Conservation Genetics of Local and Wild Pig Populations: Insight in Genetic Diversity and Demographic History

• Main Author: Medrano, Juan Manuel Herrero
• Format: Dissertation
• Language: English
• Published: ProQuest Dissertations & Theses 01-01-2013
• Subjects: Animal sciences; Demography; Endangered & extinct species; Genetics; Hogs; Mitochondrial DNA; Mutation; Phylogenetics; Sociology; Systematic biology; Wildlife Conservation
• ISBN: 9798380563949

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 development of new genotyping technologies provides unprecedented opportunities for the implementation of effective conservation programs. 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 scrofaacross Eurasia. Dispersal patterns consistent with fossil records described in other species as well as hitherto untested dispersal routes were detected. Insight in the demographic history of local pigs was obtained by using 60K SNP data. The study of regions of homozygosity (ROH) and past effective population size (Ne) showed genetic signs of past bottlenecks in some populations. The estimation of Ne revealed the bottleneck suffered by wild pigs during the last glacial maximum, and an increase of Ne of Iberian pigs may due to the domestication. 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. Within the population structure analysis, identification of admixture is a relevant issue in conservation management of livestock species. A population structure analysis combined with an analysis of ROH and the calculated inbreeding factor at the individual level provided suitable parameters to identify pigs that have been recently crossed with other breeds. I observed a high correlation between genetic diversity computed with the 60K SNP and whole genome re-sequence data. This high correlation inferred indicates that the Porcine 60K SNP Beadchip provides reliable estimates of genomic diversity in European pig populations. The study of NGS 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.