Study On The Origin Of Chinese Domestic Horses Based On Genetic Variations Of Y-chromosome

The domestic horses have played important role in human beings' activities,such as war,farming,and transportations since the wild horses were being domestictaed.The origin of Chinese domestic horses has always been controversial.Due to its male specific characterization,polymorphic markers in Y chromosome have the potential to be used for the study on the evolution of male horses.In this study,studied equids consisted of 23 Chinese indigenous breeds,4 imported breeds,1 Przewalskii,and 1 donkey,and three types of Y chromosome genetic markers including single nucleotide polymorphisms(SNPs),short tandem repeats(STRs)and copy number variations(CNVs)were employed to study the origin of Chinese indigenous horses.The results are as follows:(1)Using the techniques of Mass Spectrometry,14 loci were detected having polymorphisms.Nucleotide diversity and haplotype diversity both showed that Chinese indigenous horses had higher genetic diversity than the introduced horses.There were 20 haplotypes formed in the network,and Chinese horses distributed in all of the haplotypes.SHT1 and SHT2 were the two most popular haplotypes of local horses,and SHT4 to SHT20 were all composed of the southern local breeds.The haplotypes of SHT19 and SHT20 were derived from the mutations in the AMELY gene,and this mutation can also be detected in Przewalskii,and there were a close genetic relationship between them.It was presumed that SHT19 and SHT20 were ancient haplotypes.(2)Results of STR haplotypes showed that introduced breeds only had a uniform haplotype while northern breeds showed diversity of Y-chromosome STR and there was highest level of paternal diversity revealed in southern breeds.The haplotypes containing samples with AMELY gene mutations have close genetic relationship to asinus,which were relatively ancient haplotypes.It was presumed that these ancient haplotypes may be the retention of the local domestication of wild horses or originated from the northern horses spread to the southern regions.(3)qPCR was applied to determine CNVs of 11 loci in the 302 male samples.The resulted showed that CNVs had high level of diversity within populations.Except for locus 9,1,12 and 4,there were significant differences of median numbers among populations.FST value showed that southern horses had obvious differentiation with introduced horses compared with northern horse.The analysis of genetic distance showed that the genetic distance between the horses in North China and horses from the adjacent areas of China(Arabian and Akhal-teke horses)was closer,which indicated that the northern local breed was influenced by the breeds from the neighbour countries.Based on the results,it was presumed that early domesticated horses may be introduced into China from its northern adjacent area.The phylogenetic tree showed that the domesticated horses may spread from the north to the south in China.(4)Pyrosequencing of bases ratio of the heterozygous samples revealed that some loci showed only limited forms of bases ratio,while others had dispersive ratios.The reason why one locus had a variety of proportional forms may be attributed to the time sequence of the SNPs and CNVs occurred,or there were introduced individuals mixed in.The CNVs of SNP17A in the NSWG population was significantly different from that in the modern population,indicating that it may have different origin from other groups.(5)Based on the analysis of estimation on the number of common ancestors,there were 5 male horses participated in the establishment of initial domesticated horse group.In conclusion,the three genetic markers(horse Y chromosomal SNP,STR and CVN)were integrated to analyze the origin of Chinese horses.Our results showed that the earliest domesticated horses in China may be introduce from the adjacent areas of China,which entered northern parts of China first,and then spread into the whole country,but it can not be completely excluded that there were some local domestication events occurred in China,especially in the southern areas,where relatively high level of paternal diversity was revealed.