Genetic diversity of native Bulgarian sheep breeds based on the mitochondrial D-loop sequence analysis

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 – 192, belonging to three main haplogroups. The majority of samples showed a high prevalence of the European haplogroup B (89.6%), followed by haplogroup A (8.6%) and C (1.8%). None of the other reported mitochondrial haplogroups were observed. The number of different haplotypes, nucleotide and haplotype diversity was high (192, 0.01286, and 0.996, respectively), which is evidence for multiple maternal origins in all populations. The Tajima D-test value in all the study populations was -1.774 (p < 0.05), indicating that the abundance of rare alleles was most likely due to population expansion after a recent bottleneck. The high level of mtDNA polymorphism in the studied breeds of local sheep indicates the presence of a significant reserve of unique genotypes in Bulgaria, which is to be explored. • The sequence analysis of mtDNA D-loop region was used to infer the genetic diversity and origin of five native Bulgarian sheep breeds. • We found high haplotypes and nucleotide diversity within breeds. • A median-joining network analysis revealed the presence of B, A and C haplogroups. • The native Bulgarian sheep breeds expressed very low level of genetic differentiation.