Global gene expression profile after Salmonella enterica Serovar enteritidis challenge in two F8 advanced intercross chicken lines

A chicken 13K cDNA microarray was used to profile global gene expression after Salmonella enteritidis (SE) challenge of young chickens. Two F8 advanced intercross lines (AIL), broiler by Leghorn, and broiler by Fayoumi, were studied. Day-old chicks were orally inoculated with SE, and spleens were harvested at day 7 or 8 post-inoculation. The SE bacteria burden in the spleen was quantified. The 20% high and 20% low SE burden birds within each AIL and harvest time were studied by microarray. The loop design was used for pair-comparison between high and low SE burden challenged birds and unchallenged birds, within each AIL and harvest time. The signal intensity of each gene was globally normalized and expressed on the natural log scale. A mixed model including line, treatment, time, array (random effect), dye, and all two-way interactions among treatment, time, and line was used to identify differentially expressed candidate genes at the 1% significance level. The results suggest that genetics, time, and interaction between genetics and time play important roles in gene regulation of SE infection and colonization in chickens. The differentially expressed genes identified in the current study are candidates for detailed hypothesis-driven investigation of genes determining resistance to SE in chickens.