Background: Intramuscular fat (IMF) enhances marbling, improving meat quality and value.
Transcriptome analysis enables the identification of genes and pathways involved in IMF
deposition, supporting targeted breeding and nutritional strategies to improve beef quality.
Methods: This study used RNA-Seq to compare gene expression in high- (Hereford; Her),
moderate- (Holstein Friesian; Hf), and low-marbling (Limousine; Lim) Semitendinosus
muscle. Using Illumina’s NovaSeqX Plus, sequencing data underwent quality control with
FastQC to remove low-quality reads and adapters, followed by alignment to the bovine
genome using HISAT2. Differential expression analysis was performed using DESeq2, and
genes were filtered based on a threshold of p-value < 0.05 and |log2FC| > 0.5 to identify
significantly regulated genes. Results: A total of 21,881 expressed genes were detected,
with 3025 and 7407 significantly differentially expressed in Her and Hf vs. Lim, respectively
(|log2FC| > 0.5, p < 0.05). Protein–protein interaction analysis revealed 20 hub genes,
including SMAD3, SCD, PLIN2, SHH, SQLE, RXRA, NPPA, NR1H4, PRKCA, and IL10.
Gene ontology and KEGG pathway analyses linked these genes to lipid metabolism and
IMF-associated pathways, such as PPAR signaling, fatty acid metabolism, and PI3K–Akt
signaling. Conclusions: These findings highlight RNA-Seq’s utility in uncovering the
genetic basis of marbling and the importance of aligning beef production with consumer
demands through genetic improvements. This study aimed to identify breed-independent
molecular mechanisms of intramuscular fat deposition and shared metabolic processes in
the Semitendinosus muscle to improve beef quality