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.