Genomic characterization of the three Balkan Livestock Guardian Dogs

Balkan Livestock Guardian Dogs (LGD) were bred to help protect sheep flocks in sparsely populated, remote mountainous areas in the Balkans. The aim of this study was genomic characterization (107,403 autosomal SNPs) of the three LGD breeds from the Balkans (Karst Shepherd, Sharplanina Dog, and Tornjak). Our analyses were performed on 44 dogs representing three Balkan LGD breeds, as well as on 79 publicly available genotypes representing eight other LGD breeds, 70 individuals representing seven popular breeds, and 18 gray wolves. The results of multivariate, phylogenetic, clustering (STRUCTURE), and FST differentiation analyses showed that the three Balkan LGD breeds are genetically distinct populations. While the Sharplanina Dog and Tornjak are closely related to other LGD breeds, the Karst Shepherd is a slightly genetically distinct population with estimated influence from German Shepard (Treemix analysis). Estimated genomic diversity was high with low inbreeding in Sharplanina Dog (Ho = 0.315, He = 0.315, and FROH>2Mb = 0.020) and Tornjak (Ho = 0.301, He = 0.301, and FROH>2Mb = 0.033) breeds. Low diversity and high inbreeding were estimated in Karst Shepherds (Ho = 0.241, He = 0.222, and FROH>2Mb = 0.087), indicating the need for proper diversity management. The obtained results will help in the conservation management of Balkan LGD dogs as an essential part of the specific grazing biocultural system and its sustainable maintenance

On the origin of European sheep as revealed by the diversity of the Balkan breeds and by optimizing population-genetic analysis tools

Background: In the Neolithic, domestic sheep migrated into Europe and subsequently spread in westerly and northwesterly directions. Reconstruction of these migrations and subsequent genetic events requires a more detailed characterization of the current phylogeographic differentiation. Results: We collected 50 K single nucleotide polymorphism (SNP) profiles of Balkan sheep that are currently found near the major Neolithic point of entry into Europe, and combined these data with published genotypes from southwest-Asian, Mediterranean, central-European and north-European sheep and from Asian and European mouflons. We detected clines, ancestral components and admixture by using variants of common analysis tools: geography-informative supervised principal component analysis (PCA), breed-specific admixture analysis, across-breed f 4 profiles and phylogenetic analysis of regional pools of breeds. The regional Balkan sheep populations exhibit considerable genetic overlap, but are clearly distinct from the breeds in surrounding regions. The Asian mouflon did not influence the differentiation of the European domestic sheep and is only distantly related to present-day sheep, including those from Iran where the mouflons were sampled. We demonstrate the occurrence, from southeast to northwest Europe, of a continuously increasing ancestral component of up to 20% contributed by the European mouflon, which is assumed to descend from the original Neolithic domesticates. The overall patterns indicate that the Balkan region and Italy served as post-domestication migration hubs, from which wool sheep reached Spain and north Italy with subsequent migrations northwards. The documented dispersal of Tarentine wool sheep during the Roman period may have been part of this process. Our results also reproduce the documented 18th century admixture of Spanish Merino sheep into several central-European breeds. Conclusions: Our results contribute to a better understanding of the events that have created the present diversity pattern, which is relevant for the management of the genetic resources represented by the European sheep population

Runs of Homozygosity Reveal Genome-wide Autozygosity in the Austrian Fleckvieh Cattle

Runs of homozygosity (ROH) are recognized as potential inbreeding measure in studies on humans. Inbreeding coefficients derived from ROH (FROH) measure proportion of the genome arranged in long homozygous segments and highly correlate with those derived from pedigree (Fped). From that we assumed that ROH represent an alternative to pedigree inbreeding levels in studies on animals too, because pedigree can be incorrect, incomplete and can not fully explain what happened in meiosis. To confirm our premise we used pedigree and genotype data from 500 Austrian dual purpose Simmental bulls to determine correlation between FROH and Fped. ROH were obtainedusing Fortran 90 soft ware created by the authors. Proportions of genome in ROH were calculated for lengths of ROH of >1, >2, >4, >8 and >16 Mb. Pedigree data were analyzed and inbreeding coefficients for complete pedigree (FpedT) and five generations (Fped5) were calculated using ENDOG soft ware. We found low FpedT and Fped5 (means of 1.5% and 0.9%) while FROH for segments >1Mb suggested much higher values (9.0%) indicating old inbreeding that can not be traced using pedigree. The highest correlations were found between FROH calculated from ROH of length >4Mb and FpedT (0.68) that is consistent with studies on humans. We conclude that inbreeding coefficients derived from ROH are useful for measuring levels of inbreeding in cattle, because ROH are not subject to mistakes as pedigrees and calculations made from those

Sequence polymorphism of PrP exon 3 gene in Istrian and crossbred sheep

Polymorphisms in sheep PrP (prion protein) gene are known for scrapie susceptibility. We sequenced part of PrP exon 3 gene in 92 autochthonous Istrian (IS) and 38 crossbred sheep (CBS). ARQ, ARR and AHQ alleles were predominant with frequency of 0.674 (0.526), 0.228 (0.132) and 0.082 (0.263) in IS (CBS), respectively, while VRQ (0.011 in IS) and ARH (0.005 in IS and 0.079 in CBS) alleles were rare. We also found non-synonymous mutations at codons 112 (M→T), 127 (G→S) and 143 (H→R), and synonymous mutations at codons 231 (R) and 237 (L). Additional mutations were associated only with AHQ, ARH and ARQ alleles. The polymorphism of PrP gene in IS was not critical with respect to scrapie susceptibility and with some efforts number of “favourable” genotypes can be increased