Genetic variation and relationships in the mitochondrial DNA D-loop region of Qinghai indigenous and commercial pig breeds

Background: Bamei pigs are special germplasm resources in Qinghai. In the specific environment of the Qinghai plateau, local breeds, through long-term natural and artificial selection, have acquired a relatively stable population structure and genetic diversity. This study revealed Bamei pigs' genetic diversity at the molecular level and the degree of introgression of commercial breeds into Bamei pigs. Methods: The mitochondrial DNA D-loop region was amplified and sequenced using the ABI 3130 DNA sequencer. Sequences were collected, edited and aligned using the MEGA 5.0, DNASTAR and ClustalX 1.81 software. Haplotypes of all sequences and genetic diversity were analyzed by DnaSP 5.0 software. Results and conclusions: We identified a total of 73 polymorphic sites in our 489 novel sequences, including 1 single variable site and 72 parsimony informative sites. Genetic diversity was analyzed in this study. The results showed that haplotype diversity, nucleotide diversity and the average number of nucleotide differences of Bamei pigs were lower than those of commercial pigs. Synthetic evaluation of genetic diversity through principal component analysis indicated that Bamei pigs also showed low genetic diversity. In summary, the results of sequence analysis showed that Bamei pigs were low in genetic diversity, and the introgression of commercial pigs into Bamei pigs was serious.