A study on the genetic diversity and subpopulation structure of three Bulgarian mountainous sheep breeds, based on genotyping of microsatellite markers

Abstract

Traditional domestic breeds of domestic animals are part of the “living” wealth of the world, part of the disappearing biodiversity and a valuable local gene pool. Nowadays, they are increasingly included in the category of “rare and disappearing” breeds. Therefore, the purpose of this study was to reveal the genetic diversity and population structure of three Bulgarian mountainous sheep breeds (Rhodopean Tsigai, RT; Middle Rhodopean sheep, MRS; and Karakachan sheep, KS). A total of 113 unrelated individuals (two flocks of each breed) from different regions of the country were investigated based on 11 STR (short tandem repeat) markers. The obtained results showed a total of 116 alleles in the three sheep breeds. The mean number of alleles, effective number of alleles, and polymorphism information content (PIC) values per loci were 8.21, 4.72, and 0.79. The largest number of alleles were found in the population of MRS (9.18 ± 0.76), followed by RT (8.27 ± 0.64) and KS (7.18 ± 0.47). The largest polymorphism was found in INRA005 and INRA06 loci with 11 and 10 alleles, respectively, and the smallest polymorphic loci were noted for the locus McM042 and INRA172 with only 6 alleles. The observed heterozygosity showed the highest value in KS (0.79 ± 0.04), followed by RT (0.76 ± 0.02) and MRS (0.73 ± 0.04). The range of expected heterozygosity was from 0.77 ± 0.02 in MRS to 0.75 ± 0.03 in KS. The fixation index FST, estimated by analysis of molecular variance (AMOVA), was 0.2090, indicating moderate levels of genetic differentiation among the populations. The FST between the investigated breeds indicated a moderate value of 0.216, and the analysis of variance (ANOVA) data showed only 1% variation among the populations, whereas 99% was due to variation within breeds. The results by the STRUCTURE analysis revealed that all breeds were heterogeneous and formed three distinct clusters. The results of the genetic diversity and structure analysis of the investigated breeds provide useful information for assessing the genetic diversity of other Bulgarian autochthonous sheep breeds, serving as a cornerstone for designing effective conservation management strategies.