A limited number of highly productive populations has progressively led to many local breeds becoming endangered or extinct. Genetic characterization of the genetic resources is, thereby, needed to prevent further loss of genetic and cultural heritage. The aim of the study described in this thesis was to explore the genetic diversity and demographic history of local pig populations, and the applicability of the results for the long-term future conservation of livestock genetic resources.
In this thesis, mitochondrial DNA (mtDNA) and nuclear genetic marker systems were used to explore the past demographic history and genetic diversity of domestic and wild pigs. A Bayesian phylogeographic analysis using mtDNA allowed the detection of past dispersal events of Sus scrofa across Eurasia. The SNP panel proved to be highly efficient for population structure analyses, as it was able to differentiate 13 European local breeds and correctly assigning the pigs to their population of origin as well as to identify pigs that have been recently crossed with other breeds.
The study of whole genome re-sequence data of local and commercial European breeds demonstrated that, despite the higher inbreeding observed in many local pigs, local pigs harbour different genomic variants that may represent a valuable genetic reservoir for the livestock breeding industry in the future. This thesis provides a benchmark to address rational management and exploitation of local genetic resources. Moreover, the large representation of pig populations, the choice of genetic marker systems and the approaches utilized may benefit future studies that aim to genetically characterize livestock populations.