Selection of pigs for increased meat production or improved meat quality changes muscle mass and muscle composition. This will be related to transcriptome expression profile changes in muscle tissue, generating inter-individual differences. This study investigated the differentially expressed genes in the transcriptome profiles of the longissimus muscle of 75 Large White–Duroc cross sows and castrates. The use of a common reference design enabled to investigate the inter-individual transcriptome expression profile differences between the animals as compared with the means of all animals. The aim of the study was to identify the biological processes related to these inter-individual differences. It was expected that these processes underlie the selection effects. In total, 908 transcripts were differentially expressed. Among them, 762 were mainly downregulated and 146 were mainly upregulated. Gene Ontology and Pathways analyses indicated that the differentially expressed genes belong to three groups of processes involved in protein synthesis and amino acid–protein metabolism, energy metabolism and muscle-specific structure and activity processes. Comparing the functional biological analysis results with previously reported data suggested that the protein synthesis, energy metabolism and muscle-specific structure would contribute to meat production and the meat quality.