Transcriptome analysis of mRNA and miRNA in skeletal muscle indicates an important network for differential Residual Feed Intake in pigs

Abstract

Feed efficiency (FE) can be measured by feed conversion ratio (FCR) or residual feed intake (RFI). In this study, we measured the FE related phenotypes of 236 castrated purebred Yorkshire boars, and selected 10 extreme individuals with high and low RFI for transcriptome analysis. We used RNA-seq analyses to determine the differential expression of genes and miRNAs in skeletal muscle. There were 99 differentially expressed genes identified (q ≤ 0.05). The down-regulated genes were mainly involved in mitochondrial energy metabolism, including FABP3, RCAN, PPARGC1 (PGC-1A), HK2 and PRKAG2. The up-regulated genes were mainly involved in skeletal muscle differentiation and proliferation, including IGF2, PDE7A, CEBPD, PIK3R1 and MYH6. Moreover, 15 differentially expressed miRNAs (|log2FC| ≥ 1, total reads count ≥ 20, p ≤ 0.05) were identified. Among them, miR-136, miR-30e-5p, miR-1, miR-208b, miR-199a, miR-101 and miR-29c were up-regulated, while miR-215, miR-365-5p, miR-486, miR-1271, miR-145, miR-99b, miR-191 and miR-10b were down-regulated in low RFI pigs. We conclude that decreasing mitochondrial energy metabolism, possibly through AMPK - PGC-1A pathways, and increasing muscle growth, through IGF-1/2 and TGF-β signaling pathways, are potential strategies for the improvement of FE in pigs (and possibly other livestock). This study provides new insights into the molecular mechanisms that determine RFI and FE in pigs.

Figure 1. Validation of differentially expressed genes in LD muscles from high and low RFI pigs.

(a) qPCR results for IGF2, FABP3, RCAN, PRKAG2 and PPARGC1I genes, analyzed by the ∆∆Ct method. * significant difference between RFI_H and RFI_L pigs. (b) The log₂FC expression levels of mitochondrial DNA encoded genes. (c) qPCR results for mir1, mir30e, mir10b and mir145, analyzed by the ∆∆Ct method. * * significant difference between RFI_H and RFI_L pigs.

Figure 2. Heat map and Cluster patterns of the differentially expressed miRNAs and target gene related pathways.

Heat map of miRNAs versus pathways, miRNAs are clustered together by exhibiting similar pathway targeting patterns, and pathways are clustered together by related miRNAs. As porcine genes were not included in the current version of DIANA miRPath, prediction was performed using human miRNAs.

Figure 3. The key network of genes and miRNAs found to be differentially expressed in skeletal muscle from low RFI compared with high RFI pigs.

The network diagram was made using Cytoscape.