Genetic analysis of traits associated with domestication in rainbow trout

Domestication is a complex process by which populations evolve in the presence of humans and in response to rearing in captivity. Several behavioral and physiological differences have been detected between wild and domesticated salmonid populations. In particular, reduced stress physiology has been documented in salmonids and other domesticated species. Negative impacts of chronic stress on growth, survival, and reproduction suggest that reduced responsiveness to stress may reflect an adaptation to captivity. Growth itself is an economically trait, under complex genetic and environment control, and is the focus of continued research. This dissertation examines the genetic factors underlying these two traits using rainbow trout clonal lines. In the analysis of stress physiology, stress hormone levels, in response to handling stress, were reduced in a heavily domesticated clonal line (Arlee) relative to another heavily domesticated line (OSU) and a less domestication line (Swanson). Analysis using doubled haploids derived from clonal lines with divergent stress responses (OSU and Arlee) revealed two QTL with opposing additive effects on stress cortisol levels, and no genetic link between stress physiology and growth rate in this cross. A more detailed analysis of juvenile growth was performed using doubled haploids derived from two clonal lines with divergent growth rates and domestication histories (OSU and Swanson). Body length, mass, and condition factor were measured at two time points (89 and 194 days postfertilization), and specific growth rate was calculated for the interval between these time points. Twenty-two QTL were detected in at least 14 locations on 11 linkage groups. Several QTL affecting different growth traits mapped to similar locations suggesting the presence of loci with pleiotropic effects or closely linked loci affecting different traits. The analysis also suggests possible genotype x environment and genotype x age interactions but this could not be reliably evaluated. Finally comparisons with QTL analyses of embryonic and adult growth in rainbow trout reveals that, in some case, the same linkage groups harbor QTL affecting growth at different levels. Our findings reveal that QTL analyses of traits associated with salmonid domestication can reveal complex genetic and environmental interactions.