Diversity And Phylogenetic Relationships Of Some Chinese Goat Breeds

China has numerous native domestic goat breeds, but so far there has been no extensive study on genetic diversity, population demographic history, and origin of Chinese goats. Here, we examined the genetic diversity and phylogeographic structure of domestic goats by determining a 622-bp fragment of the first hypervariable region of mitochondrial DNA(mtDNA)control region from155 individuals representing 13 goat breeds. Phylogenetic analyses revealed that there were four mtDNA lineages (A-D) identified in 13 goat breeds. Population genetic structure and population expansion were carried out.Based on the first hypervariable region of mitochondrial DNA study, 9 samples were collected from 4 lineages, 3,4,1 and 1 samples belonged to A-Dlineages individually.15 pairs of primers overlapping in mitochondrial DNA were designed with Premair primer 5.0.After cloning and sequencing ,we analyzed characteristics of the goat mitochondrial genome and predicted the structure of mitochondrial RNA and protein in order to analyze the effect in fitness among lineages. We compared the goat with other reported species mitochondrial genome and analyzed the molecular evolution the goat mitochondrial DNA .The conclutions were as follows:1. The analysis of these sequences reveals a weak phylogeographical structure in Chinese goat breeds. The fixation index (Fst =0.21) suggested that most of the total genetic variation was due to variation within populations.2. Network profiles revealed that the lineages B displayed a star-like phylogeny with the founder haplotype in the centre, and that two star-like subclades with two founder haplotypes were identified in lineage B3. 36 lineage B sequences were presented only in the breeds of southwestern or surrounding regions of China (Shaanan White, Langkazi, Yunling Black, Maguan, Matou and Hainan Black).Multiple lines of evidence from this study and previous studies have unequivocally proved that the southwestern area of China might be one of the domestication centers of mtDNA lineage B of goats.4. We aligned and analyzed 453bp segment of mitochondrial DNA D-loop hypervariable region from 1182 sequences, neighbor-joining (NJ) tree and network showed that the sequences were divided into four distinct mtDNA lineages A-D, After the alignment of the sequences ,nucleotide position of A,B, C and D lineage specific were acquired, and included 5,6,18 and 7 variation positions respectively.5.124 SNPs were found among 4 lineages, The overall ratio of transitions:transversions (40:1) revealed a heavy transition bias in domestic goats.In region for edcoding mitochondrial protein,121 nucleotede substitutions were found and 18 nonsynonymous mutations. These nonsynonymous mutations did not affect protein function by multi-alignment and structure prediction of proteins.6. Ultraconserved sequences of The mitochondrial genome of vertebrate were found, the result revealed the 4 franment sequences had important function in vertebrate evolution.7. In region for coding tRNA and rRNA ,SNP occurred in loops, unstructured single strand, and stems which conformed with the principle of G-U pairing.So we inferred these substitution could not change secondary structure of RNAs.8. There was no positive selection on goat mitochondrial coding region according to the result ofω(0.0399-0.1591) and HKA.