SRA

RNA- sequencing was performed to compare the effect of male sex category, i.e. entire males (EM), surgical castrates (SC), and immunocastrates (IC) on differential gene expression in LD and SSC muscles. Extracted RNA from 6 randomly selected animals of each sex category and muscle were pooled together and used for library preparation and sequencing. A total of 71 and 36 differentially expressed genes (DEGs) were detected in LD and SSC, respectively (|log2(fold change) >1| and -log10(q-value) <0.005). In LD, 36 DEGs were detected between EM and IC. 29 DEGs were detected between EM and SC and only 6 DEGs were detected when comparing IC and SC. In SSC, the number of DEGs was lower compared to LD. Only 8 DEGs were detected when either EM and IC or EM and SC were compared. The number of DEGs between IC and SC was higher for SCC than for LD (20 vs. 6). In LD, downregulated genes predominated in EM compared to either IC or SC and were mainly associated with skeletal muscle tissue development, skeletal cell differentiation, and negative regulation of biological/cellular processes. When comparing IC and SC, predominantly upregulated genes were observed, and the enriched GO terms were related to various biological processes, including regulation of fibrinolysis, apoptosis, energy homeostasis, fatty acid oxidation, and behaviour. In SSC, significantly enriched GO terms were found only for predominantly upregulated genes in IC compared to SC and were related to the regulation of energy homeostasis and fatty acid oxidation, response to hormones/stimuli, and regulation of cellular ketone metabolic process. Overall design: Pigs originating from one slaughter batch (12 entire males (EM), 12 immunocastrated (IC) and 12 surgically castrated (SC) pigs) of the commercial Landrace x Pietrain crosses were used. Surgically castrated pigs were castrated within the first week of life, while immunocastrated pigs were vaccinated at the age of 12 and 21 weeks with a vaccine against GnRH (Improvac® vaccine, Zoetis). At the age of 26 weeks, animals were slaughtered and at the end of the slaughterline (45 min post mortem), approx. 1 cm3 muscle samples were taken from the central part of LD at the level of the last rib and from the SSC i.e., from the central part of its m. biventer cervicis, at the level of the 4th cervical vertebra. Muscles were sampled at the right side of the carcass, snap-frozen in liquid nitrogen and stored at –80°C until subsequent analysis