Gene expression analysis by RNA-sequencing of Longissimus dorsi muscle of pigs fed diets with differing lipid contents

We examined the effect of lipid content in the diet on the transcriptome of the Longissimus dorsi muscle in pigs. Our objective was to examine changes at the molecular level affecting economically relevant meat quality characteristics such as intramuscular fat deposition and fatty acid profile. The treatments consisted of isoproteic and isoenergetic diets with differing lipid contents due to addition of rice bran. The control diet (T0) was a normal basic diet and the test diet (T15) had 15% rice bran. The final lipid content (ether extract) in the diets was 3.4 and 4.8% in T0 and respectively. Three male piglets of the Uruguayan creole breed Pampa Rocha were used per treatment, which lasted from weaning at 42 days until 77 days of age. The animals were reared in confinement on deep bedding and were slaughtered at the end of the experiment, when muscle samples were collected. Intramuscular fat content (IMF) and fatty acid composition were analyzed to determine if diets had a phenotypic effect. Gene expression analysis was performed with RNA-seq methodology to carrying out a functional analysis of genes with differential expression between treatments. The added fat to the diet did not affect IMF or fatty acid composition. However, we identified 359 genes with differential expression between treatments. These genes participate in various metabolic pathways, some of them affecting meat quality. The most relevant genes identified in this regard were PDK4 (up-regulated with T15), which is associated with energy metabolism, FOS, ATF3, MYOD1 and MAFF (all downregulated with T15), which are associated with skeletal muscle growth, and TNC (up-regulated with T15), which is associated with extracellular matrix-receptor interactions. This study of the skeletal muscle transcriptome in pigs can help understand the genetic basis of how diet affects important production traits.