Domestication can serve as a study system of rapid evolutionary change with wide-ranging effects on traits in animals. The chicken was domesticated from the Red Junglefowl and has diverged in behaviour, morphology and life history traits. Conversely, feralisation is a more recent process when domestic animals are again exposed and respond to an environment outside of human husbandry. Linkage-based quantitative trait locus (QTL) mapping has been used to localise genetic variants that affect domestication traits in the chicken genome. Because of the limited resolution of linkage mapping, the QTL regions associated with domestication traits are often broad and contain many genes. One approach to help sort out potential causative genes is to measure gene expression as an intermediary molecular phenotype. In this dissertation, expression quantitative trait locus (eQTL) mapping of gene expression traits is used to search for potential causative genes for domestication traits in the chicken. Expression quantitative trait loci were mapped across the whole genome in bone and hypothalamus samples, and targeted at QTL regions in the base of the comb. These studies have resulted in candidate quantitative trait genes, supported by genetic and gene expression evidence, for relative comb mass, bone allocation, egg production and fearful behaviour as measured in an open field test. Secondly, a population genomics approach was used to study the molecular basis of feralisation in a free-range feral chicken population from the Pacific island of Kauai. Mitochondrial DNA sequences and phenotypic observations establish the hybrid origin of this population as a mixture of wild and domestic chickens. Genome-wide mapping of pooled heterozygosity highlight regions that may be involved in adaptation to the feral environment. The expression QTL results bring us closer to knowledge about the molecular basis of domestication traits in the chicken, suggesting plausible candidate genes and opening up for functional studies of individual loci. The population genomic study shows that feralisation has a mostly different genomic architecture than domestication, and suggests phenotypic effects, based on overlap with domestication QTL regions, for some of the identified regions.

In quantitative genetics the relationship between genetic and phenotypic variation is investigated. The identification of these variants can bring improvements to selective breeding, allow for transgenic techniques to be applied in agricultural settings and assess the risk of polygenic diseases. To locate these variants, a linkage-­‐based quantitative trait locus (QTL) approach can be applied. In this thesis, a chicken intercross population between wild and domestic birds have been used for QTL mapping of phenotypes such as comb, body and brain size, bone density and anxiety behaviour. Gene expression QTL (eQTL) mapping was also done for tissues such as comb base, medullar bone, liver and brain. By overlapping eQTL and QTL, regions were identified associated with both the gene expression levels and the phenotypes simultaneously. In this way, a number of candidate genes, underlying variation in the above-­‐mentioned phenotypes, were identified. Additionally, DNA methylation QTL (mQTL) mapping was done in the brain and the methylation landscape was assessed which indicated a decrease in methylation in the domestic breed. A small number of regions were identified which affected DNA methylation levels throughout the whole genome, so-­‐called trans hotspots. Finally, DNA methylation levels were correlated with eQTL to assess the degree to which gene expression is affected by methylation, and with gene expression in general to assess the relationship between the transcriptome and methylome. Taken together, these studies link the differences observed in various phenotypes between two populations of chicken to genetic variants coupled with gene expression correlations suggesting candidate genes. DNA methylation levels were influential in regulating variation in gene expression, both positively and negatively, but gene expression was also influential in regulating the methylation level. Epi-­‐alleles were identified which indicated genetic variants regulating methylation levels and gene expression levels either as the causal variant or in close linkage.