To take advantage of programmes to identify candidate genes for variation in traits of economic importance, methods to test these genes in selected pedigree populations need to be developed. To this end we have carried out a study of association between candidate genes and reproductive traits in a pedigree line of broiler breeders. Gonadotropin releasing hormone (GnRH), its receptor (GnRHR), growth hormone receptor (GHR) and neuropeptide Y (NPY) were selected for their role in controlling aspects of reproduction. Genetic markers for NPY, GnRHR and GHR alleles were detected using bulk PCR-restriction fragment length polymorphism or BESS-T Scan (Epicentre Technologies). Genotyping of 772 hens from one generation was by PCR-restriction fragment length polymorphism. Total number of eggs, age at first egg (AFE) and number of double yolked eggs (DY) for each hen were recorded. Additive and dominance effects were fitted for the autosomal GnRHR and NPY genes; additive effects were fitted for the sex linked GHR gene. To control for some of the background genetic variation, candidate genes were assessed within heterozygous sire families. A dominance effect of NPY (14 sire families) on AFE and an additive effect of GnRHR (36 sire families) on DY, were found (P<0.02). If the latter effect were true, selection could increase overall flock performance by 0.13 usable eggs per hen. A simplified model, omitting sires, was also fitted. This analysis gave four significant associations (P<0.05), a surprisingly large number. In conclusion it is possible to detect association between economic traits and candidate genes in a population undergoing selection, and test if a candidate gene explains some of the trait variation. However, statistical associations between trait and genes require to be treated with caution and models should account for as many genetic and environmental variables as possible
