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Genes (Basel). 2019 Mar 21;10(3). pii: E241. doi: 10.3390/genes10030241.

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

Ma H1,2,3,4, Wang S5, Zeng G6, Guo J7, Guo M8, Dong X9, Hua G10, Liu Y11,12,13,14, Wang M15,16,17,18, Ling Y19, Ding X20,21,22, Zhao C23,24,25,26,27, Wu C28,29,30,31.

Author information

1
College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China. B1303258@cau.edu.cn.
2
Equine Center, China Agricultural University, Beijing, 100193, China. B1303258@cau.edu.cn.
3
National Engineering Laboratory for Animal Breeding, Beijing, 100193, China. B1303258@cau.edu.cn.
4
Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, 100193, China. B1303258@cau.edu.cn.
5
College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China. Shengwang@cau.edu.cn.
6
Jinjiang Animal Husbandry and Veterinary Station, Fujian, 362200, China. 13655922266@163.com.
7
Jinjiang Animal Husbandry and Veterinary Station, Fujian, 362200, China. m15764251673@163.com.
8
Jinjiang Animal Husbandry and Veterinary Station, Fujian, 362200, China. guominghao_1325@163.com.
9
College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China. xgdong@cau.edu.cn.
10
College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China. hgyyxg@cau.edu.cn.
11
College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China. yliu316@cau.edu.cn.
12
Equine Center, China Agricultural University, Beijing, 100193, China. yliu316@cau.edu.cn.
13
National Engineering Laboratory for Animal Breeding, Beijing, 100193, China. yliu316@cau.edu.cn.
14
Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, 100193, China. yliu316@cau.edu.cn.
15
College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China. haohe@cau.edu.cn.
16
Equine Center, China Agricultural University, Beijing, 100193, China. haohe@cau.edu.cn.
17
National Engineering Laboratory for Animal Breeding, Beijing, 100193, China. haohe@cau.edu.cn.
18
Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, 100193, China. haohe@cau.edu.cn.
19
College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China. lingzi@cau.edu.cn.
20
College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China. xding@cau.edu.cn.
21
National Engineering Laboratory for Animal Breeding, Beijing, 100193, China. xding@cau.edu.cn.
22
Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, 100193, China. xding@cau.edu.cn.
23
College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China. cjzhao@cau.edu.cn.
24
Equine Center, China Agricultural University, Beijing, 100193, China. cjzhao@cau.edu.cn.
25
National Engineering Laboratory for Animal Breeding, Beijing, 100193, China. cjzhao@cau.edu.cn.
26
Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, 100193, China. cjzhao@cau.edu.cn.
27
Beijing Key Laboratory for Genetic Improvement of Livestock and Poultry, Beijing, 100193, China. cjzhao@cau.edu.cn.
28
College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China. chxwu@cau.edu.cn.
29
Equine Center, China Agricultural University, Beijing, 100193, China. chxwu@cau.edu.cn.
30
National Engineering Laboratory for Animal Breeding, Beijing, 100193, China. chxwu@cau.edu.cn.
31
Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, 100193, China. chxwu@cau.edu.cn.

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.

KEYWORDS:

Jinjiang horse; Single Nucleotide Polymorphism array; ancestry; origin

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