Transcriptome profiles of skeletal muscle in krškopolje and modern hybrid pigs

RNA sequencing was performed to compare two pig breeds (the Slovenian Krškopolje breed and a modern commercial breed) and to evaluate the effect of breed specific dietary protein reduction on the transcriptomic profiles of two skeletal muscles: longissimus thoracis et lumborum (LD) and semispinalis capitis (SSC). Differentially expressed genes (DEGs) were identified using the criteria |log2FC| > 1 and q value < 0.005. The effect of dietary protein reduction was minimal in both breeds and muscles, with only small numbers of DEGs detected. In Krškopolje pigs receiving medium protein (MP) or low protein (LP) diets, no DEGs were identified. In contrast, in the modern breed, 10 DEGs were detected when comparing the high protein (HP) with the MP diet group. A similar pattern was observed in SSC, where 19 DEGs were detected in Krškopolje pigs (MP vs. LP) and 16 DEGs in the modern breed (HP vs. LP). In comparison, when the LD and SSC transcriptome profiles of the modern breed were compared with those of the Krškopolje breed, the number of DEGs was substantially higher:149 in LD and 201 in SSC. The DEGs in LD of modern breed reflect a shift toward faster growing, more glycolytic muscle with distinct immune and neuromuscular regulation. Likewise, the SSC of modern breed shows stronger activation of growth related and metabolic signaling pathways.