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

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.

Figure 1

Heatmap representing associations between modules and traits (Module-trait relationships). Traits are reported on the x-axis, and modules are reported on the y-axis. The heatmap is color-coded by correlation values: green color represents a negative correlation, while red color represents a positive correlation. In the figure, “M” stands for Marinated meat, “NM” for Not Marinated, “MP” for Myofibrillar Protein, and “SP” for Sarcoplasmic protein. The complete explanation of the traits on the x-axis is reported in Zambonelli et al..

Figure 2

Macro-module functional network. This image shows the most significant functional categories identified by ClueGO Cytoscape plugin and how terms are grouped and interact with each other. Different groups of functional terms are distinguished from different colors. Terms that belong to two different groups have both colors of annotation groups to which they belong. The name in bold indicates the leading group term, according to the highest significance related to Benjamini-Hochberg.

Figure 3

Top 10 hub genes in the macro-module identified by CytoHubba Cytoscape plugin. Genes with the highest number of connections in the network are detected as hub genes. The image shows the degree of importance of hubs through a color scale ranging from red (the most important) to yellow (less important).

Figure 4

Subnetwork of hub genes extracted from CytoHubba. The figure shows the interconnections between hub genes and other genes in the macro-module.

Figure 5

Flowchart of the performed analysis. The scheme shows the steps of the gene network construction, identification of traits and modules of interest and analysis of the data obtained by WGCNA.