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Background  The improvement of feed efficiency is a key economic goal within the pig production industry. The objective of this study was to examine transcriptomic differences in both the liver and muscle of pigs divergent for feed efficiency, thus improving our understanding of the molecular mechanisms influencing feed efficiency and enabling the identification of candidate biomarkers. Residual feed intake (RFI) was calculated for two populations of pigs from two different farms of origin/genotype. The 6 most efficient (LRFI) and 6 least efficient (HRFI) animals from each population were selected for further analysis of  Longissimus Dorsi  muscle ( n  = 22) and liver ( n  = 23). Transcriptomic data were generated from liver and muscle collected post-slaughter.    Results  The transcriptomic data segregated based on the RFI value of the pig rather than genotype/farm of origin. A total of 6463 genes were identified as being differentially expressed (DE) in muscle, while 964 genes were identified as being DE in liver. Genes that were commonly DE between muscle and liver ( n  = 526) were used for the multi-tissue analysis. These 526 genes were associated with  protein targeting to membrane ,  extracellular matrix organisation  and  immune function . In the muscle-only analysis, genes associated with  RNA processing ,  protein synthesis  and  energy metabolism  were down regulated in the LRFI animals while in the liver-only analysis, genes associated with  cell signalling  and  lipid homeostasis  were up regulated in the LRFI animals.    Conclusions  Differences in the transcriptome segregated on pig RFI value rather than the genotype/farm of origin. Multi-tissue analysis identified that genes associated with GO terms  protein targeting to membrane ,  extracellular matrix organisation  and a range of terms relating to immune function were over represented in the differentially expressed genes of both liver and muscle.    Electronic supplementary material  The online version of this article (10.1186/s12864-019-5740-z) contains supplementary material, which is available to authorized users.

A comparative analysis of the transcriptome profiles of liver and muscle tissue in pigs divergent for feed efficiency