Dataset Information

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-? 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.

SUBMITTER: Jing L

PROVIDER: S-EPMC4493709 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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

Jing Lu L Hou Ye Y Wu Hui H Miao Yuanxin Y Li Xinyun X Cao Jianhua J Brameld John Michael JM Parr Tim T Zhao Shuhong S

Scientific reports 20150707

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 ...[more]

PMID: 26150313

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Project description:To identify a proper strategy for future feed-efficient pig farming, it is required to evaluate the ongoing selection scenarios. Tools are lacking for the evaluation of pig selection scenarios in terms of environmental impacts to provide selection guidelines for a more sustainable pig production. Selection on residual feed intake (RFI) has been proposed to improve feed efficiency and potentially reduce the associated environmental impacts. The aim of this study was thus to develop a model to account for individual animal performance in life cycle assessment (LCA) methods to quantify the responses to selection. Experimental data were collected from the fifth generation of pig lines divergently selected for RFI (low line, more efficient pigs, LRFI; high line, less efficient pigs, HRFI). The average feed conversion ratio (FCR) and daily feed intake of LRFI pigs were 7% lower than the average of HRFI pigs (P < 0.0001). A parametric model was developed for LCA based on the dietary net energy fluxes in a pig system. A nutritional pig growth tool, InraPorc®, was included as a module in the model to embed flexibility for changes in feed composition, animal performance traits and housing conditions and to simulate individual pig performance. The comparative individual-based LCA showed that LRFI had an average of 7% lower environmental impacts per kilogram live pig at farm gate compared to HRFI (P < 0.0001) on climate change, acidification potential, freshwater eutrophication potential, land occupation and water depletion. High correlations between FCR and all environmental impact categories (>0.95) confirmed the importance of improvement in feed efficiency to reduce environmental impacts. Significant line differences in all impact categories and moderate correlations with impacts (>0.51) revealed that RFI is an effective measure to select for improved environmental impacts, despite lower correlations compared to FCR. Altogether more optimal criteria for efficient environment-friendly selection can then be expected through restructuring the selection indexes from an environmental point of view.

Project description:Microbes and microbial components potentially impact the performance of pigs through immune stimulation and altered metabolism. These immune modulating factors can include endotoxin from gram negative bacterial outer membrane component, commonly referred to as lipopolysaccharide (LPS). In this study, our objective was to examine the relationship between intestinal barrier integrity, endotoxin and inflammation with feed efficiency (FE), using pig lines divergently selected for residual feed intake (RFI) as a model. Twelve gilts (62 ± 3 kg BW) from the low RFI (LRFI, more efficient) and 12 from the high RFI (HRFI, less efficient) were used. Individual performance data was recorded for 5 wk. At the end of the experimental period, ADFI of LRFI pigs was less (P < 0.001), ADG not different between the 2 lines (P = 0.72) but the G:F of LRFI pigs was greater than for HRFI pigs (P = 0.019). Serum endotoxin concentration (P < 0.01) and the acute phase protein haptoglobin (P < 0.05) were greater in HRFI pigs. Transepithelial resistance of the ileum, transport of fluorescein isothiocyanate labeled-Dextran and-LPS in ileum and colon, as well as tight junction protein mRNA expression in ileum, did not differ between the lines, indicating the 2 lines did not differ in transport characteristics at the intestinal level. Ileum inflammatory markers, myeloperoxidase (P < 0.05) and IL-8 (P < 0.10), were found to be greater in HRFI pigs. Alkaline phosphatase (ALP) activity was significantly increased in the LRFI pigs in ileum and liver tissues and negatively correlated with blood endotoxin (P < 0.05). Lysozyme activity in the liver was not different between the lines; however, the LRFI pigs had a twofold greater lysozyme activity in ileum (P < 0.05). Despite the difference in their activity, ALP or lysozyme mRNA expression was not different between the lines in either tissue. Decreased endotoxin and inflammatory markers and the enhanced activities of antimicrobial enzymes in the LRFI line may not fully explain the difference in the FE between the lines, but they have the potential to prevent the growth potential in HRFI pigs. Further studies are needed to identify the other mechanisms that may contribute to the greater endotoxin and acute phase proteins in the HRFI pigs and the greater FE in the LRFI pigs.

Dataset Information

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

Publications

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

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