|Abstract:||A single nucleotide polymorphism in insulin-like growth factor 2 (IGF2 intron3-G3072A) is associated with greater muscle mass and decreased subcutaneous fat deposition in pigs carrying a paternal copy of the A allele (Apat). While many studies have focused on the differences in between the gross phenotypes of these animals, relatively little has been done to understand how these animals differ at the molecular level. It was the objective of this study to compare the molecular phenotypes of animals carrying the Apat allele and those carrying the Gpat allele in order to gain insight into how those differences may result in the differences seen at the whole-animal level. RNA was extracted from longissimus (LM) samples taken from six animals of each genotype (Apat and Gpat) at four different time points, fetal day 90 (d90), birth (0d), weaning (21d), and market weight (176d). In total 46 samples were sequenced on the Illumina HiSeq 2000 with a target depth of 20 million reads per sample. Analysis of the RNA-seq data using tweeDEseq determined differentially expressed genes between Apat and Gpat pigs at each time point. Additionally, IPA analysis was used to determine if there were any differentially activated pathways between the two phenotypes. IGF2 was not found to be upregulated in Apat pigs compared to Gpat at d90 or 0d; however, IGF2 expression was found to be increased in Apat pigs compared to Gpat pigs at 21d and 176d. Though there was not differential expression of IGF2 at d90 and 0d, there was still differential expression of several other genes at these time points. At d90, Apat pigs tended to have an increase in the expression anti-apoptotic genes and a decrease in pro-apoptotic genes, possibly indicating enhanced myoblast survival, while Gpat pigs had greater expression of genes associated with protein synthesis. At 0d, there was an increased expression of genes associated with proliferation and protein synthesis in Apat pigs, and Gpat pigs appeared to have upregulation of genes involved in inflammation. At both 0d and 21d Apat and Gpat pigs had displayed upregulation of markers of myogenesis, suggesting different stages of muscle development. At 176d, Apat animals had decreased expression of genes involved in adipose signaling, including inflammation, stress, and autophagy and greater expression of genes associated with tissue development and the cell cycle. Thus, throughout the developmental timepoints, there appear to be markedly different processes taking place in the muscle tissue of Apat pigs and Gpat pigs.