Study On The Origin Of Jinjiang Horse With The Techniques Of DNAomics

Jinjiang Horses are distributed in Jinjiang,a coastal city of Fujian,Southeast China.It is the only Chinese local horse breed adapted to the humid and hot climate in the southeast coastal area.Quanzhou,the main producing area of Jinjiang Horse,was the starting point of the ancient Marine Silk Road and had frequent trade with the Arab world.Therefore,some scholars speculate that Jinjiang Horses are the descendant of the Arabian horse breed.However,the origin of the Jinjiang Horses remains unknown owing to lack of historical records.Meanwhile,due to the popularity of agricultural mechanization in recent decades,Jinjiang Horses,which is mainly used for draught,are currently at the edge of extinction.Therefore,this study intends to explore the origin of Jinjiang horse from the perspective of mitochondrial genome and nuclear genome,and also provide meaningful information for the conservation and utilization of Jinjiang Horses.The results are as follows:Results from the study on mitochondrial DNA(1)Jinjiang Horses show the same matrilineal diversity as other domestic horse breeds.The clustering results of the HVR-1 sequences formed nine major haplogroups of A-I.The Jinjiang Horses are distributed in all haplogroups except for the B haplogroup,and most of them are distributed in the A5 cluster.(2)FST analysis of the HVR-1 revealed that Jinjiang Horses have low differentiation with Baise Horses,Lijiang Horses,and Tengchong Horses,indicating that Jinjiang Horses have close relationship with horse breeds of Southwest China.The genetic differentiation between Jinjiang Horses and Arabian horse breed is relatively high.(3)Mismatch distribution results show that the population of Jinjiang Horse has undergone group expansion.(4)The mitochondrial genome sequence was used to analyze the worldwide horses,forming 18 haplogroups of Aw-Rw.The correspondence between haplotypes formed with the HVR-1 and the mitochondrial genome sequences was established.The results show that the mitochondrial sequences of Jinjiang Horses were distributed widely in the haplogroups,indicating the multi-origins of Jinjiang Horses.(5)The mitochondrial genome sequences provided high phylogenetic resolution and precise dates for the divergence of the studied maternal lineages.The sequence of the HVR-1 in Jinjiang horse was mainly distributed in the A5 cluster,which corresponds to the Aw of the whole mitochondrial sequences.The differentiation time of the Aw haplogroup was 13.6 kya,before the domestication of the horses(about 5,800 ya).Results from the study on nuclear DNA(1)In this study,the data from genotyping 24 breeds of Chinese and foreign horses with genome-wide high density SNP microarray were used to construct phylogenetic NJ trees,conduct PCA,Admixture analysis,and Treemix analysis.The results show that Jinjiang Horses have close relationship with other Chinese indigenous horse breeds.There was no gene flow between Jinjiang Horses and foreign horses.(2)According to above studies,it indicates that Jinjiang Horse is closely related to Chinese indigenous horses,therefore,merely the Chinese indigenous horses were included in the subsequent study.The clustering analysis of NJ tree of Jinjiang Horses and other China domestic horses shows that most of Jinjiang horses have close genetic relationship with Baise Horses and Lijiang Horses,while a few individuals of the breed were relevant to Northern China horses,indicating the multiple origins of Jinjiang Horses.LD decay analysis shows that Jinjiang Horses have been imposed the least selection among all Chinese horses investigated in this study,which is one of the reasons for the high diversity of Jinjiang Horses.The analyses of PCA and Admixture show that the most closely related to Jinjiang horse is the Baise horse and Lijiang horse in the southwestern horse,followed by the northern horse breed.Furthermore,the Treemix analysis reveals that there was gene flow from Chakouyi Horses to Jinjiang Horses.(3)Through the analysis of Identity by Descent(IBD),it was found that Jinjiang Horses shared the longest IBD with Southwest horses,especially with Baise Horses,while Naqu Horses shared the shortest IBD with Jinjiang Horses.(4)The f4 test with Admixtools software reveals that Baise Horses and Chakouyi Horses are the most important ancestors of Jinjiang Horses.The proportion of these two ancestors were analyzed with Alder software,and it was found that the percentage of Baise Horses and Chakouyi Horses in the ancestors of Jinjiang Horses were about 47.3%and 20.2%,respectively.In conclusion,Jinjiang Horse has a close genetic relationship with China southwest horses,especially with Baise Horse,but it has no close genitic relationship with foreign horses that investiaged in this study,especially with Arabian horse breed.There was a gene flow from Chakouyi Horse to Jinjiang Horse.Jinjiang Horse originated from other Chinese indigenous horse breeds(especially Baise Horse and Chakouyi Horse)and formed the breed under natural selection and artificial selection.