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 quantitative trait loci or eQTL. The detected eQTL can either 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. 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 build-up towards full-blown eQTL studies, we present two approaches in which gene expression studies have been combined with QTL data: a) a study where a gene expression study between broilers and layers is used to explore positional candidate genes for a pair of epistatic QTL, b) a study of the effects of a marked QTL at the gene expression level. In the latter, we have identified a positional candidate gene for a functional body weight QTL on chicken chromosome 4 in breast tissue samples from chickens with contrasting QTL genotypes.