Genomic organization and SNP identification of the porcine IRF6 gene
To characterize the genomic structure of the porcine IRF6 gene, the mRNA sequences of porcine IRF6 gene (GenBank Accession Number: AF327368) was used to search for porcine homologues with high throughput genomic sequences (HTGS) in the porcine genomic databases by BLAST (http://blast.ncbi.nlm.nih.gov) of NCBI GenBank database (http://www.ncbi.nlm.nih.gov/).
The porcine IRF6 gene consist of seven exons, using porcine genomic DNA, seven primer pairs were designed for PCR amplification of DNA sequences including all exon regions of the IRF6 gene (Table 1).
The porcine IRF6 cDNA is 2,203 bp in length (GenBank Accession Number: AF327368) and contains a 1,404 bp open reading frame (ORF) encoding a 467-amino acid polypeptide.
To determine tissue distribution of the porcine IRF6 gene, reverse transcription quantitative PCR (RT-PCR) was applied to nine different tissue samples.
Sequence comparisons of the same PCR fragment among three pig populations detected one SNP (HQ026023:1383 G>C) in exon7 and two SNPs (HQ026023:130 G>A; 232 C>T) in the 5 promoter region of the porcine IRF6 gene.
Association analysis of porcine IRF6 gene in three pig populations
On the other hand, the results of association analysis between SNPs and immune traits also showed that the SNP (HQ026023:1383 G>C) of IRF6 gene was significantly associated with the level of IFN-[gamma] (d 20) in serum (p = 0.038) and the ratio of IFN-[gamma] to IL10 (d 20) in serum (p = 0.041) (Table 4).
IRF6 plays an important role in initiating cellular interferon-stimulated gene-mediated antiviral responses and in the transforming growth factor-p signaling pathway.