Whole transcriptome analysis of the porcine muscle tissue of breeds differing in muscularity and meat quality traits

In pigs, an intense research have been performed in order to select genetic markers, which could be associated with important production traits and may be included in breeding program. The aim of the present study was to compare the whole gene expression profile of semimembranosus muscle from three pig breeds differing in muscularity, fatness traits and meat quality. The RNA-seq analysis was performed on 16 animals: Pietrain (5), Polish Landrace - PL (4) and Pulawska pigs (7). The transcriptome sequencing of muscle tissue (m. semimembranosus) was carried out on HiScanSQ System (Illumina) with 50 single-end cycles. The validation of obtained results and exact estimation of transcript abundance was performed by real-time PCR method. The present study showed the differential expression of 229 genes between Pulawska and PL pigs, and 87 between Pulawska and Pietrain (p <= 0.05). The Pulawska breed was characterized by significantly higher expression of only 9 and 43 genes compared to Pietrain and PL pigs, respectively. Accordingly to functional annotation of DEGs, several novel genes were proposed which were involved with processes such as purine and pirymidine biosynthesis, cell cycle, protein transport and metabolism. These genes may be potentially responsible for muscle cell growth and development. On the other hand, the up-regulation of genes involved in immune processes, observed in native Pulawska pigs, may be related with a very good resistance to diseases of this breed. The different expression profile of selected genes may illustrate the effect of long-term selection to improve the meat content in carcasses conducted on pigs. (C) 2015 Elsevier B.V. All rights reserved.