Bioinformatic Interpretation through Upstream and Functional Analysis of Global Gene Expression Associated with Feed Efficiency in Broiler

Feed efficiency (gain:feed) is an important genetic trait in commercial poultry and livestock breeding programs since feed represents 60 to 70% of the total cost in raising an animal to market weight. Within a single male line of broilers (meat type chickens) individually phenotyped for feed efficiency (FE), broiler males with low FE (LFE) have consistently exhibited higher protein oxidation that is likely due to higher mitochondrial ROS production compared to high FE (HFE) broilers. Thus, the gene expression in the LFE phenotype is the result of inherent gene expression that is modulated by mitochondrial ROS. Using upstream and functional analysis in a commercial on-line software program (Ingenuity Pathway Analysis) applied to cDNA microarray and shotgun proteomic analyses obtained on muscle tissue of HFE and LFE broiler phenotypes, we have identified proteins associated with antioxidant protection (SOD2) as well as inhibition of muscle damage and cell death along with genes associated with formation and development of muscle fibers or muscle cells. Results of these analyzes provide additional insight into phenotypic expression of feed efficiency in broilers.