Gene expression profiling of longissimus dorsi and adipose tissue in pigs with differing post-weaning growth rate

Abstract Text: Weaning transition is a stressful event in the pig’s life. While most pigs recover rapidly from this stressor, a portion of the population lags behind their contemporaries in growth performance. The underlying biological and molecular mechanisms involved in post-weaning differences in growth performance are poorly understood. The objective of this experiment was to use transcriptional profiling of skeletal muscle and adipose tissue to develop an understanding of the possible metabolic basis for poor weaned-pig transition. A total of 1,054 pigs were reared in commercial conditions and weighed at birth, weaning, and 3 weeks post-weaning. Transition ADG (tADG) was calculated as the average daily gain for the 3-week period post-weaning. Nine pigs from the lowest 10^th percentile (low tADG) and the 60^th-70^th percentile (high tADG) were harvested at 3 weeks post-weaning. Total RNA was extracted from longissimus dorsi muscle (LM) and subcutaneous adipose tissue and transcriptional profiles of both tissues were developed using RNAseq. Statistical analysis of RNAseq read counts were performed using the QuasiSeq package in R. The model included the effects of tADG, parity, and birth weight. The Storey-Tibshirani method was used to correct for multiple testing and to calculate a q-value estimating false discovery rate. In LM, 622 genes were differentially expressed (317 with higher expression in low tADG and 305 with higher expression in high tADG pigs; q ≤ 0.10, fold change ≥ 1.2). There were no differentially expressed transcripts in adipose tissue. To identify biological functions potentially underlying the effects of tADG on skeletal muscle metabolism and physiology, functional annotation analysis of the differentially expressed genes was conducted using DAVID analytic tools. Genes with higher expression in low tADG LM produced 3 enriched clusters of biological function terms including protein catabolic processes, ubiquitin-dependent protein catabolism, and regulation of translational initiation (enrichment score ≥ 1.3; P < 0.05). Genes with higher expression in LM of high tADG pigs produced 6 significant annotation clusters related to muscle contraction, the glycolysis pathway, cytoskeleton organization, muscle development, and blood vessel development (enrichment score ≥ 1.3; P< 0.05). These results indicate a shift to decreased protein synthesis, increased protein degradation, and reduced glucose metabolism in the LM of low tADG. Many of the gene expression differences between poor transitioning pigs and their contemporaries may be related to low availability of energy and amino acids in low tADG pigs.

Keywords: post-weaning growth, RNAseq, pig