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

Lu Jing,Jianhua Cao,Yuanxin Miao,Xinyun Li,John Michael Brameld,Hui Wu,Ye Hou,Shuhong Zhao,Tim Parr

doi:10.1038/srep11953

Lu Jing, Jianhua Cao + Show 7 more

Open Access

https://doi.org/10.1038/srep11953

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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.

Highlights

Feed accounts for more than 60% of the costs for pig production, improving feed efficiency (FE) is one of the major ways to reduce costs in the pig industry
Two assessments of body fat, average back fat (ABF) thickness and intramuscular fat (IMF) content, showed no significant differences, suggesting that changes in residual feed intake (RFI) or feed conversion ratio (FCR) were not mediated by significant changes in body fat
We found that HK2 and Protein kinase, AMP-activated, gamma 2 non-catalytic subunit (PRKAG2), which is a member of AMPK gamma subunit family, were both down regulated in low RFI pigs

Summary

Introduction

Feed accounts for more than 60% of the costs for pig production, improving feed efficiency (FE) is one of the major ways to reduce costs in the pig industry. 10 SNPs identified using high-density SNP chip analysis[8] had significant association with FCR in a Duroc pig population, 2 of them were on SSC4 and the others were on SSC 14. 161 genes were differentially expressed between animals with high and low RFI. These genes were related with several gene networks, including cell growth and differentiation, lipid metabolism and carbohydrate metabolism[11]. One SNP of the stearoyl-CoA desaturase (SCD) gene, within a predicted target site for 2 miRNAs (ssc-miR-185 and ssc-miR-491), was significantly associated with daily body weight gain and FCR in cattle[15]. To our knowledge there are as yet no studies relating porcine FE and miRNA expression

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