If it is not of the Mongolian origin, this horse could have been imported via the Paekche State (its territory is roughly a predecessor of the Jeolla Province of Korea), the Puyo State in Northeast China with later Paekche connections, whose former population underwent assimilation by the Machengzi culture, which should be autosomally not dissimilar to the ancient sample of Shandong Bianbian, judging by the PCA of “The deep population history of northern East Asia from the Late Pleistocene to the Holocene”. “Kingdom of Puyŏ”-related populations was scattered by the Mongolic Xianbei or incorporated into the Mongolic Xianbei (including Daur-, Buryat-related ones), according to “Bio-Archaeological Research of the Ethnicity of Lamadong Sanyan Burials” and according to Mark E. Byington (“The Ancient State of Puyŏ in Northeast Asia”).


Comprehensive genome and transcriptome analyses reveal genetic relationship, selection signature, and transcriptome landscape of small-sized Korean native Jeju horse
Krishnamoorthy Srikanth, Nam-Young Kim, WonCheoul Park, Jae-Min Kim, Kwon-Do Kim, Kyung-Tai Lee, Ju-Hwan Son, Han-Ha Chai, Jung-Woo Choi, Gul-Won Jang, Heebal Kim, Youn-Chul Ryu, Jin-Wu Nam, Jong-Eun Park, Jun-Mo Kim & Dajeong Lim

Abstract
The Jeju horse, indigenous to the Jeju Island in Korea may have originated from Mongolian horses. Adaptations to the local harsh environment have conferred Jeju horse with unique traits such as small-sized body, stocky head, and shorter limbs. These characteristics have not been studied previously at the genomic level. Therefore, we sequenced and compared the genome of 41 horses belonging to 6 breeds. We identified numerous breed-specific non-synonymous SNPs and loss-of-function mutants. Demographic and admixture analyses showed that, though Jeju horse is genetically the closest to the Mongolian breeds, its genetic ancestry is independent of that of the Mongolian breeds. Genome wide selection signature analysis revealed that genes such as LCORL, MSTN, HMGA2, ZFAT, LASP1, PDK4, and ACTN2, were positively selected in the Jeju horse. RNAseq analysis showed that several of these genes were also differentially expressed in Jeju horse compared to Thoroughbred horse. Comparative muscle fiber analysis showed that, the type I muscle fibre content was substantially higher in Jeju horse compared to Thoroughbred horse. Our results provide insights about the selection of complex phenotypic traits in the small-sized Jeju horse and the novel SNPs identified will aid in designing high-density SNP chip for studying other native horse breeds.

Archeological evidence suggests that horses were present in the Jeju island prior to the introduction of the Mongolian horses in the 12th century10, and there are reports of size similarity between the Jeju Horse and horses in Southern Japan47, and phylogenetic analysis based on mitochondrial genome sequence had placed the Jeju Horse with European and Middle eastern breeds rather than the Mongolian breeds, these results along with our findings, leads us to speculate that the Jeju Horse has an ancestry independent of the Mongolian Horse, however since 2 of the 12 Jeju Horse samples used in this study showed some admixture with Mongolian Horse, a future study with a larger number of Jeju Horse samples must be carried out, to verify if there is a population substructure within the Jeju Horse, one with no admixture with Mongolian horse and another with admixture.