Discovering genetic biomarkers associated with disease resistance and enhanced immunity is critical to developing advanced strategies for controlling viral and bacterial infections in different species. Macrophages, important cells of innate immunity, are directly involved in cellular interactions with pathogens, the release of cytokines activating other immune cells and antigen presentation to cells of the adaptive immune response. IFNγ is a potent activator of macrophages and increased production has been associated with disease resistance in several species. This study characterizes the molecular basis for dramatically different nitric oxide production and immune function between the B2 and the B19 haplotype chicken macrophages.A large-scale RNA sequencing approach was employed to sequence the RNA of purified macrophages from each haplotype group (B2 vs. B19) during differentiation and after stimulation. Our results demonstrate that a large number of genes exhibit divergent expression between B2 and B19 haplotype cells both prior and after stimulation. These differences in gene expression appear to be regulated by complex epigenetic mechanisms that need further investigation.

Disease resistance and susceptibility has been associated with the major histocompatibility complex (MHC) in several species. This study aimed to better characterize the molecular basis for dramatically different nitric oxide production and associated immune function between the B2 and the B19 haplotype chicken macrophages in response to IFNγ stimulation, previously shown by our laboratory. A next generation RNA sequencing approach was employed to analyze gene expression from purified macrophages from each haplotype group (B2 vs. B19) across 9 time points spanning seven days. Ultimately, our data shows global dysregulation of gene expression in B19 haplotypes correlating with increased disease susceptibility of this haplotype. Our results demonstrate that transcription factors (TF) exhibit divergent expression between B2 and B19 haplotype cells both prior to and after stimulation. Our results also reveal that miRNAs exhibit divergent expression between B2 and B19 haplotype cells both, prior to, and after stimulation with IFNγ. In contrast to TFs, miRNAs can modulate gene product levels post-transcriptionally. We also identify ubiquitin-related enzymes and factors that exhibit divergent expression between B2 and B19 haplotype cells. Some of our results indicate that snoRNAs exhibit divergent expression between B2 and B19 haplotype cells, which is noteworthy because snoRNAs can modulate genes epigenetically. Taken together our results suggest that the global dysregulation of gene expression observed in B19 haplotypes can at least in part be attributed to differential epigenetic regulation.