Microsatellite Variation in Jeju and American horses and their Phylogenetic Relationship

The aim of this study was to evaluate the microsatellite (Ms) variation in Jeju and American horses and their phylogenetic relationship, and to establish a lineage-based breeding plan for domestic American miniature horse (AMH) and Quarter horse (QH) in Korea. A total of 83 horse samples (27 AMHs, 32 QHs, and 24 Jeju horses [JHs]) were genotyped with 17 Ms markers. The observed number of alleles per locus ranged from 4 (HTG7) to 12 (ASB17), with an average value of 7.71, 7.41, and 6.11 in AMH, QH, and JH, respectively. Of the 17 Ms markers, HTG4, HTG6, HTG7, HMS1 markers had relatively low PIC values (<0.6) in AMH and HMS1 in QH, and ASB2, HMS7, HTG4, ASB23, HMS1, HTG10 in JH. An average level of genetic variation was as follows: AMH, H_E= 0.7300 and H_O= 0.7317; QH, H_E= 0.7505 and H_O= 0.7011; and JH, H_E = 0.6917 and H_O= 0.7011. QH and JH had a genetic distance of 0.3831, and JH and AMH had a genetic distance of 0.2883. Of the three breeds, QH and JH formed clearly near groups and the AMH formed clearly different groups. This study is judged to be suitable for individual identification and parentage testing for registration of the lineage of AMH and QH. Therefore, the results of this study are an effective tool for genetic research and preservation of these horse breeds.