Gene expression patterns associated with processing yield of marinated breast meat in broilers affected by white striping and wooden breast defects

White striping (WS) and wooden breast (WB) severely affect the technological properties of chicken meat. Several studies investigated their effects on both marinated and nonmarinated meat, showing a reduction in marination uptake and retention of the affected fillets. In the present study, we performed a weighted gene co-expression network analysis (WGCNA) to exploit relationships between genes and the reduced processing yields in marinated meat affected by WS and WB. The analysis was performed using the microarray profiles and phenotypic evaluations referring to the marination process (uptake %; cook losses %; and overall processing yield %) of 12 broiler Pectoralis major muscles (6 normal vs. 6 affected by both WS/WB). In particular, a parallelepiped meat cut (8×4×2 cm) weighing about 60 g was excised from the middle part of each fillet and individually labeled and tumbled with a 20% (wt/wt) sodium chloride (6%) and sodium tripolyphosphate (1.8%) marinade solution, and subsequently cooked in a water bath at 80°C for 25 min. Marinade uptake, cook losses and processing yield (calculated as ratio between weights of raw meat before tumbling and after cooking) were calculated for each sample. WGCNA identified 212 clusters of co-expressed genes (i.e., modules) associated with the phenotype “processing yield” (P<.0001). Among them, the modules most significantly correlated (r>|0.8|; P<.0001) with this phenotype were selected for further analyses: darkgreen, khaki4, and midnightblue. Functional analyses were carried out using both DAVID tool and ClueGO Cytoscape plug-in to explore the biological function of selected modules. DAVID analysis identified terms related to the spliceosome and extracellular exosome (P=.07). ClueGO analysis evidenced terms related to oxidative phosphorylation; proteoglycan metabolic process; fatty acid oxidation; and targeted protein degradation (P<.05). Also, hub genes were identified as those with the highest gene significance (GS) and module membership (MM) values (>|0.8|). Genes encoding a specific type of fibroblast growth factor (FGF16), myosin (MYO18B), and collagen (COL12A1), as well as genes related to obesity in humans (PPP1CB and GPD1L) were found as hubs. In conclusion, our results evidenced that gene expression patterns significantly related to the variability of processing yield of marinated meat affected and not affected by WB/WS mainly resemble molecular pathways related to the onset and progression of these defects.