Weighted gene co-expression network analysis identifies molecular pathways and hub genes involved in broiler White Striping and Wooden Breast myopathies

Abstract

Abstract In recent years, the poultry industry has experienced an increased incidence of myopathies affecting breasts of fast-growing broilers, such as White Striping (WS) and Wooden Breast (WB) defects. To explore the molecular mechanisms and genes involved in WS and WB onset, we decided to perform a Weighted Gene Co-expression Network Analysis (WGCNA) using the gene expression profile and meat quality parameters of Pectoralis major muscles analysed in our previous study. Among the 212 modules identified by WGCNA, the red, darkred, midnightblue and paleturquoise4 modules were chosen for subsequent analysis. Functional analysis evidenced pathways involved in extracellular matrix (ECM) organization, collagen metabolism, cellular signaling and unfolded protein response. The hub gene analysis showed several genes coding for ECM components as the most interconnected nodes in the gene network (e.g. COL4A1, COL4A2, LAMA2, LAMA4, FBLN5 and FBN1). In this regard, this study suggests that alterations in ECM composition could somehow activate the cascade of biological reactions that result in the growth-related myopathies onset, and the involvement of Collagen IV alterations in activating the endoplasmic reticulum (ER) stress response may be hypothesized. Therefore, our findings provide further and innovative knowledge concerning the molecular mechanisms related to the breast abnormalities occurrence in modern broilers.