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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 L, Hou Y, Wu H, Miao Y, Li X, Cao J, Brameld JM, Parr T, Zhao S - Sci Rep (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, P. R. China.

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.

No MeSH data available.


Related in: MedlinePlus

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.
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f1: 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.

Mentions: To validate the differential expression of genes, eight genes were selected for qRT-PCR analysis. Compared with the RFI_H group, expression of FABP3, RCAN, PPARGC1, and PRKAG2 mRNA were all lower in RFI_L muscles, whereas expression of IGF2 mRNA was higher in RFI_L muscles (Fig. 1a). Expression of 4 of the selected genes (IGF2, RCAN, PPARGC1 and PRKAG2) showed significant differences between the RFI_H and RFI_L groups. Hence the qRT-PCR analyses largely confirmed the RNA-seq data, with the correlation coefficient of the fold-change (FC) values from the two methods being 0.99 and the R2 for the linear regression also being 0.99, indicating the reliability of the RNA-seq analysis.


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

Jing L, Hou Y, Wu H, Miao Y, Li X, Cao J, Brameld JM, Parr T, Zhao S - Sci Rep (2015)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4493709&req=5

f1: 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.
Mentions: To validate the differential expression of genes, eight genes were selected for qRT-PCR analysis. Compared with the RFI_H group, expression of FABP3, RCAN, PPARGC1, and PRKAG2 mRNA were all lower in RFI_L muscles, whereas expression of IGF2 mRNA was higher in RFI_L muscles (Fig. 1a). Expression of 4 of the selected genes (IGF2, RCAN, PPARGC1 and PRKAG2) showed significant differences between the RFI_H and RFI_L groups. Hence the qRT-PCR analyses largely confirmed the RNA-seq data, with the correlation coefficient of the fold-change (FC) values from the two methods being 0.99 and the R2 for the linear regression also being 0.99, indicating the reliability of the RNA-seq analysis.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, P. R. China.

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.

No MeSH data available.


Related in: MedlinePlus