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Background  Supplementing farm animals diet with functional ingredients may improve the nutritional quality of meat products. Diet composition has been also demonstrated to influence the gene expression with effect on biological processes and pathways. However, the knowledge on the effect of nutrients at the molecular level is scant. In particular, studies on the effects of antioxidants and polyphenols dietary supplementation have been investigated mainly in rodents, and only scarcely in farm animals so far. RNA-Seq with next-generation sequencing is increasingly the method of choice for studying changes in the transcriptome and it has been recently employed also in pig nutrigenomics studies to identify diet-induced changes in gene expression. The present study aimed to investigate the effect of diets enriched with functional ingredients (linseed, vitamin E and plant extracts) on the transcriptome of pig  Longissimus thoracis  to elucidate the role of these compounds in influencing genes involved in muscle physiology and metabolism compared to a standard diet.    Results  Eight hundred ninety-three significant differentially expressed genes (DEGs) (FDR adjusted  P- value ≤ 0.05) were detected by RNA-Seq analysis in the three diet comparisons (D2-D1, D3-D1, D4-D1). The functional analysis of DEGs showed that the diet enriched with  n -3 PUFA from linseed (D2) mostly downregulated genes in pathways and biological processes (BPs) related to muscle development, contraction, and glycogen metabolism compared to the standard diet. The diet supplemented with linseed and vitamin E/Selenium (D3) showed to mostly downregulate genes linked to oxidative phosphorylation. Only few genes involved in extracellular matrix (ECM) organization were upregulated by the D3. Finally, the comparison D4-D1 showed that the diet supplemented with linseed and plant extracts (D4) upregulated the majority of genes compared to D1 that were involved in a complex network of pathways and BPs all connected by hub genes. In particular,  IGF2  was a hub gene connecting protein metabolism, ECM organization, immune system and lipid biosynthesis pathways.    Conclusion  The supplementation of pig diet with  n -3 PUFA from linseed, antioxidants and plant-derived polyphenols can influence the expression of a relevant number of genes in  Longissimus thoracis  muscle that are involved in a variety of biochemical pathways linked to muscle function and metabolism.    Electronic supplementary material  The online version of this article (10.1186/s40104-018-0297-2) contains supplementary material, which is available to authorized users.

journal of animal science and biotechnology/journal of animal science and biotechnology

Effect of diets supplemented with linseed alone or combined with vitamin E and selenium or with plant extracts, on Longissimus thoracis transcriptome in growing-finishing Italian Large White pigs