The objective of this study was to investigate, both empirically and deterministically, the ability to explain genetic variation resulting from a copy number polymorphism (CNP) by including the CNP, either by its genotype or by a continuous derivation thereof, alone or together with a nearby single nucleotide polymorphism (SNP) in the model. This continuous measure of a CNP genotype could be a raw hybridization measurement, or a predicted CNP genotype. Results from simulations showed that the linkage disequilibrium (LD) between an SNP and CNP was lower than LD between two SNPs, due to the higher mutation rate at the CNP loci. The model R2 values from analysing the simulated data were very similar to the R2 values predicted with the deterministic formulae. Under the assumption that x copies at a CNP locus lead to the effect of x times the effect of 1 copy, including a continuous measure of a CNP locus in the model together with the genotype of a nearby SNP increased power to explain variation at the CNP locus, even when the continuous measure explained only 15% of the variation at the CNP locus.

Mapping quantitative trait loci (QTL) within commercial populations circumvents the need to verify segregation of QTL detected under experimental crosses. Variance component (VC) mapping combines information from all relationships within a pedigree to provide a breeding value for the animal and QTL with immediate potential for marker assisted selection. Variance components are estimated by modelling the covariance structure between relatives sharing alleles identical by descent (IBD). Commercial poultry data and simulation will be used as a model to explore how VC methodology behaves under varying population structures. Data is available from the Cobb Vantress broiler population to evaluate extensions to the additive QTL model. Computer simulation will be used to test models including additive, dominance, epistatic and imprinting effects over a range of pedigree structures including family sizes and number of generations.

This study investigated whether quantitative trait loci (QTL) identified in experimental crosses of chickens provide a short cut to the identification of QTL in commercial populations. A commercial population of broilers was targeted for chromosomal regions in which QTL for traits associated with meat production have previously been detected in extreme crosses. A three-generation design, consisting of 15 grandsires, 608 half-sib hens and over 15000 third-generation offspring, was implemented within the existing breeding scheme of a broiler breeding company. The first two generations were typed for 52 microsatellite markers spanning regions of nine chicken chromosomes and covering a total of 730 cM, approximately one-fifth of the chicken genome. Using half-sib analyses with a multiple QTL model, linkage was studied between these regions and 17 growth and carcass traits. Out of 153 trait×region comparisons, 53 QTL exceeded the threshold for genome-wide significance while an additional 23 QTL were significant at the nominal 1% level. Many of the QTL affect the carcass proportions and feed intake, for which there are few published studies. Given intensive selection for efficient growth in broilers for more than 50 generations it is surprising that many QTL affecting these traits are still segregating. Future fine-mapping efforts could elucidate whether ancestral mutations are still segregating as a result of pleiotropic effects on fitness traits or whether this variation is due to new mutations.

A statistical analysis strategy for the detection of quantitative trait loci (QTLs) in half-sib populations is outlined. The initial exploratory analysis is a multiple regression of the trait score on a subset of markers to allow a rapid identification of possible chromosomal regions of interest. This is followed by multiple marker interval mapping with regression methods within and across families fitting one or two QTLs. Empirical thresholds are determined by experiment-wise permutation tests for different significance levels and empirical confidence intervals for the QTLs' positions are obtained by bootstrapping methods. For traits with evidence for a significant single-QTL effect, an approximate maximum likelihood analysis is performed to obtain estimates of QTL effect and the probability of the QTL genotype for each parent of a group of half-sibs. The strategy is demonstrated in an analysis of previously published data on chromosome 6 and five production traits from a granddaughter design in dairy cattle. The results confirm and extend evidence for QTLs affecting protein percentage. Informativeness of markers limited the possibility of mapping more than one QTL on the same linkage group.

Several empirical studies suggest that exposure in vivo and response prevention have a differential treatment effect on the complaints presented by patients with Obsessive-Compulsive Disorder (OCD). In the present study it was hypothesized that exposure in vivo would result in a greater decrease of obsessional fear, whereas response prevention would result in a greater decrease of rituals. Forty patients, diagnosed with OCD, participated in the study. Half of the patients received exposure in vivo alone, followed by response prevention alone, and half received response prevention alone, followed by exposure in vivo alone. No differential treatment effects between exposure in vivo alone and response prevention alone could be found, although ritualistic behaviour was less strongly affected by exposure in vivo following response prevention.