Transcriptomics pathway analysis with cellular signaling pathways as a key tool to improve marbling in beef cattle

Red meat is as an important dietary source that provides part of the nutritional requirements such as proteins, minerals, B-complex vitamins and essential fatty acids. Intramuscular fat is located throughout skeletal muscles. It is responsible for the marbling seen in certain cuts of beef. Marbling is a trait of major economic relevance that positively influences sensory quality aspects, including flavor, juiciness and tenderness of meat. the objective of this study was to identify cellular signaling pathways regulating muscle marbling in beef cattle using microarray gene expression data.Materials & Methods publicly available preprocessed transcriptomics data (E-GEOD-46411) from a study by Sadkowski et al [1] was used. They measured gene expression in skeletal muscle of well-marbled beef and lean-marbled beef using Agilent microarrays. The data quality was evaluated using ArrayAnalysis [2]. All arrays passed quality control and were analyzed further. pathway analysis on differentially regulated genes was performed with the pathway visualization and analysis tool, PathVisio [3], a free open-source pathway analysis tool.Results and Discussion The regulation of marbling is possibly the result of interaction of signaling pathways in muscle, fat and intramuscular connective tissue [4], identifying these processes with pathway analysis can help to decipher the key marbling processes. Pathway analysis revealed 17 pathways that showed differences in expression (z-score > 1.96) between well-marbled and lean marbled beef (Table 1). MAPK ((WP998) and P38 MAPK (WP1037) signaling, two pathways well known two affect lipid metabolism, were enriched in the well marbling breed (fig, 1). In addition, the signaling pathways Hypertrophy Model , microRNAs in cardio myocyte hypertrophy and Physiological and pathological hypertrophy of the heart that play a role in tissue development were affected. Interestingly, the analyses also demonstrated that pathways related to immune response (IL signaling, TCR signaling and Toll-like receptor signaling pathways) and insulin signaling, mitochondrial gene expression and Vitamin D metabolism were enriched and might act together with pathways related to lipid metabolism.