Abstract
The Jinjiang horse is a unique Chinese indigenous horse breed distributed in the southern coastal areas, but the ancestry of Jinjiang horses is not well understood. Here, we used Equine SNP70 Bead Array technology to genotype 301 horses representing 10 Chinese indigenous horse breeds, and we integrated the published genotyped data of 352 individuals from 14 foreign horse breeds to study the relationships between Jinjiang horses and horse breeds from around the world. Principal component analysis (PCA), linkage disequilibrium (LD), runs of homozygosity (ROH) analysis, and ancestry estimating methods were conducted to study the population relationships and the ancestral sources and genetic structure of Jinjiang horses. The results showed that there is no close relationship between foreign horse breeds and Jinjiang horses, and Jinjiang horses shared a similar genetic background with Baise horses. TreeMix analysis revealed that there was gene flow from Chakouyi horses to Jinjiang horses. The ancestry analysis showed that Baise horses and Chakouyi horses are the most closely related ancestors of Jinjiang horses. In conclusion, our results showed that Jinjiang horses have a native origin and that Baise horses and Chakouyi horses were key ancestral sources of Jinjiang horses. The study also suggested that ancient trade activities and the migration of human beings had important effects on indigenous horse breeds in China.
Highlights
There are over five million horses in China, the majority of which are indigenous horses that are distributed widely across the rural areas of China
The genotype data of the Chinese indigenous horses from the 10 breeds, which were generated in the present study, as well as that of the 14 breeds of foreign horses from the previous study were used in the phylogenic analysis
The Jinjiang horses were assigned into two clusters, one of which was close to the Chakouyi horses and another clustered with the Southwest breed group consisting of the Tengchong horses, the Lijiang horses, the Baise horses, and the Zhaotong horses
Summary
There are over five million horses in China, the majority of which are indigenous horses that are distributed widely across the rural areas of China. The largest horse populations exist in the northern and southwestern provinces [1]. The Jinjiang horse is the only Chinese indigenous horse breed (CHB). Located in the southeast coastal areas of Fujian Province, and it is named for the prefecture of the river and the city where Jinjiang horses are mainly distributed. Most Jinjiang horses have chestnut or bay coat colors, while a few show buckskin, black, or pinto colorations. Genes 2019, 10, 241 their breeding activities, in which stallions and mares were not intensively selected and for whom there are no systematic and well-designed breeding strategies.
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
