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MC4R gene was proved to play important roles in body weight regulation in many mammals and the mutation in its coding and regulatory regions significantly correlated to the restricted feeding weight, fat deposition and energy balance, also exhibit higher homology among different species. ORF sequences of MC4R gene of Bos grunniens were sequenced in this work, and the sequences of Bos grunniens and Bos taurus were aligned and edited on line by using Clustalw. Nucleotide and amino acid sequences of the coding region of MC4R gene were explored and analyzed by using MEGA 4. SWISS-MODEL was employed to analyze and predict the spatial structure of MC4R Finally, we find the gene sequences and protein spatial structure of MC4R gene is highly homologous between Bos grunniens and Bos taurus, which illustrates the functional proteins in different species are highly conservative. We also analyzed the phylogenetic relationships of yak and other mammals based on MC4R gene. All the sequences were clustered into phylogenetic clades representing different orders or families. The individuals of Bos grunniens, Bos taurus and Ovis aries belonged to the family of Bovidae and diverged from the other clades. Therefore, bovid animals may have branched out from the phylogenetic tree earlier than other mammals during 450 million years of vertebrate evolution.

Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0 was employed to analyze 217 mitochondrial DNA (mtDNA) D-loop sequences of Chinese cattle to reveal phylogenetic evolution of them. These sequences exhibited 122 polymorphic sites and 100 haplotypes were defined. These mtDNA D-loop sequences fell into two distinct lineages: taurine Bos taurus and zebu Bos indicus. Therefore, Chinese cattle displayed abundant genetic diversity and were originated from Bos taurus and Bos indicus in maternal lineages. The cattle population from Bos taurus and Bos indicus were both experienced population expansion.