Identifying key pathways and genes in the progression of wooden breast across multiple broiler lines using weighted gene co-expression network analysis

1. Wooden breast (WB) is a common muscle abnormality in the pectoralis major (PM) muscle of broilers that results in significant economic losses for the poultry industry, although its incidence varies in different broiler lines. However, there are few reports on the genes and pathways involved in WB using RNA-seq or microarray data across multiple lines.2. The current study obtained three datasets (GSE127806, GSE144000 and GSE79276) from different broiler lines in the Gene Expression Omnibus (GEO) database. Weighted gene co-expression network analysis (WGCNA) was then performed using GSE127806 and GSE144000 datasets and identified consensus modules significantly correlated with WB (p ≤ 0.05). Preservation analysis showed that one consensus module was strongly preserved (Zsummary < 2), and two others were moderately preserved (2 < Zsummary < 10) in the GSE79276 dataset.3. Functional enrichment analysis revealed seven key genes (FN1, SPP1, CD44, TNC, BAK1, TNFRSF1A and CTSK) related to WB were significantly enriched in the extracellular matrix (ECM)-receptor interaction pathway and in the apoptosis pathway in one consensus module. The genes ACO2, MDH2 and SUCLG1 were significantly enriched in the tricarboxylic acid cycle (TCA) cycle pathway. From the protein-protein interaction analysis, hub genes linked to WB were identified. Seven of these genes are known to participate in muscle contraction (TNNI1, TNNT1, TNNT2, TNNT3, TPM3, TMOD3 and TMOD4) and three others in the TCA cycle (ACO2, MDH2 and SUCLG1).4. This study identified key genes and pathways associated with WB, deepening the understanding of the mechanism by which fibrosis (mediated by genes such as FN1) influences WB. It further revealed the important role of the TCA cycle and apoptosis in the pathogenesis of WB.