| The samples were collected from 8 Chinese yellow cattle breeds, including Qinchuan cattle (QC), Xizhen cattle (XZ), Jinnan cattle (JN), Yueyang cattle (YY), Mongolian cattle (MG), Nanyang cattle (NY), Jiaxian cattle (JX) and China Holstein cattle (BW) from Shaanxi, Shanxi, Hunan, Mongolian and Henan Province or Autonomous region in China. In order to amplify the complete control region (D-loop) sequence of mtDNA in Chinese cattle by PCR technique, the specific primers was designed by ourself in reference to Loftus (1991) Si Wu (2000). The complete mitochondrial D-loop sequence, 910bp in length, in 22 individuals from 8 cattle breeds were aligned by Clustal W (1.82) software and analyzed, the results showed that:1.1 Comparisons of these D-loop sequences revealed five types of mutation of nucleotide sites in Chinese cattle: transition, transversion, insertion, deletion and coexistence of transition and transversion. The nucleotide transitions existed mainly in T<=>C with 62.96%, A<=>G with 37.04%. A special polymorphic site of 266 position with C<=>G<=>A<=>T was revealed, of the 22 individual sites, 12 represented base G with 54.55%, 6 represented base A with 27.27%, 3 represented base C with 13.64%, 1 represented base T with 4.55%, the 266 position was named as coexistence site of transition and transversion.1.2 In the complete mitochondrial D-loop sequence, 910bp in length of 22 individuals from 8 Chinese cattle breeds, A% + T% was about 61.65%, G% +C% was about 38.35% and 66 polymorphic nucleotide sites were observed, with the percentage of 7.25% of 910bp. Of the 66variable positions, 54 represented transition with 81.82%, 4 represented transversion with 6.06%, 4 represented insertion with 6.06%, 3 representeddeletion with 4.54% and 1 represented coexistence site of transition and transversion with 1.52%.1.3 Complete mtDNA D-loop of Bos Taurus (Anderson, 1982) was as a control, 3 groups were divided according to the average percentage of mtDNA D-loop nucleotide variation in 8 Chinese cattle breeds. The first group with the lowest percentage of D-loop nucleotide variation, including Xizhen cattle (XZ) , Mongolian cattle (MG), China Holstein cattle (BW) and Qinchuan cattle (QC) with 0.37%, 0.44%, 0.52%, 0.66% respectively; the second group with the percentage of D-loop nucleotide variation, including Nanyang cattle (NY) and Jiaxian cattle (JX) with 1.91%, 2.02% respectively and the third group with the highest percentage of D-loop nucleotide variation, including Jinnan cattle (JN), Yueyang cattle (YY) with 4.47% , 4.73% respectively.1.4 An examination of the distribution of nucleotide mutations in the bovine whole D-loop revealed two major hypervariable regions in China cattle, the first major hypervariable regions was the same as that of the European Bos Taurus (Loftus, 1994), 370bp in length between the 241-610bp, containing almost 60.00% of the overall number of nucleotide mutations, and the second, less variable region, 138bp in length between the 713-850bp, containing almost 20.00% of mutations.1.5 The average sequence divergence estimated from total D-loop within breeds varied from 0.55%~5.39% in Chinese cattle. The average levels of divergence were seen within 8 cattle breeds: the lowest (0.55%) and the highest (above 5.0%) among Mongolian cattle, Nanyang cattle and Jiaxian cattle, respectively. The average sequence divergence estimated from total D-loop among breeds varied from 1.21%~6.59%. The average sequence divergence estimated from total D-loop from the 370bp and 138bp hypervariable region among breeds varied from 0.54%~9.46% and 0.74%~8.82%, respectively.1.6 Comparisons of these 22 complete D-loop sequences revealed 19 mitochondrial haplotypes in Chinese cattle, one haplotype sequence was shared by NY1, QC1 and QC3, another by JN1 and YY1. The haplotype rate is 86.36%, demonstrating that Chinese cattle existed abundant mitochondrial genetic diversity.1.7 Phylogenetic trees were constructed using the neighbor-joining algorithm (NJ) in complete mt...
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