Genetical genomics: combining gene expression with marker genotypes in poultry

Microarrays have been widely implemented across the life sciences, although there is still debate on the most effective uses of such transcriptomics approaches. In genetical genomics, gene expression measurements are treated as quantitative traits, and genome regions affecting expression levels are denoted as expression QTL (eQTL). The detected eQTL can represent a locus that lies close to the gene that is being controlled (cis-acting) or one or more loci that are unlinked to the gene that is being controlled (trans-acting). One powerful outcome of genetical genomics is the reconstruction of genetic pathways underlying complex trait variation. Because of the modest size of experiments to date, genetical genomics may fall short of its promise to unravel genetic networks. We propose to combine expression studies with fine mapping of functional trait loci. This synergistic approach facilitates the implementation of genetical genomics for species without inbred resources but is equally applicable to model species. Among livestock species, poultry is well placed to embrace this technology with the availability of the chicken genome sequence, microarrays for various platforms, as well as experimental populations in which QTL have been mapped. In the buildup toward full-blown eQTL studies, we can study the effects of known candidate genes or marked QTL at the gene expression level in more focused studies. To demonstrate the potential of genetical genomics, we have identified the cis and trans effects for a functional BW QTL on chicken chromosome 4 in breast tissue samples from chickens with contrasting QTL genotypes.