Genetic Diversity and Phylogenetic Relationships of Russian Pig Breeds Based on the Analysis of mtDNA D-Loop Polymorphism

A decrease in the level of genetic diversity is one of the main genetic problems in pig breeding worldwide. In Russia, some local breeds are endangered because of their low number. A strong directional selection can lead to a decrease in the diversity in transboundary breeds. In this regard, the aim of our study was to estimate the genetic diversity and to establish phylogenetic relationships in nine pig breeds reared in Russia by the analysis of mtDNA D-loop sequences. In total, 273 nucleotide sequences of mtDNA D-loop were sequenced in pigs of the following breeds: Breit, Kemerovo, Livni, Murom, Urzhum, Mangalitsa, Large White, Landrace, and Duroc. In the entire sample, 84 haplotypes, including 55 in local and 29 in transboundary breeds, and 104 variable sites were identified. Local breeds were characterized by a lower average number of nucleotide differences between the haplotypes than transboundary ones (K = 6.272 and K = 9.934). Of the studied pigs, 78.8% belonged to the haplogroup E; haplogroups D (20.5%) and A (0.7%) were found less frequently. The AMOVA analysis demonstrated that 43.88% of total genetic variability was due to the differences between the studied breeds. The analysis of the median network structure demonstrated that the Kemerovo breed was the most differentiated among local breeds, while the Mangalitsa breed entered the cluster of transboundary breeds owing to its European origin. The results obtained can be useful monitoring the genetic diversity in transboundary breeds, as well as for developing evidence-based programs for local pig breed conservation.

Automated summary

A decrease in genetic diversity is a major genetic concern in pig breeding worldwide. This study aimed to assess the genetic diversity and phylogenetic relationships among nine pig breeds in Russia using mtDNA D-loop sequences. The results showed that local breeds had lower nucleotide differences compared to transboundary breeds. The Kemerovo breed was the most differentiated among local breeds, while the Mangalitsa breed clustered with transboundary breeds due to its European origin. These findings are important for monitoring genetic diversity in transboundary breeds and developing conservation programs for local pig breeds.