Transcriptomic analysis gains insights into the gene expression profiles of broiler breast muscles affected by growth-related myopathies

Growth-related myopathies remain a worldwide concern in terms of fast-growing chicken welfare, meat quality, and sustainability. As part of a bigger project aimed at deepening the knowledge about the wooden breast (WB) underpinning biological mechanisms, this study represents a first step focused on a new characterization of the transcriptomic profiles of myopathic breasts collected from male fast-growing broilers (45-d-old; 3.2 kg) at a commercial processing plant in 2024. In detail, 180 breast fillets (90/group) were classified according to their macroscopic appearance as affected by severe WB or not affected (normal; N), and their classification was validated through multivariate analysis of meat quality data (i.e., pHu, color, WHC, and shear force). Among the collected muscles, 10 samples/group were used for total RNA extraction and sequencing. Raw-reads quality control, trimming, alignment to the reference genome, and read counting were performed on the High-Performance Computing platform provided by ELIXIR-IIB HPC@CINECA. After raw-reads processing, a differential analysis was performed (q-value<0.01 and log2 fold change>|1.5|). A total of 193 differentially expressed genes (DEGs) were identified, with 174 being up-regulated and 19 down-regulated in WB samples. Among those, PTX3, a key regulator of inflammation and modulator of extracellular matrix deposition and angiogenesis, has been found as the top up-regulated gene in WB. Also, genes encoding for striated muscle function and contraction (e.g., LMOD2 and MYH15), growth factor activity (e.g., MDK), stress response (e.g., CRH), and extracellular matrix remodeling (e.g., MMP9) were some of the top up- and down-regulated genes. To gain insights into the functional annotation of DEGs, Gene Ontology (GO) and KEGG pathway enrichment analyses were performed. GO analysis identified terms related to muscle contractions and neuromuscular transmissions (e.g., “sarcomere”, “contractile muscle fiber”, and “neuron projection”). Also, “Phagosome”, “ECM-receptor interaction”, and “PPAR signaling pathway” were found as significant KEGG pathways. In conclusion, despite years of efforts to mitigate growth-related myopathies, our results largely highlighted persisting alterations in terms of muscular and neuromuscular functions in WB-affected breast muscles, suggesting the persistence of still unknown triggering factors underlying the observed gene expression patterns. Further investigations comparing past and recent transcriptomic profiles may help identify fundamental biological alterations associated with the WB condition. Research supported by NextGenerationEU, National Grant PRIN2022 (Prot. n. 2022EPWEPW).