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

作　　者：任一帆 赵雪艳[1] 张大龙 王彦平[1] 李菁璇 王继英[1] REN Yifan;ZHAO Xueyan;ZHANG Dalong;WANG Yanping;LI Jingxuan;WANG Jiying(Institute of Animal Husbandry and Veterinary Medicine/Key Laboratory of Animal Disease Prevention and Breeding in Shandong Province/Key Laboratory of Livestock and Poultry Biogenomics of Ministry of Agriculture and Rural Affairs,Shandong Academy of Agricultural Sciences,Jinan 250100,China;Jinan Academy of Agricultural Sciences,Jinan 250316,China)

机构地区：[1]山东省农业科学院畜牧兽医研究所/山东省畜禽疫病防治与繁育重点实验室/农业农村部畜禽生物组学重点实验室,济南250100 [2]济南市农业科学研究院,济南250316

出　　处：《中国农业大学学报》2025年第3期153-165,共13页Journal of China Agricultural University

基　　金：山东省重点研发计划(2022LZGC003,2022LZGCQY007);山东省生猪产业技术体系(SDAIT-08-03);山东省农业科学院农业科技创新工程(CXGC2023A23)。

摘　　要：为筛选影响莱芜猪肉色的关键候选基因,本研究利用莱芜猪转录组数据,通过加权基因共表达网络分析(Weighted gene co-expression network analysis,WGCNA)对33头莱芜猪测定了45 min及24 h的肉色(包括L、a、b),对其背最长肌样本开展了转录组测序,挖掘影响猪肉色的关键基因。结合转录组数据和表型数据利用R语言WGCNA软件包开展了WGCNA分析,在剔除2个离群样本后利用31个样本数据构建基因共表达网络,筛选目标模块及模块中的关键基因。结果表明:1)通过WGCNA分析,共获得20个共表达模块,其中4个模块与2个及以上肉色性状显著相关(|相关性系数|≥0.35且显著性P<0.01),分别为Floral white、Dark green、Pink及Orangered 4模块。2)功能富集分析发现,目标模块内基因显著富集在线粒体结构和功能、蛋白修饰、脂肪沉积和代谢、肌肉结构和功能等相关的GO项和通路中。3)以模块基因表达量与模块特征值的相关性系数绝对值>0.85且基因表达量与至少2个肉色性状的相关性系数绝对值>0.3为标准筛选目标模块基因,并将筛选到的基因进行蛋白互作分析,最终从4个模块中筛选到8个影响肉色的候选基因MYO9A、NDUFA13、COX5B、MRPL12、RPL8、ROBO4、EGFL7和CIDEC。综上,本研究通过WGCNA分析鉴别到影响肉色的4个目标模块及8个候选基因,为猪肉色分子调控机制研究与肉色育种改良奠定了理论基础。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 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|correlation coefficient|≥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

关 键 词：莱芜猪 肉色 转录组测序 WGCNA 

分 类 号：S828[农业科学—畜牧学]