Polymorphism and promoter methylation-regulated mRNA expression of IFI6 gene affect meat quality in pigs

Abstract

This study examined the association, promoter methylation of Interferon alpha-inducible protein 6 (IFI6) gene, and their effects on mRNA expression and meat quality traits in pig. Muscle samples (n=300) were randomly collected from the Longissimus thoracis et lumborum (LTL) to determine meat quality traits including drip loss, thawing loss, cooking loss, meat pH [at 45 minutes (pH45min) and at 24 hours (pH24h) post-mortem], shear force (for tenderness), and lightness (L*) in pigs. Genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Muscle samples (5 per group) with divergent meat pH (low vs high) were selected for promoter methylation study using bisulfate and pyrosequencing. Muscle samples from animals (5 per group) with divergent phenotypes (low vs high meat pH and low vs high drip loss) were used for mRNA expression study by quantitative real-time polymerase chain reaction (qRT-PCR). Results showed that a polymorphism in IFI6 gene (g.370A>G) was significantly (P < 0.01) associated with meat pH24h. Furthermore, four CpG regions were identified in IFI6 promoter, of which DNA methylation in a CG site was higher in low meat pH24h group compared to high meat pH24h group (P < 0.05). The mRNA expression of IFI6 gene was significantly (P < 0.01) downregulated in low meat pH24h group than high meat pH24h group. This result postulated that high DNA methylation at CG site in the promoter region might downregulate the IFI6 gene expression, hence lower the muscle pH that might lead to higher drip loss and lower tenderness. Therefore, porcine IFI6 gene might be a potential candidate gene for meat quality trait in pig. Nevertheless, further research is needed to confirm the role of IFI6 gene in controlling meat quality traits in other commercial populations.

HIGHLIGHTS

• This study analysed association of a SNP in IFI6 gene with meat quality traits, and promotor methylation and transcriptome expression of IFI6 gene in relation to meat pH.

• The result suggested that polymorphism affects meat pH.

• The high DNA methylation at a specific CG site in the IFI6 promoter is involved in IFI6 gene downregulation in low meat pH.

Keywords:

• IFI6
• SNP
• methylation
• expression
• meat pH

Ethical approval

The meat samples in this study were taken from a local meat supplier, which did not need contact with animals. This study did not involve any invasive procedure on animals; therefore, ethical approval was not required.

Disclosure statement

No potential conflict of interest relevant to this article is reported.

Data availability statement

The data presented in this study are available on request from the corresponding author upon reasonable request.

Additional information

Funding

This work was financially supported by the Office of the Ministry of Higher Education, Science, Research and Innovation; and the Thailand Science Research and Innovation through the Kasetsart University Reinventing University Program 2021 (grant no RUP2.2/Con-CASAF PD 08) and The Thailand Research Fund (grant no MRG 5680077).