Study On The Genetic Variety , Origion And Divergence Using Mitochondrial DNA Sequences Of Chinese Domestic Goats

In the study, complete sequence of mitochondrial DNA(mtDNA) control region (CR, D-loop) was sequenced in 96 individuals from 16 domestic goat breeds (strains) raised in China (include 4 foreign breeds). The complete sequence of mtDNA CR is 1,212 or l,213bp(base pair). 90 sites were polymorphic (7.43% in 1,212) with 69 parsimony informative polymorphic sites, 20 singleton polymorphic sites and one insertion/deletion in 1075 sites. All polymorphic sites were two variants with transitition .The curve of nucleotide mismatch distributions in domestic goats population took on unimodal and wavilness. Tajima's test of selective neutrality was not significant (P > 0.10 or 0.05 < P < 0.10) .It revealed that all sequence of domestic goats were selective neutrality and that goat population did not undergo expansions. High nucleotide diversity (Pi=0.977) and haplotype diversity(H=1.608%)were manifested either in Chinese goat or in foreign goat populations. All sequence polymorphic sites defined 54 haplotypes with 16 haplotypes within 4 foreign breeds , 41 within 11 Chinese breeds. Chinese indigenous goats showed higher haplotype diversity(0.973) than foreign breeds(0.913), while nucleotide diversity, pairwise distance and average number of nucleotide differences among haplotypes were less than foreign breeds. These results suggested richer genetic diversity within Chinese goat populations. The hierarchical components of mtDNA variation computed under the analysis of molecular variance(AMOVA) framework showed that smaller but not significant percentage existed among breeds(24.22%;P>0.05) .The AMOVA results revealed that there were no significant divergence and far weaker genetic structure among breeds.Only 3 haplotypes existed within Chinese goat populations by analyzing 96 sequences in the study, combined 16 domestic goats and 2 wild goats(Copra aegagrus and Capra falconeri) reported in documents. The average number of nucleotide differences , average number of nucleotide subs, per site between breeds were 19.475(7.50~30.42) and 1.607%(0.619%~2.512%), respectively. The Kimura 2-parameter distance between breeds varied from 0.0008 to 0.0315. Many breeds had its unique haplotypes and only 10 haplotypes were shared among some breeds. The distributions and frequencies were unequilibrium either among breeds or within breeds.Maximum parsimony tree and. maximum-likehood tree were constructed by using PAUP4.0 software , including 56 haplotypes and 2 wild capra sequences. While minumumevolution tree was established by MEGA software. All trees tested by 1000 times bootstrap replications. Three phylogenetic trees had same branch structure and higher confidence probabilities .All domestic haplotypes were divided three high obvious divergent clusters (I , II and III ) that showed multiple maternal origins of Chinese domestic goat population. More and deeper research should be continued if we want to get specific answer to some questions, for example, which wild capra maternal origins contributed to Chinese domestic goats ? Whether wild Capra crossed before domestication or independent domestication and subsequent introgression?The rate of cytochrome b (cyt &) evolution is relatively moderate. The cytochrome b genes that the only cytochrome coded by mitochondrial DNA, even small fragment sequence, contains phylogenetically informative and unlikely to be severely compromised by saturation effects. So it is thought to be variable enough for population level questions, and conserved enough for clarifying deeper phylogenetic relationships. In the study , cyt b gene were sequenced in 42 individuals from 16 domestic goat breeds(strains) in China. The complete sequence was l,140bp that coded 379 amino acid and one termination. 17 sites were polymorphic with 7 singleton polymorphic sites ,10 parsimony informative which caused 3 amino acid change at 215,242 and 302 sites. Rich adenine(A) presented in the 1st and 3rd codons, while the 2nd had rich thymine(T). The base composition showed more bias at 3rd codon that guanine (G) cont...