中国农业大学学报2025，Vol.30Issue(3)：153-165,13.DOI:10.11841/j.issn.1007-4333.2025.03.14
基于WGCNA分析挖掘调控莱芜猪肉色相关基因
Identification of genes regulating meat color in Laiwu pigs based on WGCNA
摘要
Abstract
To screen for key candidate genes that affect the color of pork in Laiwu pigs,this study utilized transcriptome data from Laiwu pigs and identified key genes affecting pork color using weighted gene co-expression network analysis(WGCNA).The color of the meat,including L,a,and b,was measured at 45 m and 24 h postmortem for a total of 33 Laiwu pigs.RNA sequencing was conducted on the longissimus dorsi muscles of these pigs.Based on the transcriptome data and phenotype data,WGCNA analysis was conducted using the WGCNA package of R.After removing two outlier samples,31 samples were used to construct a gene co-expression network for the identification of target modules and key genes.The results showed that:1)Through WGCNA analysis,a total of 20 co-expression modules were identified.Among these modules,Floral white,Dark green,Pink,and Orangered 4 demonstrated significant correlations with two or more meat color traits,with a Icorrelation coefficientl ≥0.35 and a significance P value＜0.01.2)Functional enrichment analysis revealed that genes within the target module were significantly enriched in GO terms and pathways related to mitochondrial structure and function,protein modification,fat deposition and metabolism,muscle structure and function,etc.3)Identification of key genes in the target module involved applying an absolute correlation coefficient greater than 0.85 between gene expression and module eigengene,as well as an absolute correlation coefficient greater than 0.3 between gene expression and meat color traits for at least two traits.Subsequently,these genes were carried out protein-protein interaction analysis.A total of eight candidate genes affecting meat color,including MYO9A,NDUFA13,COX5B,MRPL12,RPL8,ROBO4,EGFL7,and CIDEC,were obtained from the four target modules.In summary,this study identified four target modules and eight candidate genes regulating meat color in Laiwu pigs through WGCNA,laying the foundation for exploring the molecular regulatory mechanisms of pig meat color trait and making advancements in meat color improvement through breeding.关键词
莱芜猪/肉色/转录组测序/WGCNAKey words
Laiwu pigs/meat color/RNA sequencing/WGCNA分类
农业科技引用本文复制引用
任一帆,赵雪艳,张大龙,王彦平,李菁璇,王继英..基于WGCNA分析挖掘调控莱芜猪肉色相关基因[J].中国农业大学学报,2025,30(3):153-165,13.基金项目
山东省重点研发计划(2022LZGC003,2022LZGCQY007) （2022LZGC003,2022LZGCQY007）
山东省生猪产业技术体系(SDAIT-08-03) （SDAIT-08-03）
山东省农业科学院农业科技创新工程(CXGC2023A23) （CXGC2023A23）
