Differential expression of mRNA isoforms in the skeletal muscle of pigs with distinct growth and fatness profiles

Tainã Figueiredo Cardoso,Raquel Quintanilla,Rayner González-Prendes,Ángela Cánovas,Anna Castelló,Marcel Amills

doi:10.1186/s12864-018-4515-2

Abstract

BackgroundThe identification of genes differentially expressed in the skeletal muscle of pigs displaying distinct growth and fatness profiles might contribute to identify the genetic factors that influence the phenotypic variation of such traits. So far, the majority of porcine transcriptomic studies have investigated differences in gene expression at a global scale rather than at the mRNA isoform level. In the current work, we have investigated the differential expression of mRNA isoforms in the gluteus medius (GM) muscle of 52 Duroc HIGH (increased backfat thickness, intramuscular fat and saturated and monounsaturated fatty acids contents) and LOW pigs (opposite phenotype, with an increased polyunsaturated fatty acids content).ResultsOur analysis revealed that 10.9% of genes expressed in the GM muscle generate alternative mRNA isoforms, with an average of 2.9 transcripts per gene. By using two different pipelines, one based on the CLC Genomics Workbench and another one on the STAR, RSEM and DESeq2 softwares, we have identified 10 mRNA isoforms that both pipelines categorize as differentially expressed in HIGH vs LOW pigs (P-value < 0.01 and ±0.6 log2fold-change). Only five mRNA isoforms, produced by the ITGA5, SEMA4D, LITAF, TIMP1 and ANXA2 genes, remain significant after correction for multiple testing (q-value < 0.05 and ±0.6 log2fold-change), being upregulated in HIGH pigs.ConclusionsThe increased levels of specific ITGA5, LITAF, TIMP1 and ANXA2 mRNA isoforms in HIGH pigs is consistent with reports indicating that the overexpression of these four genes is associated with obesity and metabolic disorders in humans. A broader knowledge about the functional attributes of these mRNA variants would be fundamental to elucidate the consequences of transcript diversity on the determinism of porcine phenotypes of economic interest.

Highlights

The identification of genes differentially expressed in the skeletal muscle of pigs displaying distinct growth and fatness profiles might contribute to identify the genetic factors that influence the phenotypic variation of such traits
In the CLC Bio analysis, we found evidence of the existence of alternative transcripts in 2066 genes (11.7% of protein-coding genes expressed in the gluteus medius (GM) muscle of HIGH and LOW swine) which produced 5835 messenger ribonucleic acid (mRNA) isoforms (2.8 transcripts per gene)
We have demonstrated that around 10.9% of genes expressed in the porcine skeletal muscle produce alternative transcripts, generating an average of 2.9 different mRNA isoforms per gene

Summary

Introduction

The identification of genes differentially expressed in the skeletal muscle of pigs displaying distinct growth and fatness profiles might contribute to identify the genetic factors that influence the phenotypic variation of such traits. In White Duroc × Erhualian F2 intercross pigs, a mutation in a splice acceptor site of intron 9 (g.8283C > A) of the porcine phosphorylase kinase catalytic subunit gamma 1 (PHKG1) gene has been shown to drive the synthesis of an aberrant transcript subjected to nonsense-mediated decay [7] This results in the inactivation of this enzyme, which plays a key role in the degradation of glycogen, and in the production of a low quality meat with a poor water-holding capacity [7]. Koltes et al [8], identified a mutation located in the pig guanylate binding protein 5 (GBP5) gene that introduces a new splice acceptor site that results in the insertion of five additional nucleotides, altering the open reading frame and introducing a premature stop-codon This mutation has a major effect on the host response to the porcine respiratory and reproductive syndrome virus [8]

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