| There are numerous domestic horse breeds in China, but there has been no extensive study on genetic diversity, population demographic history and origin of Chinese horses.In this study, three kinds of molecular genetic markers including autosomal microsatellites, mitochondrial DNA and Y–DNA, were used to analyze the genetic diversity, and origin of Chinese domestic horse, and results of this study further provide scientific basis for its conservation and utilization.1. Genetic variation at 27 microsatellite loci was investigated for 1,273 individuals from 26 Chinese indigenous horse populations and two introduced horse populations. Genetic variation parameter statistics, population differentiation analysis and clustering analysis were carried out to determine the genetic diversity and evolutionary relationships among Chinese horse populations. The number of alleles, PIC and heterozygosity in this reseach showed that there was abundant genetic variation in Chinese indigenous horses. The mean Observed heterozygosity (Ho) was 0.743, and the mean Polymorphism information content (PIC) was above 0.69 in each Chinese horse population. Genetic diversity of Chinese horses was higher than Thoroughbred horse based on most genetic diversity estimators. However, the genetic differentiation in Chinese native horses was low and only 2.4% of the total genetic variance existed among populations.Dendrogram analysis showed that the genetic differentiation and genetic relationships between Chinese horse populations were almost consistent with their geographic distribution, and five groups were recognized: Yangtze River group, Qinghai-Tibet Plateau group, Northwest group, Northeast group and Inner Mongolia group. Cluster analysis was performed by the Multivariate Statistical Packsge (MVSP) and Structure analysis.2. 659 domestic horse and 28 Przewalskii'horse D-loop sequences were sequenced. Statistics showed that there were 82 variation sites and 178 haplotypes in domestic horses. There were only two haplotypes in Przewalskii'horses. Haplotype diversity (Hd) and Nucleotide diversity (Pi) showed abundant genetic variation in Chinese domestic horses. Phylogenetic analysis showed nine haplogroups (A-I) in Chinese domestic horses based on 178 haplotypes of domestic horse. The two haplogroups of new definition were Haplogroup H and Haplogroup I. There was high sample proportion in A, D and F haplogroups of Chinese domestic horses. NETWORK analysis supported the results of phylogenetic analysis. There was geographical bias of the distribution of the nine haplogroups in Chinese domestic horses. The samples of F haplogroup in north of the Yangtze River were more than the samples in the south of the Yangtze River. The samples of G haplogroup in south of the Yangtze River were more than the samples in other area. Abundant genetic diversity and wide haplogroup distribution of mtDNA showed that China is likely to be one of the horse domestication centers, and supported there were wide maternal origin of the domestic horses in China.Added 334 sequences from GenBank, a total of 1021 sequences from Europe, the Middle East, and Asian were analysed. Results of analysis showed that there was different distribution of haplogroups in different area. This concordance of haplogroup F with the Far Eastern population origin was highly significant. Samples of Haplogroup I in Asian were more than other aera. These results indicated the F and I haplogroups maybe correlated with domestication of Chinese horses.3. Genetic variations of the six equine Y-DNA microsatellites were assessed in the male domestic horses, male Przewalski horses and male domestic donkeys. And there were obvious allele differences between domestic horse, Przewalski's horse and donkey. Though the six Y-specific microsatellites displayed limited genetic variation in the domestic horse breeds, this was the first time polymorphism was found in non-recombinant horse Y-DNA. Moreover, Chinese domestic horse breeds carrying two alleles were only in the southern area of the Yangtze River, mainly in the southwest of China. Horse breeds in these regions have distinct appearances from those in the North of China. |
