| Horse,as a kind of livestock,has a great effect in human history.In terms of human society,the domestication of horse is propitious to economic and cultural intercourse between different countries and regions.Moreover,it also has a profound impact on the political and military affairs.With human-selective breeding,the breeds of domestic horses are increased while genetic structure of horse is modified to some extent.An origin research on domesticated horses will contribute us to learn the emergence and development of animal husbandry in the early period of human civilization.We worked whole-genome resequencing and population genome evolution analysis on the 104 domestic horses with 13 breeds collected on a global scale during this study,which afford the expansive inherited bases for uncovering evolutionary history and domestic livestock origin in equine.By Illumina Hi Seq X Ten sequencing platform,the whole-genome resequencing on104 modern domesticated horses were completed at the high cover.We further obtained the high-quality data of genome sequence which average sequencing depth was 17.59 x,based on quality control of the raw sequence data.Combined with the published sample data of extra 62 horses of 14 breeds in the equine family,we performed SNP detection on the genome sequences of all the 166 horses with 22 breeds,selecting 9,626,234high-quality SNP sites as hallmark to subsequent population structure analysis.In our work,we implemented the population structure,population history and population genetic polymorphisms analyses in equine by bioinformatics methods and tools.Based on population genetic structure analyses,we found out that the horse populations of East Asian had distinct regional divisions compared to the horse populations of central Eurasia and of Western Europe.In accordance with distribution trends of horses in population genetic structure analyses and in geography,the findings intimate that domestic horse might migrate to western Eurasia from eastern Eurasia.Based on all the 166 horeses with 22 breeds,we reconstructed the population history while the estimated divergence time between Przewalski’s horse and domestic horse was forty to fifty thousand years ago.The effective population size of modern domestic horses was basically consistent until about 3500 years ago.By calculating the divergence time,we propose that a part of domestic-horse ancestor migrated to western zones from eastern zones in Eurasia while another part of domestic-horse ancestor,staying in eastern Eurasia,began to diffuse.By using various analytical methods,we proved that the horsepopulations of eastern Eurasia had higher genetic diversity,which may indicate that these horses are the older existent breeds in equine and less influenced by artificial selection.Combining relevant archaeological data,we speculate that East Asia is probably one of the origins,focused on the acclimation of domesticated horses,while domestication events of horses may be arising about ten thousand years ago in East Asia.In order to explore the effect of domestication process on horse genome,we selected two subbreeds of Mongolian horse,including Abaga horse with fast-running ability and Wushen horse with slower running speed,to compare their genomic data.We discovered that most of the positively selected genes,particularly exercise-related,of Abaga horse and Wushen horse were concentrated on chromosome 4,which imply that the chromosome 4 may be associated with the domestication of the Mongolian horse to be used to further research on athletic performance.The exercise-related pathways and genes were significantly enriched while the unique mechanism of physiological regulation is possible on athletic performance in Abag horses.So,we suggest that the directional change of genomic structure may be mainly in response to artificial exercise-related-selection during domestication process of Abag horses. |
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