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Genes 2019, 10(3), 241;

The Origin of a Coastal Indigenous Horse Breed in China Revealed by Genome-Wide SNP Data

1,2,3,4,†, 1,†, 5, 5, 5, 1, 1, 1,2,3,4, 1,2,3,4, 1, 1,3,4,*, 1,2,3,4,6,* and 1,2,3,4
College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
Equine Center, China Agricultural University, Beijing 100193, China
National Engineering Laboratory for Animal Breeding, Beijing 100193, China
Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing 100193, China
Jinjiang Animal Husbandry and Veterinary Station, Fujian 362200, China
Beijing Key Laboratory for Genetic Improvement of Livestock and Poultry, Beijing 100193, China
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Received: 2 January 2019 / Revised: 3 March 2019 / Accepted: 4 March 2019 / Published: 21 March 2019
(This article belongs to the Special Issue Equine Genetics)
PDF [19633 KB, uploaded 27 March 2019]


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. View Full-Text
Keywords: Jinjiang horse; origin; ancestry; Single Nucleotide Polymorphism array Jinjiang horse; origin; ancestry; Single Nucleotide Polymorphism array

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Ma, H.; Wang, S.; Zeng, G.; Guo, J.; Guo, M.; Dong, X.; Hua, G.; Liu, Y.; Wang, M.; Ling, Y.; Ding, X.; Zhao, C.; Wu, C. The Origin of a Coastal Indigenous Horse Breed in China Revealed by Genome-Wide SNP Data. Genes 2019, 10, 241.

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