Gene coexpression network analysis reveals the genes and pathways in pectoralis major muscle and liver associated with wooden breast in broilers.

Wooden breast (WB) is a myopathy mainly affecting pectoralis major (PM) muscle in modern commercial broiler chickens, causing enormous economic losses in the poultry industry. Recent studies have observed hepatic and PM muscle injury in broilers affected by WB, but the relationships between WB and the 2 tissues are mostly unclear. In the current study, the RNA-seq raw data of PM muscle and liver were downloaded from GSE144000, and we constructed the gene coexpression networks of PM muscle and liver to explore the relationships between WB and the 2 tissues using the weighted gene coexpression network analysis (WGCNA) method. Six and 2 gene coexpression modules were significantly correlated with WB in the PM muscle and liver networks, respectively. TGF-beta signaling, Toll-like receptor signaling and mTOR signaling pathways were significantly enriched in the genes within the 6 gene modules of PM muscle network. Meanwhile, mTOR signaling pathway was significantly enriched in the genes within the 2 gene modules of liver network. In the consensus gene coexpression network across the 2 tissues, salmon module (r = -0.5 and p = 0.05) was significantly negatively correlated with WB, in which Toll-like receptor signaling, apoptosis, and autophagy pathways were significantly enriched. The genes related with the 3 pathways, myeloid differentiation primary response 88 (MYD88), interferon regulatory factor 7 (IRF7), mitogen-activated protein kinase 14 (MAPK14), FBJ murine osteosarcoma viral oncogene homolog (FOS), jun proto-oncogene (JUN), caspase-10, unc-51 like autophagy activating kinase 2 (ULK2) and serine/threonine kinase 11 (LKB1), were identified in salmon module. In this current study, we found that the signaling pathways related with cell inflammation, apoptosis and autophagy might influence WB across 2 tissues in broilers.