Mitochondrial Diversity and Phylogenetic Relationship of Eight Native Bulgarian Sheep Breeds

Abstract

Simple Summary Mitochondrial DNA (mtDNA) is one of the most often used genetic markers in animal population studies. Its relevance as a genetic marker is due to the high mutation rate and variability, the maternal inheritance, and the supposedly nearly neutral mode of evolution. Therefore, mtDNA diversity is typically assumed to reflect demographic effects, i.e., variations in population size between species or populations, which makes it a popular tool for conservation purposes. Thus, mtDNA diversity allows a better understanding of the evolutionary plasticity and provides insights into the molecular and evolutionary mechanisms modeling mitochondrial genomes. Abstract The geographical, geomorphological, and climatic characteristics of Bulgaria are particularly favorable for animal breeding and, above all, for pastoral farming and sheep breeding. These conditions created prerequisites for the creation of about 30 unique local breeds of sheep. In this study we investigated the genetic diversity of eight of the most popular Bulgarian native breeds, based on the sequence analysis of a part of the mitochondrial D-loop region. An almost entire mitochondrial DNA (mtDNA) D-loop region (1180 bp) was amplified and sequenced. The obtained results showed the presence of a large number of haplotypes–225, belonging to two main haplogroups. The majority of samples showed a high prevalence of the European haplogroup B (95.2%) while the remaining individuals were assigned to haplogroup A (4.8%). None of the other reported mitochondrial haplogroups were observed. The number of polymorphic sites, nucleotide and haplotype diversity was high (240, 0.01237, and 0.9968, respectively), which is evidence for multiple maternal origins in all populations. The Tajima D-test value in all the study populations was −1.905 (p < 0.05), indicating that the abundance of rare alleles was most likely due to population expansion after a recent bottleneck. The Median joining network showed that almost all haplotypes belonging to haplogroup B formed a star-like network, which revealed a weak genetic differentiation and a large gene flow between the Bulgarian native breeds.