Abstract
We have used a RNA-seq approach to investigate differential expression in the skeletal muscle of swine (N = 52) with divergent lipid profiles i.e. HIGH (increased intramuscular fat and muscle saturated and monounsaturated fatty acid contents, higher serum lipid concentrations and fatness) and LOW pigs (leaner and with an increased muscle polyunsaturated fatty acid content). The number of mRNAs and non-coding RNAs (ncRNAs) expressed in the porcine gluteus medius muscle were 18,104 and 1,558, respectively. At the nominal level of significance (P-value ≤ 0.05), we detected 1,430 mRNA and 12 non-coding RNA (ncRNA) transcripts as differentially expressed (DE) in the gluteus medius muscle of HIGH vs LOW pigs. This smaller contribution of ncRNAs to differential expression may have biological and technical reasons. We performed a second analysis, that was more stringent (P-value ≤ 0.01 and fold-change ≥ 1.5), and only 96 and 0 mRNA-and ncRNA-encoding genes happened to be DE, respectively. The subset of DE mRNA genes was enriched in pathways related with lipid (lipogenesis and triacylglycerol degradation) and glucose metabolism. Moreover, HIGH pigs showed a more lipogenic profile than their LOW counterparts.
Highlights
Ensembl ID ENSSSCG00000005648 ENSSSCG00000027946 ENSSSCG00000017232 ENSSSCG00000005935 ENSSSCG00000003379 ENSSSCG00000011740 ENSSSCG00000001931 ENSSSCG00000011444 ENSSSCG00000007574 ENSSSCG00000007745 ENSSSCG00000000293 ENSSSCG00000007133 ENSSSCG00000028814 ENSSSCG00000006277 ENSSSCG00000007554 ENSSSCG00000003105 ENSSSCG00000010529 ENSSSCG00000006245 ENSSSCG00000013579 ENSSSCG00000008232 ENSSSCG00000030165
76 of these 1,430 mRNA-encoding genes were identified as differentially expressed (DE) by Cánovas et al.[7] when they compared the gene expression of HIGH and LOW pigs retrieved from the same population employed by us (Supplementary Figure 1, Supplementary Table S2)
By comparing the mRNA expression of HIGH and LOW pigs by RNA-seq, we have identified 96 loci displaying differential expression (P-value ≤ 0.01 and FC ≥ 1.5)
Summary
Ensembl ID ENSSSCG00000005648 ENSSSCG00000027946 ENSSSCG00000017232 ENSSSCG00000005935 ENSSSCG00000003379 ENSSSCG00000011740 ENSSSCG00000001931 ENSSSCG00000011444 ENSSSCG00000007574 ENSSSCG00000007745 ENSSSCG00000000293 ENSSSCG00000007133 ENSSSCG00000028814 ENSSSCG00000006277 ENSSSCG00000007554 ENSSSCG00000003105 ENSSSCG00000010529 ENSSSCG00000006245 ENSSSCG00000013579 ENSSSCG00000008232 ENSSSCG00000030165. Our goal was to determine the relative contributions of protein-coding and non-coding RNAs to differential expression in the skeletal muscle of pigs with distinct lipid profiles
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