RNA-Seq Study on the Longissimus thoracis Muscle of Italian Large White Pigs Fed Extruded Linseed with or without Antioxidants and Polyphenols

Abstract

The addition of n-3 polyunsaturated fatty acids (n-3 PUFAs) to the swine diet increases their content in muscle cells, and the additional supplementation of antioxidants promotes their oxidative stability. However, to date, the functionality of these components within muscle tissue is not well understood. Using a published RNA-seq dataset and a selective workflow, the study aimed to find the differences in gene expression and investigate how differentially expressed genes (DEGs) were implicated in the cellular composition and metabolism of muscle tissue of 48 Italian Large White pigs under different dietary conditions. A functional enrichment analysis of DEGs, using Cytoscape, revealed that the diet enriched with extruded linseed and supplemented with vitamin E and selenium promoted a more rapid and massive immune system response because the overall function of muscle tissue was improved, while those enriched with extruded linseed and supplemented with grape skin and oregano extracts promoted the presence and oxidative stability of n-3 PUFAs, increasing the anti-inflammatory potential of the muscular tissue.

Keywords: antioxidant; methodological approach for RNA-seq data analysis; polyphenols; polyunsaturated fatty acid (PUFA); selenium; swine; transcriptome; vitamin E.

Figure 1

Cytoscape Gene networks achieved with stringApp for the DEGs obtained comparing D1 vs. D3 diets on the left (a) and D1 vs. D4 diets on the right (b). Over-expressed genes were colored in shades of blue, from the lightest (least over-expressed) to the darkest (most over-expressed). Down-expressed genes were colored in shades of red, from the lightest, least under-expressed to the darkest, most under-expressed. The genes indicated with a gray ellipse are additional interactor genes selected by Cytoscape.