Identification of Meat Quality Determining Marker Genes in Fibroblasts of Bovine Muscle Using Transcriptomic Profiling

In the present study, we comparatively analyzed the transcriptomic profiling of fibroblasts derived from two different muscles, biceps femoris and longissimus dorsi with significant difference in the meat quality and tenderness. EBSeq algorithm was applied to analyze the data, and genes were considered to be significantly differentially expressed if the false discovery rate value was <0.05, the P value was <0.01, and the fold change was >0.585. The results revealed that 253 genes were differentially expressed genes (DEGs) (170 genes were upregulated, and 83 were downregulated) and more than 100 DEGs were probably associated with intramuscular fat deposition, tenderness, and toughness, which are driving the meat quality and were involved in biological processes such as collagen synthesis, cell differentiation, and muscle tissue and fiber development; molecular functions such as chemokine activity and collagen activity; cellular components such as cytoplasm and myofibril; and pathways such as collagen signaling and metabolic pathways. A gene-act network and a co-expression network revealed the close relationship between intramuscular fat deposition and meat tenderness. The expressions of 20 DEGs were validated by real-time PCR, and the results suggested that the DEGs are correlated with RNA-seq data and play crucial roles in muscle growth, development processes, toughness, and tenderness of the meat. Together, the genome-wide transcriptome analysis revealed that various genes are responsible for toughness and tenderness variance in the difference muscles of beef.