted to dinucleotide repeat polymorphic band patterns using a Fragment Manager (Amersham Biosciences).
Estimation of Genetic Distances and the Construction of a Phylogenetic Tree
Alleles were designated according to PCR product size and allele frequencies were estimated by direct counting. Genetic differences among populations were estimated by calculating the DA distance (Nei 1983) and (
µ)2 distance (Goldstein et al. 1995). A neighbor-joining (NJ) tree was constructed from the distances (Saitou and Nei 1987), and 1,000 bootstrap replicates were generated.
| Results |
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Heterozygosities and the Number of Alleles
Polymerase chain reaction amplification of 20 (CA/TG)n microsatellites, which were mainly isolated from the thoroughbred horse genome, was successful with minor modifications of the original condition for the 13 horse populations studied. Allele frequencies and heterozygosities were calculated. (The allele frequencies are available from the senior author upon request.) Despite possible inbreeding, most loci displayed polymorphism between individuals. Allele frequency distributions and heterozygosities of 20 microsatellites showed unique features for each population. Although the other populations were polymorphic, with 2 to 10 alleles at all loci, the Misaki and Tokara populations were monomorphic at three loci (HTG7, HMS3, and HMS8) and six loci (HTG5, HTG6, HTG7, HMS8, ASB1, and ASB2), respectively; these loci also showed relatively less polymorphism than the other loci when the other horse populations were analyzed.
A total of 130 alleles were detected in this study and the average number of alleles was 4.6 (Table 1). The observed number of alleles and average heterozygosities for all populations are shown in Tables 1 and 2. The average heterozygosity was 0.62, ranging from 0.34 in the Tokara population of Japanese horses to 0.77 in the Bajandzargalan population of Mongolian horses. Four populations of Japanese horses (Misaki, Noma, Tokara, and Yonaguni) showed lower heterozygosity than the average value. Similar to the heterozygosity data, the observed number of alleles ranged from 42 in the Tokara population to 125 in the Dzaamar population, and the average allele number was 4.6. The average allele numbers of the aforementioned four populations were lower than the average value. In particular, low heterozygosities and a small number of alleles were observed in the Tokara and Misaki populations. Conversely, high heterozygosities and a large number of alleles were observed in three populations of Mongolian horses. Three populations of Mongolian horses had more alleles than the other populations at 17 loci. The average heterozygosity for Japanese horses was less than for any other population. Furthermore, the number of alleles per locus also tended to be fewer among Japanese horses.
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Genetic Distances and Population Relationships
Estimates of the genetic distances among the 13 populations based on the allele frequency data on 20 microsatellites are presented in Table 3. The DA values always range between 0 and 1 and are nonlinearly related to the number of gene substitutions. Mean genetic distances ranged from 0.057 (Bajandzargalan to Garshar populations), 0.065 (Bajandzargalan to Garshar populations), and 0.075 (Bajandzargalan to Garshar populations) to 0.491 (Tokara to thoroughbred populations) and 0.481 (Misaki to Noma populations), while the (
µ)2 distance ranged from 0.057 (Bajandzargalan to Garshar populations), 0.065 (Bajandzargalan to Garshar populations), and 0.075 (Bajandzargalan to Garshar populations) to 0.491 (Tokara to thoroughbred populations) and 0.481 (Misaki to Noma populations). Considering all distance measures, the three populations of Mongolian horses were closest.
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DA and (
µ)2 distance matrices were used to build phylogenetic trees with the NJ method. The NJ method for constructing evolutionary trees from distance data has been reported to be one of the most effective methods (Saitou and Nei 1987). Figures 2 and 3 show the phylogenetic tree obtained from DA and (
µ)2 distance values using the NJ method. However, these trees showed some differences from each other. In order to test the reliability of the tree topography, dendrograms from 1,000 replications of resample loci were constructed using both distances. High bootstrap values were obtained when using the DA distance, which indicated the high confidence of the obtained trees. The DA distance clustered together both European populations with a bootstrap value of 99%, and Mongolian populations with bootstrap values of 89% and 92%. Hokkaido and Kiso horses clustered with a bootstrap value of 91%.
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| Discussion |
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The task of resolving the genetic relationships among Japanese horses is a difficult one, because each population size of Japanese horses is small and Japanese horses had substantial gene flow between the populations (Nozawa 1992). Recently, many microsatellites were isolated from the horse genome (Tozaki et al. 2000a, 2000b, 2000c, 2001b), and the microsatellites showed multiple alleles as well as high heterozygosity among European horse breeds such as thoroughbreds. Microsatellites may be a useful approach for resolving the relationships of Japanese horse populations.
In this study we analyzed the allele frequencies and genotype distributions of Japanese horses to investigate a phylogenetic relationship among the populations. In addition, we analyzed the allele frequencies and genotype distributions among Mongolian and Korean horses to consider the ancestral populations for Japanese horse populations.
