Phylogenetic analysis of mitochondrial DNA D-loop region for excavated horse bones at the Asian archaeological sites

Abstract Horses have played a significant role in the development of human society. As an important domestic animal, horses have been used for transport, labor, food and recreation. It is widely accepted that the horse was probably first domesticated on the Eurasian steppes from Ukraine to Turkestan between the fifth and fourth millennium BC, and the earliest domesticated horses subsequently spread out from their original range. However, we currently have little genetic evidence to demonstrate whether Korean domestic horse breeds originated in Korea or if it came into the area via an ancient migration route. In the present study, to obtain more knowledge of the origin and genetic diversity of Korean domestic horses, we analyzed seventeen 247-bp mitochondrial DNA (mtDNA) D-loop sequences of ancient horse bones excavated from seven archaeological sites located in the southern Korean Peninsula and Mongolia, aged between the fifth century B.C and nineteenth century A.D. The seventeen ancient horses revealed 9 variable positions when compared with the reference sequence (GenBank X79547). All the substitutions were transitions, and defined a total of 11 unique haplotypes with the haplotype diversity value of 0.9118±0.056. Among the 11 haplotypes, 3 haplotypes were detected more than once and were thus shared by individuals from the same or close archaeological sites. The largest haplotype consisted of 5 individuals, with another two haplotypes containing 2 individuals respectively, and eight haplotypes were singletons. The data indicate an abundant genetic diversity of the Korean ancient horses, and also suggest that the origin of Korean domestic horses is complex, and several maternal lines were introduced into the gene pool of Korean horses after their initial domestication.