Genetic Relationship among the Korean Native and Alien Horses Estimated by Microsatellite Polymorphism

Microsatellite polymorphism and the genetic relationship were estimated using genotype information of 305 horses from 11 microsatellite loci. The breeds include the indigenous Korean breeds, Korean native horse (102) and Jeju racing horse (56) together with Japan Hokkaido horse (5), Mongolian horse (19), Thoroughbred horse (108), Quarter horse (11) and Przewalskii horse (4). Allelic frequencies, the number of alleles per locus were estimated by direct counting from observed genotype, and genetic variability was computed using the CERVUX software and DISPAN. The number of alleles per locus varied from 6 (HMS6) to 18 (ASB17) with an average value of 10.45 in horse breeds. The expected total heterozygosity ($H_T$) and coefficient of gene differentiation ($G_{ST}$) ranged 0.764-0.921 (the average value was 0.830) and 0.102-0.266 (the average value was 0.180) in horse breeds, respectively. Four populations (Przewalskii horse, Japan Hokkaido horse, Quarter horse, Thoroughbred horse) showed lower heterozygosity than the average value (the average value was 0.710). The expected heterozygosity within breed ($H_S$) and mean no. of observed alleles ranged from $0.636{\pm}0.064$ (Japan Hokkaido horse) to $0.809{\pm}0.019$ (Mongolian horse), and from 2.73 (Przewalskii horse) to 8.27 (Korean native horse), respectively. The polymorphic information content (PIC) ranged from 0.490 (Przewalskii horse) to 0.761 (Mongolian horse) with an average value of 0.637 in horse breeds. The results showed three distinct clusters with high bootstrap support: the Korean native horse cluster (Korean native horse, Mongolian horse), the European cluster (Przewalskii horse, Thoroughbred horse), and other horse cluster (Jeju racing horse, Japan Hokkaido horse, and Quarter horse). A relatively high bootstrap value was observed for the Korean native horse cluster and European cluster (87%), and the Korean native horse and Mongolian horse (82%). Microsatellite polymorphism data were shown to be useful for estimating the genetic relationship between Korean native horse and other horse breeds, and also be applied for parentage testing in those horse breeds.