The aim throughout this thesis has been to investigate the underlying genetics of behaviours and feather colour and plumage patterns by using chickens as a model organism. Chickens are extremely important as a food source, both in terms of egg, as well as meat production. As such there is a large research interest for them, and they provide an excellent model to study the effects of domestication and evolution, since the ancestor to our domestic breeds the Red Junglefowl can still be found living freely in the wild. This allows us to set up long term crossing experiments where we can harness the power of recombination events and genome wide sequencing to perform genome wide mapping studies. I also want to take the opportunity to integrate the results from all of my work and consider it in perspective of the domestication syndrome.

In Paper I we investigated the Social Reinstatement behaviour which combines aspects of sociality and anxiousness. We detected several QTL and some overlap with Open Field behaviour from previous work within the group. By combining genomic and transcriptomic methods three strong candidate genes were found: TTRAP, ACOT9 and PRDX4.

In Paper II Tonic Immobility, another classic behaviour was examined. Once more there was some overlap with the QTL regions discovered in earlier work, and it turns out that two of the most well supported candidate genes for Tonic Immobility is ACOT9 and PRDX4. These two genes had also been implicated with a pH dependent meat quality trait. Therefore, we conducted experiments in an additional smaller scale test cohort to investigate any potential link between the two traits. Following statistical multiple testing corrections, no significant association was found.

The remaining papers in the thesis investigated different types of feather patterning and colour. In Paper III we determined that the underlying genetic mechanism behind the striped appearance of the sex-linked barring feathers is likely caused by cyclic depletion and renewal of the pigment producing melanocyte cells during feather growth, which is a consequence of specific mutations in the gene CDKN2A.

Paper IV took a quantitative approach to colour by measuring and quantifying the pheomelanic colour ranging from dark red to yellow. We identified five main candidate genes for the intensity of red colouration, CREBBP, WDR24, ARL8A, PHLDA3 and LAD1. They are all regulated by a trans-acting eQTL located within the QTL region previously associated with behaviours in Paper I and Paper II.

Finally, in Paper V we turned our attention from pigment-based colour traits to an iridescent structural colour. Here we followed up the QTL mapping performed in our F8 lab intercross with a Genome Wide Association Study in two feral populations from the islands of Kauai and Bermuda. RNA-sequencing was then performed in selected individuals from both feral populations in addition to individuals from the F3 generation of our domestic x wild intercross. The main region of interest is located between 17.4 -17.5Mb on chromosome Z, with the main candidate genes being MAP3K1, Zinc finger RNA binding protein 2, and Zinc finger protein. After integrating and viewing the results from the work conducted as a part of this thesis from the perspective of the Domestication Syndrome, I have found that there are a lot of potential connections between the traits that I have studied. For instance, the same QTL region on chromosome 10 is detected in association with the behaviour traits in Paper I and Paper II and the quantitative colour trait in Paper IV. I believe that the domestication syndrome is caused by the underlying functional arrangement of the genome, which causes correlated responses in nearby genes and their associated traits, when selective forces such as domestication are applied on the primary trait.