Genetic Diversity and Population Structure of Bulgarian Autochthonous Sheep Breeds Revealed by Microsatellite Analysis.

This study attempts to provide a deeper insight into the current genetic status of 12 Bulgarian autochthonous sheep breeds using microsatellite (SSR) markers. A total of 600 individuals from 50 flocks were analyzed using a panel of 13 SSR markers. In total, 228 alleles were found in the studied microsatellite loci. The mean number of alleles, the effective number of alleles, and the polymorphic information content (PIC) values per locus were 17.54, 5.250, and 0.799, respectively. The expected heterozygosity (He) for all breeds ranged from 0.70 to 0.82. The within-population heterozygote deficit (Fis) varied from -0.03 to 0.1, reflecting significant levels for 10 of the 12 breeds. The average genetic differentiation (Fst) was 0.046, revealing a low discrimination between the breeds. The genetic distance, principal coordinate analysis, and the structure analysis showed that two of the studied breeds-Local Stara Zagora/SZ/ and Local Karnobat/MK/-were the most distinct sheep populations. The Bayesian clustering approach suggested poor breed differentiation for the remaining 10 sheep breeds. The results suggest that proper management strategies and specific breeding policies need to be implemented in Bulgaria to avoid the intermixing of breeds and to reduce the erosion of breed purity observed in some breeds.

Large-scale mitogenome sequencing reveals consecutive expansions of domestic taurine cattle and supports sporadic aurochs introgression.

The contribution of domestic cattle in human societies is enormous, making cattle, along with other essential benefits, the economically most important domestic animal in the world today. To expand existing knowledge on cattle domestication and mitogenome diversity, we performed a comprehensive complete mitogenome analysis of the species (802 sequences, 114 breeds). A large sample was collected in South-east Europe, an important agricultural gateway to Europe during Neolithization and a region rich in cattle biodiversity. We found 1725 polymorphic sites (810 singletons, 853 parsimony-informative sites and 57 indels), 701 unique haplotypes, a haplotype diversity of 0.9995 and a nucleotide diversity of 0.0015. In addition to the dominant T3 and several rare haplogroups (Q, T5, T4, T2 and T1), we have identified maternal line in Austrian Murbodner cattle that possess surviving aurochs' mitochondria haplotype P1 that diverged prior to the Neolithization process. This is convincing evidence for rare female-mediated adaptive introgression of wild aurochs into domesticated cattle in Europe. We revalidated the existing haplogroup classification and provided Bayesian phylogenetic inference with a more precise estimated divergence time than previously available. Occasionally, classification based on partial mitogenomes was not reliable; for example, some individuals with haplogroups P and T5 were not recognized based on D-loop information. Bayesian skyline plot estimates (median) show that the earliest population growth began before domestication in cattle with haplogroup T2, followed by Q (~10.0-9.5 kyBP), whereas cattle with T3 (~7.5 kyBP) and T1 (~3.0-2.5 kyBP) expanded later. Overall, our results support the existence of interactions between aurochs and cattle during domestication and dispersal of cattle in the past, contribute to the conservation of maternal cattle diversity and enable functional analyses of the surviving aurochs P1 mitogenome.

Conservation of a domestic metapopulation structured into related and partly admixed strains.

Preservation of genetic diversity is one of the most pressing challenges in the planetary boundaries concept. Within this context, we focused on genetic diversity in a native, unselected and highly admixed domesticated metapopulation. A set of 1,828 individuals from 60 different cattle breeds was analysed using a medium density SNP chip. Among these breeds, 14 Busa strains formed a metapopulation represented by 350 individuals, while the remaining 46 breeds represented the global cattle population. Genetic analyses showed that the scarcely selected and less differentiated Busa metapopulation contributed a substantial proportion (52.6%) of the neutral allelic diversity to this global taurine population. Consequently, there is an urgent need for synchronized maintenance of this highly fragmented domestic metapopulation, which is distributed over several countries without sophisticated infrastructure and highly endangered by continuous replacement crossing as part of the global genetic homogenization process. This study collected and evaluated samples, data and genomewide information and developed genome-assisted cross-border conservation concepts. To detect and maintain genetic integrity of the metapopulation strains, we designed and applied a composite test that combines six metrics based on additive genetic relationships, a nearest neighbour graph and the distribution of semiprivate alleles. Each metric provides distinct information components about past admixture events and offers an objective and powerful tool for the detection of admixed outliers. The here developed conservation methods and presented experiences could easily be adapted to comparable conservation programmes of domesticated or other metapopulations bred and kept in captivity or under some other sort of human control.