Identification of Key Modules and Hub Genes Involved in Regulating the Color of Chicken Breast Meat Using WGCNA

SIMPLE SUMMARY: To explore the gene networks and key genes involved in the regulation in meat color of chicken breast muscle, weighted gene co-expression network analysis (WGCNA) was performed based on transcriptome data from the pectoralis major muscle of two yellow feather chicken breeds. The results suggest that genes involved in the regulation of mitochondrial activity and lipid oxidation may play a crucial role in the formation of meat color. The present study advanced our understanding of the molecular mechanisms contributing to meat color and identified potential molecular markers for breeding chicken breast meat color. ABSTRACT: Meat color is one of the most important economic traits in chickens. However, the gene network and regulatory mechanisms contributing to meat color traits in chickens remain largely unknown. In the present study, we performed weighted gene co-expression network analysis (WGCNA) based on RNA-Seq datasets of 16 pectoralis major muscle samples from two yellow-feather chicken breeds to identify the modules and hub genes related to meat color in chickens. A total of 18,821 genes were used to construct the weighted gene co-expression network, and 29 co-expression gene modules were identified. Among these modules, five modules including blue, brown, steel blue, paleturquoise and orange modules were found to be significantly correlated with meat color traits. Furthermore, several genes within the association module involved in the regulation of mitochondrial activity (e.g., ATP5L, UQCR10 and COX7C) and lipid oxidation (e.g., CAV3, RBP4A and APOH) were identified as hub genes that may play a crucial role in the regulation of meat color. These results provide valuable information to improve our understanding of gene expression and regulation in relation to meat color traits and contribute to future molecular breeding for improving meat color in chickens.