Genetic diversity in the mitochondrial DNA D-loop region of global swine (Sus scrofa) populations.

Increased global use of highly productive commercial breeds has reduced genetic diversity in indigenous breeds. It is necessary to protect local porcine breeds. We therefore assessed the level of genetic diversity in global swine populations. In this study, the mitochondrial DNA D-loop region was examined in 1010 sequences from indigenous pigs and commercial swine as well as 3424 publicly available sequences We identified 334 haplotypes and 136 polymorphic sites. Genetic diversity was analyzed based on basic parameters, including haplotype diversity, nucleotide diversity and the average number of nucleotide differences, and also assessed by principal component analysis. A comparison of nucleotide diversity and the average number of nucleotide differences between indigenous breeds and commercial breeds showed that indigenous pigs had a lower level of diversity than commercial breeds. The principle component analysis result also showed the genetic diversity of the indigenous breeds was lower than that of commercial breeds. Collectively, our results reveal the Southeast Asian porcine population exhibited the higher nucleotide diversity, whereas Chinese population appeared consistently lower level in Asia. European, American and Oceanian pigs had a relatively higher degree of genetic diversity compared with that of Asian pigs. In conclusion, our findings indicated that the introgression of commercial into indigenous breeds decreased indigenous breeds' genetic diversity.