Despite intense selection there is evidence to suggest that there is still much variation that might be exploited within commercial populations [1, 2]. The effectiveness of selection procedures utilising genomic information can be increased by correctly identifying the mode of inheritance of desired variants. For example, Hayes and Miller  show that including dominance effects in mate selection can be a powerful tool for exploiting previously untapped genetic variation while Dekkers and Chakraborty  discuss maximization of crossbred performance by incorporating information from overdominant QTL.
Historically, much of the success in commercial poultry breeding and many other agricultural species has relied on utilizing heterosis and reciprocal effects [5–8], yet the underlying genetic architecture is still not clear. It appears that both maternal effects and dominant or over-dominant genes play a role . Tuiskula-Haavisto and Vilkki  suggest that there is also recent evidence for the role of parentally imprinted mechanisms in poultry to explain the underlying mechanism for reciprocal effects.
Despite increasing evidence for parent of origin effects in crosses between divergent lines of poultry, imprinting in poultry remains a contentious issue.
Genomic imprinting affects many mammalian genes  and is brought about by epigenetic instructions or imprints that are laid down in the parental germ cells . Imprinting is most prevalent in foetal development and until recently was considered best described by the parental conflict hypothesis . In viviparous animals this occurs where the male exerts selection pressure for offspring to maximise use of maternal resources whereas the female limits this allocation of resources to preserve herself and future offspring. As there is no apparent parental conflict, the presence of imprinting was not thought to occur in oviparous species. Furthermore, IGF2 has been shown to be imprinted and expressed from paternal allele in man rabbit, mice, pig, and sheep [14, 15], but not in the chicken . There is, however, recent evidence for imprinted genes in birds and lower vertebrates and for shared orthologues with mammalian imprinted genes [17, 18]. Different species may also have species specific imprinted genes . Current theory suggests that the evolution of imprinted genes is a dynamic step-wise process with orthologues present on separate chromosomes before imprinting arose. These conserved orthologues were selected during vertebrate evolution becoming imprinted only as the need arose [18, 20]. Lawton et al.,  show that transcriptional silencing at imprinted loci has evolved along independent trajectories in mammals and marsupials. Imprinted genes are characteristically found in a clustered organization with 80% physically linked with other imprinted genes. These clusters are conserved in mammals, marsupials and flowering plants. . Studies reporting QTL with parent of origin effects in chicken show a similar pattern tending to cluster on a few macrochromosomes with 78% of imprinted gene orthologues residing on chicken chromosomes 1, 3, and 5 [10, 18].
Both dominant and imprinted QTL effects have been identified in poultry for economically important production and disease resistance traits. Ikeobi et al.,  found that 1/3 of QTL found for fat related traits in a broiler-layer cross showed dominance effects; Yonash et al.,  found both partial and overdominance QTL effects for resistance to Marek's disease, while Kerje et al.,  and Tuiskula-Haavisto et al.,  report dominant effects for egg production traits. Parent of origin effects in poultry are reviewed by Tuiskula-Haavisto et al.,  and have been found for bodyweight, carcass and egg production traits [26–28].
All of these studies have involved crosses between lines or divergent populations, reviewed by Hocking  and Abasht et al.,. Detection of QTL effects, however, within model organisms or experimental populations is costly and potentially of limited relevance to populations under selection. It is of much greater benefit to directly explore QTL segregating within commercial populations. A variance component or pedigree based approach can be applied to map QTL directly within the population under selection and by simple extension of genetic models can potentially also be used to dissect the mode of inheritance at the QTL. Here we use a variance component approach to look for dominant and imprinted QTL associated with bodyweight and conformation score measured at 40 days in a two-generation commercial broiler population.