Genetic Diversity Of Mitochondrial DNA In Six Yak Populations From Qinghai And Xinjiang

Mitochondrial DNA(mtDNA),a form of maternal genetic material,has been widely used to study the genetic diversity of mammals.So far,studies on clustering and network relationships in Chinese yak populations have focused on the cytochrome b(cytb)genes and mtDNA control region(D-loop region).The D-loop region is usually used to study phylogenetic relationships at the subspecies level because of its fast mutation rate.Complete mtDNA sequences contain more genetic information than any single sequence fragment in mtDNA sequences,and are more effective in assessing mammalian phylogenetic relationships than cytb genes,D-loop region sequences,or protein-coding genes.In this study,mtDNA sequencing was performed on 5 yak populations(Yushu yak n=73,Qilian yak n=89,Xueduo yak n=69,Huanhu yak n=21and Tianjun yak n=50)from Qinghai Province and 1 yak population(Pamir yak n=70)from Xinjiang Uygur Autonomous Region.The genetic diversity of 6 yak populations was evaluated by analyzing the mtDNA D-loop region of 6 yak populations and the complete mtDNA of 5 yak populations(Yushu n=20,Qilian n=22,Xueduo n=23,Huanhu n=21 and Pamir n=25 yaks).The main findings are as follows:1.The sequence length of mtDNA D-loop region of 6 yak populations in Qinghai and Xinjiang was different with different individuals,and its length ranged from892～895 bp.The proportion of each base in 6 yak populations were T 28.6%,A 32.5%,G 13.7% and C 25.2%,A+T content was 61.1%,G+C content was 38.9%.The complete mtDNA sequences(16,321～16,325 bp)of 111 individuals from 4 Qinghai yak populations and 1 Xinjiang yak population consisted of T 27.3%,C 25.8%,A 33.7%and G 13.2%,and A+T content was 61% and G+C content was 39%.These results indicated that the mitochondrial genome of yak has similar base composition and rich in A+T,which is consistent with the bias of base composition.2.A total of 91 haplotypes were defined by mtDNA D-loop sequences of 372 yak individuals from 6 populations in Qinghai and Xinjiang,and 78 haplotypes were defined by mtDNA sequences of 111 yak individuals from 5 populations.Shared haplotypes were found among all 6 yak populations in the D-loop region sequence,while shared haplotypes were found among 4 yak populations in Qinghai province in the complete mtDNA sequence,but no shared haplotypes were found between Pamir yak in Xinjiang and 4 yak populations in Qinghai province.3.The D-loop region of 6 yak populations and the complete mtDNA sequence genetic diversity of 5 yak populations were analyzed.It was found that the haplotype diversity in the D-loop region of the six populations was as follows: Huanhu yak(0.943±0.039),Tianjun yak(0.929±0.018),Xueduo yak(0.915±0.024),Qilian yak(0.909±0.024),Pamir yak(0.829±0.033)and Yushu yak(0.823±0.031).The nucleotide diversity in the D-loop region of the six populations was as follows: Tianjun yak(0.01792±0.00362),Pamir yak(0.01657±0.00278),Huanhu yak(0.01317±0.00473),Qilian yak(0.01255±0.00321),Xueduo yak(0.01171±0.00377)and Yushu yak(0.00951±0.00256).The haplotype diversity of intact mtDNA in five yak populations were Huanhu yak(0.905±0.048),Pamir yak(0.990±0.014),Qilian yak(0.948±0.036),Xueduo yak(0.992±0.015)and Yushu yak(0.963±0.033),respectively.The nucleotide diversity of intact mtDNA in five yak populations were Huanhu yak(0.00220±0.00061),Pamir yak(0.00309±0.00018),Qilian yak(0.00273±0.00043),Xueduo yak(0.00232±0.00051),and Yushu yak(0.00276±0.00047),respectively.The results indicated that the 6 yak populations in this experiment had rich genetic diversity.4.The genetic distances between 6 yak populations in Qinghai and Xinjiang were0.011～0.018,and the genetic distances between 5 yak populations were 0.002～0.003 with complete mtDNA sequences.The genetic distance between any two populations was not 0,indicating that there were differences in genetic development between yak populations.The complete mtDNA sequence haplotype similarity analysis of yak showed that the haplotype similarity between Pamir yak and Qinghai yak populations was 0,indicating that there was no or almost no genetic communication between Pamir yak and Qinghai yak populations.However,mtDNA D-loop sequence analysis of haplotype similarity among populations showed that haplotype similarity between Pamir yak and Qinghai yak populations was not 0,and was not the lowest.According to the haplotype similarity data,the results of complete mtDNA sequences were more consistent with the geographical distance between yak populations.5.Phylogenetic analysis showed that the D-loop sequences of yak mtDNA were clustered into two categories,and the complete mtDNA sequences were clustered into three categories.Compared with previous studies,a new phylogenetic branch of domesticated yak was identified in the complete mtDNA sequences in this study.The complete mtDNA sequences of yaks were divided into three haplogroups by haplotype clustering analysis,of which haplogroup A and B had a star-like distribution,and haplogroup C had a dendritic distribution.