A genomic variant in IRF9 is associated with serum cytokine levels in pig

The interferon regulatory factor 9 (IRF9) gene is a member of the IRF family and has been shown to play functionally diverse roles in the regulation of the immune system. Previous study revealed the IRF9 gene resides within the reported quantitative trait locus (QTLs) for cytokine levels. The aims of this study were to identify genomic variants in IRF9 and to test the association between the variants and cytokine levels in pig. A synonymous single-nucleotide polymorphism (c.459A > G) was identified in exon 4 of the IRF9 gene. Association analysis in 300 piglets (Landrace, n = 68; large white, n = 158; and Songliao black, n = 74) showed that this variant was significantly associated with the level of interferon (IFN)-gamma and the ratio of IFN-gamma to IL-10 in serum (P < 0.05). Relative quantification of messenger RNA (mRNA) revealed that spleen had the highest expression level and individuals with genotype AA had higher expression than those with genotype AG. Transfection-based mRNA stability assay analysis further showed that the mutant allele G could reduce the RNA stability of IRF9. These findings suggest that the SNP (c.459A > G) could be a causative mutation for the association between IRF9 and the serum cytokine levels in swine.