Construction of a co-expression network affecting intramuscular fat content and meat color redness based on transcriptome analysis

Binbin Wang; Liming Hou; Wen Yang; Xiaoming Men; Keke Qi; Ziwei Xu; Wangjun Wu

doi:10.3389/fgene.2024.1351429

Construction of a co-expression network affecting intramuscular fat content and meat color redness based on transcriptome analysis

Front Genet. 2024 Feb 13:15:1351429. doi: 10.3389/fgene.2024.1351429. eCollection 2024.

Authors

Binbin Wang¹, Liming Hou², Wen Yang², Xiaoming Men¹, Keke Qi¹, Ziwei Xu¹, Wangjun Wu²

Affiliations

¹ Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
² College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.

Abstract

Introduction: Intramuscular fat content (IFC) and meat color are vital indicators of pork quality. Methods: A significant positive correlation between IFC and redness of meat color (CIE a* value) indicates that these two traits are likely to be regulated by shared molecular pathways.To identify candidate genes, hub genes, and signaling pathways that regulate these two traits, we measured the IFC and CIE a* value in 147 hybrid pigs, and selected individuls with extreme phenotypes for transcriptome analysis. Results: The results revealed 485 and 394 overlapping differentially expressed genes (DEGs), using the DESeq2, limma, and edgeR packages, affecting the IFC and CIE a* value, respectively. Weighted gene co-expression network analysis (WGCNA) identified four modules significantly correlated with the IFC and CIE a* value. Moreover, we integrated functional enrichment analysis results based on DEGs, GSEA, and WGCNA conditions to identify candidate genes, and identified 47 and 53 candidate genes affecting the IFC and CIE a* value, respectively. The protein protein interaction (PPI) network analysis of candidate genes showed that 5 and 13 hub genes affect the IFC and CIE a* value, respectively. These genes mainly participate in various pathways related to lipid metabolism and redox reactions. Notably, four crucial hub genes (MYC, SOX9, CEBPB, and PPAGRC1A) were shared for these two traits. Discussion and conclusion: After functional annotation of these four hub genes, we hypothesized that the SOX9/CEBPB/PPARGC1A axis could co-regulate lipid metabolism and the myoglobin redox response. Further research on these hub genes, especially the SOX9/CEBPB/PPARGC1A axis, will help to understand the molecular mechanism of the co-regulation of the IFC and CIE a* value, which will provide a theoretical basis for improving pork quality.

Keywords: RNA-seq; functional enrichment analysis; hub gene; intramuscular fat content; meat color redness.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was financially supported by the National Natural Science Foundation of China (32302695), the Project of Seed Industry Revitalization in Jiangsu Province (JBGS2021024), the Zhejiang Science and Technology Major Program on Agricultural New Variety Breeding (2021C02068), the Key R & D projects of Zhejiang Province (2021C02007), and the China Agriculture Research System of MOF and MARA (CARS36).