Domestication is one of the best models of evolution available, eliciting a range of behavioural, morphological and life history changes both in traits under selection and in other, correlated, traits. However, it remains unclear whether the same genes underpin the changes seen across different traits. Though there is some evidence for pleiotropic effects (where one gene has effects on multiple traits) from artificial selection experiments, these have yet to identify any of the loci involved. Using a large F2 intercross between White Leghorn layers and wild red junglefowl chickens in a marker-dense Quantitative Trait Loci (QTL) mapping experiment, we identified 41 significant (genome wide P<0.05) and 46 suggestive (P<0.2) QTL for a variety of behavioural (for example, fear avoidance behaviour), morphological (body weight, bone density measures, comb size) and life history (fecundity) phenotypes. The behavioural tests in this instance were specifically related to fear avoidance, and comprised of a tonic immobility test, latency to approach a novel object, a restraint test (to measure anxiety) and an open field test. Of the QTL found, 59 were found in 7 'hotspots', with 27 of these QTL statistically indistinguishable from pleiotropy (i.e. either in pleiotropy or close linkage). Therefore these regions consist of a pleiotropic or tightly linked 'core' surrounded by a set of more loosely linked loci. Evolutionarily, this indicates that genetic variation in domesticated animals may be due to linked groups of genes (potentially with a pleiotropic core), rather than a few genes that affect numerous traits. The findings offer possible explanations for how selection for a particular trait during domestication (for example, low fearfulness) can simultaneously cause cascades of phenotypical effects on unselected traits. This knowledge could also be of profound importance in breeding and selection programs, especially those trying to select specific characteristics and exclude others.