Using whole-genome sequencing data for demographic and functional evaluations of small managed populations

Summary:

Genetic diversity forms the basis for selection to act upon a population: without diversity, evolution can not occur and species can not adapt to changing environments. In livestock populations, the rapid decline in genetic diversity calls for immediate and effective conservation measures to prevent future breeds to go extinct. However, parameters related to, for instance, genetic diversity and inbreeding should be estimated upfront in order to successfully intervene.

The aim of this thesis was to explore the use of whole-genome sequencing data to characterize, from a demographic and functional perspective, livestock diversity to guide conservation efforts. Local chicken breeds were the main breeds of interest. Results showed, among others, that (1) recent inbreeding and genetic drift are important threats in small populations, (2) the genetic basis of some of the phenotypic variation has a complex evolutionay history, and that (3) genetic diversity can and should be measured at multiple levels to best manage populations and genetic resources.