Effect of rearing systems and dietary protein levels on the skeletal muscle histomorphology and transcriptome profiles in indigenous Krškopolje PigVrecl, Milka (Avtor) Škrlep, Martin (Avtor) Poklukar Žnidaršič, Klavdija (Avtor) Fazarinc, Gregor (Avtor) Štrbenc, Malan (Avtor) Čandek-Potokar, Marjeta (Avtor) RNA sequencespigsadipose tissuehigh throughput sequencingRNAtranscriptome profilesgene expressionlocel breedshybrid breedsdatadata setRNA-sequencing was performed to compare the effects of production systems (conventional indoor, vs. outdoor) and diets (standard protein, HP, vs. low protein, LP) within each rearing system on the transcriptomic profiles of two skeletal muscles, longissimus thoracis et lumborum (LL) and semispinalis capitis (SSC). Differentially expressed genes (DEGs) were identified with |log2FC| > 1 and q-value < 0.005. The effect of rearing system (indoor vs. outdoor) resulted in 354 DEGs in LL and 334 DEGs in SSC. The effect of diet within individual rearing system was less pronounced. In LL, HP vs. LP resulted in 23 DEGs under indoor and none under outdoor rearing system. In SSC, HP vs. LP resulted in 28 DEGs under indoor and 30 DEGs under outdoor rearing system. Pathway enrichment analysis revealed 42 pathways significantly enriched for HP vs. LP in the outdoor rearing system (across both muscles); additionally, 11 pathways were altered specifically in SSC for HP vs. LP under indoor rearing system, and 27 pathways were altered specifically in LL for HP vs. LP under outdoor rearing systemGene Expression Omnibus (GEO)20262026-03-20 08:34:59Neznano28453sl