| The mitochondrial DNA control region complete sequence of 22 individuals from five different Chinese water breeds or strains were individually sequenced. The results showed:The complete sequence of mtDNA D-loop of Chinese water buffalo was 927 bp, 928bp ,929 bp,930 bp and 931 bp. The average length was 929.8 bp. We found that T/A and C/G content were 58.6% and 41.4% respectively. 70 sites were polymorphic (7.4% in 910) with 9 singleton polymorphic sites(1%) and 63 parsimony informative polymorphic sites(4.6%). There were five types of mutation of nucleotide. They were transition, transversion, insertion/deletion and the coexistence of transition and transversion. This research defined 17 haplotypes, in which haplotype H17 is major haplotypes of Chinese water buffalo, which was shared by DeChang and FuLing water buffalo, other 13 haplotypes belongs to individual breeds respectively. The intro-breeds average haplotypes diversity was 0.965±0.028. Average nucleotide differences and nucleotide diversity of intro-breeds was 15.238 and 1.651% respectively. Nucleotide divergence rang from 0.638% to 2.042%, in which the least divergence presents between YunNan water buffalo and FuLing water buffalo. Kimura 2-parameter distance between 5 Chinese water buffalo breeds was -0.160%- 0.528%, the variation of distance is relatively small with between AnHui and DeChang , FuLing and YunNan water buffalo exception. The Jukes-Cantor distance in 17 haplotypes variation is low, ranging from 0.00108 to 0.020414, in which Jukes-Cantor distance is highest (0.04234). These results indicated that genetic diversity of Chinese water buffalo was relatively abundant.This research adopted D-loop's haplotypes of Chinese water buffalo, pooled with published data in gene bank of 3 swamp buffalo(Carabao) and 3 river buffalo(Murrah) D-loop complete sequence haplotypes, using software Paup4.0 and Mega2.1 to construct MP-tree and NJ-tree of D-loop complete sequence of water buffalo, In the process of...
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