Muscle Transcriptome Analysis Reveals Molecular Pathways Related to Oxidative Phosphorylation, Antioxidant Defense, Fatness and Growth in Mangalitsa and Moravka Pigs

Abstract

This work was aimed at evaluating loin transcriptome and metabolic pathway differences between the two main Serbian local pig breeds with divergent characteristics regarding muscle growth and fatness, as well as exploring nutrigenomic effects of tannin supplementation in Mangalitsa (MA) pigs. The study comprised 24 Mangalitsa and 10 Moravka (MO) males, which were kept under identical management conditions. Mangalitsa animals were divided in two nutritional groups (n = 12) receiving a standard (control) or tannin–supplemented diet (1.5%; MAT). Moravka pigs were fed the standard mixture. All animals were slaughtered at a similar age; 120 kg of average live weight (LW) and loin tissue was used for RNA-seq analysis. Results showed 306 differentially expressed genes (DEGs) according to breed, enriched in genes involved in growth, lipid metabolism, protein metabolism and muscle development, such as PDK4, FABP4, MYOD1 and STAT3, as well as a relevant number of genes involved in mitochondrial respiratory activity (MT-NDs, NDUFAs among others). Oxidative phosphorylation was the most significantly affected pathway, activated in Mangalitsa muscle, revealing the basis of a different muscle metabolism. Also, many other relevant pathways were affected by breed and involved in oxidative stress response, fat accumulation and development of skeletal muscle. Results also allowed the identification of potential regulators and causal networks such as those controlled by FLCN, PPARGC1A or PRKAB1 with relevant regulatory roles on DEGs involved in mitochondrial and lipid metabolism, or IL3 and TRAF2 potentially controlling DEGs involved in muscle development. The Tannin effect on transcriptome was small, with only 23 DEGs, but included interesting ones involved in lipid deposition such as PPARGC1B. The results indicate a significant effect of the breed on muscle tissue gene expression, affecting relevant biological pathways and allowing the identification of strong regulatory candidate genes to underlie the gene expression and phenotypic differences between the compared groups.

Changes in Biceps femoris Transcriptome along Growth in Iberian Pigs Fed Different Energy Sources and Comparative Analysis with Duroc Breed

“…In fact, this gene is considered to be a candidate gene for fattening traits, and its structural variation has been associated with IMF and muscle water content and other meat quality traits in pigs [ 103 ]. This gene was also found to be upregulated in the fatty Mangalitsa breed in a comparison between the muscle transcriptomes of Mangalitsa and Moravka pig breeds [ 104 ]. These results are concordant with the known high lipogenesis potential of fat pig breeds, such as the Iberian [ 1 , 105 ].…”

Hypothalamic transcriptome analysis reveals male-specific differences in molecular pathways related to oxidative phosphorylation between Iberian pig genotypes

“…RNA obtained from the 19 animals employed for RNA-seq was used to perform the technical validation of five genes affected by genotype and/or sex ( GRPEL2 , PDKZ1 , SGCA , TBCD and UQCRC2 ). The genes GAPDH and ACTB were selected for normalization after testing their stability with Genorm software (0.271 < M < 0.363) [ 37 ]. Additional information on the selected genes and amplification primers can be found in S2 Table .…”

“…Primers were designed using Primer Select Software (DNASTAR, Madison, WI, USA) from the available ENSEMBL sequences. Quantitave PCR (qPCR) was performed as previously described [ 37 ].…”

Genes Related to Fat Metabolism in Pigs and Intramuscular Fat Content of Pork: A Focus on Nutrigenetics and Nutrigenomics

“…Nutrigenetics and nutrigenomics are distinct fields providing a holistic approach in unravelling how nutrient intake affects the entire genome response and molecular mechanisms involved in fat deposition [ 18 , 19 , 20 ]. Nutrigenetics and nutrigenomics as fields of nutritional genomics research integrate computational systems biology (bioinformatics) with high-throughput functional genomic technologies (transcriptomics, proteomics, metabolomics and muscle biochemistry) in understanding how the cellular pathways and the entire genome respond to nutritional programming in farm animals [ 7 , 21 , 22 , 23 , 24 ].…”