Dissecting the Gene Expression Networks Associated with Variations in the Major Components of the Fatty Acid Semimembranosus Muscle Profile in Large White Heavy Pigs

Abstract

To date, high-throughput technology such as RNA-sequencing has been successfully applied in livestock sciences to investigate molecular networks involved in complex traits, such as meat quality. Pork quality depends on several organoleptic, technological, and nutritional characteristics, and it is also influenced by the fatty acid (FA) composition of intramuscular fat (IMF). To explore the molecular networks associated with different IMF FA compositions, the Semimembranosus muscle (SM) from two groups of Italian Large White (ILW) heavy pigs divergent for SM IMF content was investigated using transcriptome analysis. After alignment and normalization, the obtained gene counts were used to perform the Weighted Correlation Network Analysis (WGCNA package in R environment). Palmitic and palmitoleic contents showed association with the same gene modules, comprising genes significantly enriched in autophagy, mitochondrial fusion, and mitochondrial activity. Among the key genes related to these FAs, we found TEAD4, a gene regulating mitochondrial activity that seems to be a promising candidate for further studies. On the other hand, the genes comprised in the modules associated with the IMF contents of oleic, n-6, and n-3 polyunsaturated FAs (PUFAs) were significantly enriched in Mitogen-Activated Protein Kinase (MAPK) signaling, in agreement with previous studies suggesting that several MAPK players may have a primary role in regulating lipid deposition. These results give an insight into the molecular cascade associated with different IMF FA composition in ILW heavy pigs. Further studies are needed to validate the results and confirm whether some of the identified key genes may be effective candidates for pork quality.

Keywords: RNA sequencing; WGCNA; co-expression network; fat; intramuscular fat; mRNA; meat; muscle acidic composition; pork; swine.

Figure 1

The heatmap graphically displaying the correlations between the gene modules and the studied traits. The scale bar on the left shows the strength of the correlations: the darker the color, the stronger the correlation. Correlations in light colors are of small magnitude and not significant.

Figure 2

Functional enrichment analysis of the genes included in the modules significantly associated with palmitic and palmitoleic acids in pig Semimembranosus muscle. Different colors are used to highlight the significant Gene Ontology (GO) terms and the main genes entering in each GO term.

Figure 3

Functional enrichment analysis of the genes included in the modules significantly associated with oleic acid, n-6, and n-3 polyunsaturated fatty acids in pig Semimembranosus muscle. Different colors are used to highlight the significant Gene Ontology (GO) terms and the main genes entering in each GO term.