Mitochondrial DNA diversity and origins of domestic goats in Southwest China (excluding Tibet)

Southwest China contains about one third Chinese indigenous goat breeds representing special economic and ecological characteristics. Mitochondrial DNA (mtDNA) D-loop sequences of 312 individuals (including 109newindividuals, 203 individuals retrieved from GenBank) from 18 Chinese domestic goat breeds were used to investigate breed genetic diversity, origin and phylogeography. All goat breeds in this study proved to be extremely diverse, average haplotype diversity and nucleotide diversity being 0.9829±0.0027 and 0.03615±0.03257, respectively. The 312 sequences gave 148 different haplotypes. Phylogenetic analyses revealed that there were two mtDNA haplogroups identified in domestic goats in Southwest China, in which haplogroup A was predominant. Mismatch analysis showed haplogroup A had experienced population expansion events, whereas haplogroup B did not. Amova analysis showed there was no significant geographical structuring. Almost 86.23% of genetic variation was included in the within-breed variance component and only 3.5% was observed among the four geographic provinces. The results of this study contribute to the knowledge of the genetic structure and origin of domestic goats in Southwest China.