| To develop effective conservation and utilization proposal of genetic resources in farm animal,we must first understand the genetic structure clearly.One recently developed and useful analysis method to study the genetic structure,population expansion history,and phylogenetic relationship of domestic animals is refered to the mitochondrial genomes sequence variation.The michondrial DNA(mtDNA) is the genetic basis for cytoplasmic inheritance effect,and to study the correlation of SNPs of mtDNA with important economic traits is significiant to perform marker-assisted selection.In this study,we seuqneced the mtDNA genome entire sequence of Chinese indigenious cattles,and studied the matrilineal components,population expansion history,and phylogeographical pattern of Bos taurus combined with available data from GenBank.In addition,we studied the SNPs distribution in the mtDNA ATPase 8 and ATPase 6 genes and the correlation with milk production traits in Holstein.The results are followed:1.After dissecting the matrilineal components of Bos taurus based on mitochondrial genomes sequence variation,we detected two new haplogroups as well as four already reported T1,T2,T4,and T5 haplogrous.The two new haplogroups separated by 16119th and 16122nd mutations,respectively,were defined by T16119 and T16122.All modern Bos taurus were clustered together with low genetic divergence,and in which T16119 and T16122 haplogroups presented comparable phylogenetic location with T4 haplogroup.The results suggested that the complete mitochondrial genome sequence variation could be used to dissect systematically matrilineal components of Bos taurus.2.The five new complete mtDNA sequences of Tonjiang cattle from Southwest China were perfectly clustered into T1,T2,T3,T4,and T16119 haplogrous, respectively,which is consistent with former reports studied by mtDNA D-loop sequence variation.This is the first report to verify the African haplogroup(T1) exist in the Chinese indigenious cattle population based on the mitochondrial genome entire sequence.3.The occurrence frequency of T16119 haplogroup was only inferior to T3 haplogroup.The network profile of T16119 haplogroup was the star-like shape,and the Fs value of neutrality test was-25.98045(P＜0.00001).In T16119 haplogroup, about 70%samples came from China and 23%from Northeast Asia.The highest frequency of T16119 haplogroup occurred in Southwest China,and followed by the middle and upstream region of the Yellow River,Korea region,and Japan region.The results suggested that T16119 haplogroup might have undergone population expansion in the past,which would occur in Southwest China.Subsequently,T16119 haplogroup spread north to Northeast Asia.4.The network profile of T16122 haplogroup was the star-like shape,in which more than 80%samples was from Northeast Asia.The Fs value of neutrality test was -8.2383(P=0.00500).The results suggested that T16122 haplogroup might have undergone population,and perhaps occurred in Northeast Asia.Five samples from North China region was also detected in T16122 haplogroup,which suggested that the influence of T16122 haplogroup presented in North China region.5.Although network profile of T1 haplogroup almost showed the star-like shape,all the samples could be clustered into two potential central nodes with one mutation distance,which were further occurred by East Asian and European samples, respectively.Then we proposed that T1 haplogroup was introduced into East Asia and Europe regions with independent events,and the one nucleotide mutation already existed before initial diffusion.6.97%samples in T4 haplgroup came from China(37 individuals) and Northeast Asia(46 individuals).The results suggested that the distribution of T4 haplgroup was not only in Northeast Asia but also in China with comparable frequency.7.Two extinct anrochsen mtDNA haplogroups(P and Q) were detected in China and Northeast Asia cattle population with much low frequency.The results suggested the influence of Aurochs on modern cattle population would be not restricted only in Europe region.8.Whichever geographical classifications were adopted,about 85-90%of the genetic variation was distributed within breeds when the Bos taurus and Bos indicus type samples were separately studied.The population pairwise FST value was about 0.15.The genetic variation within breeds and FST value were changed to 79%and 0.21 in all Bos taurus and Bos indicus samples,respectively.Then we proposed that the genetic difference of Chinese cattle among ecologically geographical areas was resulted from the different influence degree of Bos indicus on these geograpchical populations.For Bos taurus type alone,there was no significiant genetic difference among ecologically geographical areas.9.As one case study,total five haplogroups(T1-T4,T16119) were detected in Tongjiang cattle with 54 samples.We proposed that there was no haplogroup-specific breed for Chinese indigenious cattle.The difference of matrilineal components of Chinese cattle populations would be only referred to different occurrence frequency of haplogroups.10.Total 139 parsimony informative sites were detected in complete mtDNA sequence.Among them,92 sites were distributed in coding region,and the Cyt b gene was the secondary mutational hot spots fragment.11.Total 18 polymorphism sites were detected in the 936 bp fragment of ATPase 6 and ATPase 8 genes,which further determined six haplogroups(H1-H6).The least squares analyses revealed that the haplotypes had no significant influence on fat content and somatic cell count(SCC) traits.In contrast,the protein content and 305 days milk production differed significantly among haplotypes(P＜0.05).Haplotype H2 had the highest protein content and haplotype H4 ocurred by the highest 305 days milk production.The results suggested that H2 and H4 haplotypes could be used as candidate gentypes for protein content and 305 days milk production traits,which should be further confirmed.
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