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. 2019 Feb 20;14(2):e0212449.
doi: 10.1371/journal.pone.0212449. eCollection 2019.

Functional analysis finds differences on the muscle transcriptome of pigs fed an n-3 PUFA-enriched diet with or without antioxidant supplementations

Marika Vitali  1 , Rubina Sirri  1 , Martina Zappaterra  2 , Paolo Zambonelli  1   2 , Giulia Giannini  2 , Domenico Pietro Lo Fiego  3   4 , Roberta Davoli  1   2
Affiliations

Functional analysis finds differences on the muscle transcriptome of pigs fed an n-3 PUFA-enriched diet with or without antioxidant supplementations

Marika Vitali et al. PLoS One. .

Abstract

Supplementing pig diets with n-3 polyunsaturated fatty acids (n-3 PUFA) may produce meat products with an increased n-3 fatty acid content, and the combined antioxidants addition could prevent lipid oxidation in the feed. However, to date, the effects of these bioactive compounds at the molecular level in porcine skeletal muscle are mostly unknown. This study aimed to analyse changes in the Longissimus thoracis transcriptome of 35 pigs fed three diets supplemented with: linseed (L); linseed, vitamin E and Selenium (LES) or linseed and plant-derived polyphenols (LPE). Pigs were reared from 80.8 ± 5.6 kg to 151.8 ± 9.9 kg. After slaughter, RNA-Seq was performed and 1182 differentially expressed genes (DEGs) were submitted to functional analysis. The L vs LES comparison did not show differences, while L vs LPE showed 1102 DEGs and LES vs LPE 80 DEGs. LPE compared to the other groups showed the highest number of up-regulated genes involved in preserving muscle metabolism and structure. Results enlighten that the combined supplementation of bioactive lipids (n-3 PUFA from linseed) with plant extracts as a source of polyphenols increases, compared to the only addition of linseed, the expression of genes involved in mRNA metabolic processes and transcriptional regulation, glucose uptake and, finally, in supporting muscle development and physiology. These results improve the knowledge of the biological effect of bioactive compounds in Longissimus thoracis muscle, and sustain the growing interest over their use in pig production.

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Conflict of interest statement

In order to disclose any potential competing interest, I declare that I am part of the Editorial Board of PLOS ONE journal. The other authors declare that they have no competing interests. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

Figures

Fig 1
Fig 1
Venn diagram showing the distribution of DEGs in the three diet comparisons before (a) and after (b) the Log2FC cut-off application.
Fig 2
Fig 2. Cytoscape functional analysis of L vs LPE comparison.
squares = pathways; circles = biological processes; shape size = according to the P-value of the term in its own group; red colour = up-regulated (cluster #1); green colour = down-regulated (cluster #2); grey colour = same number of up- and down-regulated genes (none specific cluster); font size = according to the P-value of the term in its own group; interaction line thickness = according to Kappa Score value, represents the strength of the interactions, lighter colour corresponds to a lower strength while darker colour to a higher strength.
Fig 3
Fig 3. Cytoscape functional analysis of L vs LPE comparison displaying hub DEGs.
Significant GO terms are graphically summarized using REVIGO. squares = pathways; circles = biological processes; shape size = according to the P-value of the term in its own group; red colour = up-regulated (cluster #1); green colour = down-regulated (cluster #2); grey colour = same number of up- and down-regulated genes (None specific cluster); fill colour transparency = according to the percentage of genes belonging to the term, lighter colour corresponds to a lower percentage while darker colour to a higher percentage; font size = according to the P-value of the term in its own group; interaction line thickness = according to Kappa Score value, represents the strength of the interactions, lighter colour corresponds to a lower strength while darker colour to a higher strength.
Fig 4
Fig 4. Cytoscape functional analysis of LES vs LPE comparison.
squares = pathways; circles = biological processes; shape size = according to the P-value of the term in its own group; red colour = up-regulated (cluster #1); green colour = down-regulated (cluster #2); grey colour = same number of up- and down-regulated genes (none specific cluster); font size = according to the P-value of the term in its own group; interaction line thickness = according to Kappa Score value, represents the strength of the interactions, lighter colour corresponds to a lower strength while darker colour to a higher strength.
Fig 5
Fig 5. Cytoscape functional analysis of LES vs LPE comparison displaying hub DEGs.
Significant GO terms are graphically summarized using REVIGO. squares = pathways; circles = biological processes; shape size = according to the P-value of the term in its own group; red colour = up-regulated (cluster #1); green colour = down-regulated (cluster #2); grey colour = same number of up- and down-regulated genes (None specific cluster); fill colour transparency = according to the percentage of genes belonging to the term, lighter colour corresponds to a lower percentage while darker colour to a higher percentage; font size = according to the P-value of the term in its own group; interaction line thickness = according to Kappa Score value, represents the strength of the interactions, lighter colour corresponds to a lower strength while darker colour to a higher strength.
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