Comprehensive co-expression analysis reveals candidate regulatory genes associated with carcass and meat quality traits in Neijiang and Large White pigs

Objective: The Neijiang indigenous pig breed of China and the Western Large White pig breed have unique meat quality and carcass characteristics. However, the genetic factors and mechanisms influencing their distinct meat and carcass traits are still not well understood. Therefore, using weighted gene co-expression network analysis (WGCNA), this study aimed to identify key genes influencing these traits. Methods: Transcriptome data from 17 Neijiang and 22 Large White pigs, along with their carcass weight, backfat thickness, eye muscle area, meat color, and muscle pH phenotypic data, were analyzed using WGCNA. A total of 9,249 genes were used to construct a weighted gene co-expression network. Results: Twenty-two co-expression gene modules were identified. Genes in the top modules were enriched in processes relevant to carcass and meat quality, such as protein transport. Further analysis identified six key genes, including HSPH1, HSPA4, DNAJA4, MRPL3, SEC63, and SRP54, for the Neijiang breed. Also, five key genes, consisting of EP300, SETD2, NIPBL, NAT10, and VCP, were identified for the Large White population. These genes were involved in biological processes related to mitochondrial function, protein targeting, chromatin organization, and morphogenesis. Conclusion: The findings from this study elucidate the regulatory mechanisms influencing the carcass and meat characteristics of the Neijiang and Large White pigs. The key genes could serve as potential biomarkers for enhancing breeding strategies aimed at improving pork quality.