The physiological drivers of commercial broiler chicken performance uncovered with transcriptomics analyses and a novel pathway activation method.

Factors contributing to sub-optimal animal performance are often subtle and difficult to identify. This proof-of-concept study generated transcriptomics profiles from chickens' jejunum and liver tissues to understand differences among broiler flocks with varying final growth performance. Two pathway analysis methods were used and compared, including an enrichment method (Gene Set Enrichment Analysis, GSEA) and a topology-based, Quantitative Pathway Activation method (QPA, Biofractal, Portugal). Straight run Ross-708 broilers were selected from four different farms within a commercial broiler integration that differed in historic FCR at 28 days of age. Farms were retrospectively assigned to a performance category (High Performing (HP) n = 2 or Low Performing (LP) n = 2) according to performance at the end of the cycle (63 d). Final FCR were 1.901 and 1.914 for the HP farms and 1.923 and 1.951 for the LP farms. Final BW were 4,246 and 4,309 g/bird for the HP farms and 4,096 and 4,188 g/bird for the LP farms. Birds from HP farms had lower crypt depth (270 µm vs 381 µm) and greater villi length to crypt depth ratio (3.95 vs 2.69) than LP farms (P < 0.05). The GSEA and QPA analyses showed that LP birds had activation of immune function and inhibition of nutrient metabolism in the jejunum and liver compared to birds from HP farms. QPA results suggested a relatively lower nutritional state in the LP birds compared to HP birds including inhibited energy, lipid, and amino acid metabolism in the liver, and inhibited digestion and absorption processes in the jejunum. Both the GSEA and QPA data suggested that LP birds were exposed to cellular stress. Whilst GSEA recorded this stress as pathways related to heat stress, the QPA method detected hypoxia and oxidative stress as sources of cellular stress that were directly associated with reduced final BW in LP birds. In conclusion, transcriptomics data from commercial broiler farms demonstrated potential to provide in-depth insights into the health and nutrition of broiler chickens. Quantitative pathway activation methods and improved functional annotation of biochemical pathways demonstrated high potential for field applications such as detection of limitations for performance and evaluating the effectiveness of nutritional interventions.