Twenty microsatellites, which were isolated from the thoroughbred genome, showed high heterozygosity and were used for analyzing allele frequencies of Asian horse populations, Anglo-Arab breeds, and thoroughbreds. The average heterozygosity within populations analyzed in this study was 0.62 (range 0.340.77). Nozawa et al. (1998) investigated genetic variation among Asian horses using 22 blood protein polymorphisms; this study showed an average heterozygosity between 0.0584 and 0.1257. The microsatellites tested in our study were therefore effective tools in analyzing the genetic population structure of Asian horses.
The average heterozygosity within each population of Mongolian horses ranged from 0.75 to 0.77. Mongolian horses had the highest values in all populations, demonstrating that Mongolian horses have retained the largest amount of genetic variation of all the populations studied.
In contrast, the average heterozygosity within each population of Japanese horses ranged between 0.34 and 0.66. In addition, Mongolian horses possessed all the alleles found in Japanese horses. These results are attributed to the fact that Mongolian horses are descended from the ancestral populations of Japanese horses. This assumption is supported by the historical fact that native horses on the Asian continent were frequently transported to Japan through the Korean peninsula.
The Tokara population showed the lowest heterozygosity in this study. Furthermore, the Tokara population showed the lowest value of protein polymorphisms (Nozawa et al. 1998). According to the literature, the population size of the Tokara group has decreased to low numbers in the past, but has recently increased due to breeding. Thus the main reason for this low-level genetic variation is most likely the population bottleneck.
The phylogenetic reconstructions using DA and (
µ)2 gave similar clustering results. However, the different clustering was not unexpected since the bootstrap values in both trees were low. The DA tree showed much higher values than the (
µ)2 tree. This difference can be explained by the fact that (
µ)2 is based on the assumption that microsatellites follow a stepwise mutation model, while DA is based on the infinite allele model. All the populations in Japan were derived from one original horse population, which was transported about 2,000 years ago through the Korean peninsula. Furthermore, these populations localized to the particular areas in Japan mentioned in this article. After localization, the populations were affected by the gene flow of each other. Thus allele frequencies of Japanese horses might not be the effect of a stepwise mutation of microsatellites, indicating that the DA tree might be suitable for this study. In addition, Takezaki and Nei (1996) studied the efficiencies of several genetic distance measures, such as DA (Nei 1983), DC (Cavalli-Sforza and Edwards 1967), DSW (Shriver et al. 1995), and (
µ)2 (Goldstein et al. 1995), when applied to microsatellites. Their computer simulation showed that the DA and DC distances are most efficient in obtaining the correct tree topology (Takezaki and Nei 1996).
In this study, our phylogenetic tree showed several clusters, including the European cluster (Anglo-Arab, thoroughbreds), the Hokkaido-Kiso cluster, and the Mongolian cluster, because of high bootstrap values. The relationship of the clusters to each other corresponds to their geographical distributions. In particular, the Hokkaido and Kiso populations clustered with a high bootstrap value. This relationship corresponds to the historical fact that the Hokkaido population was made up of horses transported from Honshu, Japan's mainland, for the purpose of agriculture. The Kiso population is geographically located in the area nearest to the Hokkaido population in Japan. Although Misaki and Tokara populations have long branch lengths and low bootstrap values, these populations were clustered into one group close to the Yonaguni population. The long branch lengths for the Tokara and Misaki populations in the tree might be caused by a bottleneck effect. The Misaki, Tokara, and Yonaguni populations were also close to the Noma population genetically. Furthermore, the genetic relationship of the Taishu population was close to the Mongolian, Korean, Hokkaido-Kiso groups, and the four populations. The genetic relationships constructed in this study corresponded to geographical distribution in Japan. Furthermore, the correspondence between the genetic relationship and the geographical distribution supports the hypothesis that Japanese horses are descended from Mongolian horses through the Korean peninsula and have spread all over Japan, because there were no horses in Japan about 2,000 years ago, according to the literature.
In conclusion, we analyzed the genetic variation and phylogenetic relationship of Asian and Japanese horses using microsatellites, and we support the view that Japanese horses originated from Mongolian horses through the Korean Peninsula. The genetic relationship of Japanese horses to each other corresponds to their geographical distribution. Our results also show that several horse populations in Japan have low genetic variation. Because almost all Japanese horses are in small populations, breeders should monitor genetic variation to protect these horse populations. Genetic marker data, as described here, could be an effective tool.
In the future, an investigation of the pedigree of populations and the genetic variations in those populations will be necessary. As our data show, microsatellites are a useful tool for studying the genetic relationships among closely related horse breeds. Since the microsatellites in this study are highly polymorphic, they can also be applied for parentage testing. Thus we believe that using microsatellites is important in the evaluation of genetic variations.
| Acknowledgments |
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We thank Dr. M. Sakagami for coordinating this project and for helpful discussion. We are grateful to Drs. N. Oguri, T. Oyunsuren, and Y. Lim for collecting blood samples of Asian and Japanese horses. We are also grateful to the staff of the blood-typing section of the Laboratory of Racing Chemistry for collecting blood samples of Japanese horses.
| Footnotes |
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Corresponding Editor: Oliver A. Ryder
Received August 29, 2002
Accepted May 31, 2003
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