Molecular Characteristics And Phylogenetic Analysis Of Chinese Cattle From Maternal And Perternal Lineages

To clarify the maternal origin and phylogenetic relationships of Chinese indigenous cattle, as well as mtDNA distribution and introgression in China, we carried out phylogenetic analysis of 18 breeds from 14 provinces by employing mitochondrial DNA (mtDNA) polymorphisms. The complete mitochondrial cyt b gene and D-loop region sequences were determined for a total of 136 and 84 individuals, respectively. On the other hand, polymorphisms of 11 Y chromosome specific satellites were analyzed among 310 bulls from 15 indigenous breeds. Based on the investigation of Bos taurus and Bos indicus specific Y chromosome satellites makers of UMN2404 and UMN0103, in conjunction with the published data resulted from the study of Y chromosome morphologies of 66 bulls from 10 breeds, we revealed the distribution and genetic introgression of male indicine and taurine in China.1. mtDNA cyt b gene diversity and phylogenetic evolution of Chinese cattle1.1 136 sequences of the cyt b gene in full length for 18 cattle breeds spanned 1140 bp, started with an ATG codon and ended with an AGA codon. No insertion/deletion or length variation was observed in these sequences. The average nucleotide composition of A+T (56.7%) is higher than that of G+C (43.4%), so the cyt b gene sequences are rich in A and T. The third codon of the cyt b genes presented a highest content of A (44.6%) but a lowest of G (3.5%), resulting in a strong composition bias index of 0.45. In contrast, the highest frequency of T (40.5%) was observed at the second codon, with a composition bias index of 0.21.1.2 Analysis of 136 sequences of cyt b gene showed 105 polymorphic sites, representing 9.2% of the total DNA sequence analysed (1140 bp). These sequences belonged to 47 haplotypes defined by polymorphisms at 105 polymorphic sites. The overall nucleotide diversity and haplotype diversity of the cyt b genes in Chinese cattle samples analyzed were 0.00923 and 0.848, respectively, which were higher than the reports from other studies. Among the 105 polymorphic sites, 65 were transitions and 39 were transversions. Transition and transversion coexisted in the cyt b genes in Chinese cattle at the site 15615 scored by the reference sequence of mtDNA genome (Accession no. V00654). The overwhelming majority of substitutions at the third codon were sense mutations, while those at the first and second codon were missense mutations. Compared with transitions, transversions resulted in a...