The Chakouyi horse is an ancient Chinese indigenous horse breed distributed in Gansu Province in northwestern China, and is also one of the key breeds protected by the government. However, the origin of the Chakouyi horse remains unclear. As it is distributed in a key region of the Silk Road, it was speculated that the origin of the Chakouyi horse might involve the foreign horse breeds found along this ancient commercial artery. In this study, whole-genome resequencing data of 12 horse breeds, including both indigenous and foreign horses, were applied to reveal the genetic relationships between the Chakouyi horse and other breeds, as well as the ancestry of this ancient breed. An analysis of the population structure and admixture showed that there is no close genetic affinity between the Chakouyi horse and the foreign horses while Chinese indigenous horse populations were grouped together in accordance with their geographic locations, and the Chakouyi horse showed a closer relationship with Kazak horses, Mongolian horses, and Tibetan horses. The results from the ancestral composition prediction indicated that the Kazak horse and the Mongolian horse might be two ancestors of the Chakouyi horse. Furthermore, the genome-wide selection signature analysis revealed that the DMRT3 gene was positively selected in the Chakouyi horse and related to the gait trait of the breed. Our results provide insights into the native origin of the Chakouyi horse and indicate that Kazak and Mongolian horses played important roles in the formation of the Chakouyi horse. Genetic communication between the Chakouyi horse and other horse populations could be attributed, at least partially, to population migrations and trade activities along the ancient commercial routes.
Keywords: Chakouyi horse; DMRT3; origin; population structure; selection signature; the ability to pace.