Differences in loin tenderness of Iberian pigs explained through dissimilarities in their transcriptome expression profile

Tenderness is one of the most important meat quality traits and it can be measured through shear force with Warner-Bratzler test. In the current study, we use RNA-seq technique to analyse the transcriptome of Longissimus dorsi (LD) muscle in two groups of Iberian pigs (Tough and Tender) divergent for shear force breeding values. We identified 200 annotated differentially expressed genes (DEGs) and 245 newly predicted isoforms. The RNAseq expression results of 10 genes were validated with qPCR. Functional analyses showed an enrichment of DE genes in biological processes related with proteolysis (CTSC, RHOD, MYH8, ACTC1, GADD45B, CASQ2, CHRNA9 and ANKRD1), skeletal muscle tissue development (ANKRD1, DMD, FOS and MSTN), lipid metabolism (FABP3 and PPARGC1A) and collagen metabolism (COL14A1). The upstream analysis revealed a total of 11 transcription regulatory factors that could regulate the expression of some DEGs. Among them, IGF1, VGLL3 and PPARG can be highlighted since they regulate the expression of genes involved in biological pathways that could affect tenderness. The experiment revealed a set of candidate genes and regulatory factors suggestive to search polymorphisms that could be incorporated in a breeding program for improving meat tenderness. Twelve Iberian individuals with divergent breeding values for tenderness were selected (six per group), samples of Longissimus dorsi were collected after the slaughter, RNA from these samples was extracted, pair-end libraries were constructed