结合WGCNA鉴定与猪肌纤维和肌内脂肪相关的中枢基因  

Identification of hub genes associated with porcine muscle fibers and intramuscular fat by WGCNA

作　　者：刘娟[1] 王舒 左周 路畅 杨阳 蔡春波 赵燕[1] 郭晓红[1] 曹果清[1] 李步高[1] 高鹏飞[1] Liu Juan;Wang Shu;Zuo Zhou;Lu Chang;Yang Yang;Cai Chunbo;Zhao Yan;Guo Xiaohong;Cao Guoqing;Li Bugao;Gao Pengfei(College of Animal Science,Shanxi Agricultural University,Taigu 030801,China)

机构地区：[1]山西农业大学动物科学学院,山西太谷030801

出　　处：《山西农业大学学报（自然科学版）》2021年第4期109-118,共10页Journal of Shanxi Agricultural University(Natural Science Edition)

基　　金：国家自然科学基金(31872336);山西省农业重点研发项目(201803D221022-1);山西省重点基础研究项目(20101D211376;20101D211369)。

摘　　要：[目的]肌纤维直径和肌内脂肪含量是影响猪肉质性状的重要因素之一,中国本土猪品种和国外猪品种在肌肉发育和性能性状方面存在很大差异,本研究将课题组前期猪肌肉发育转录组数据随机分为训练集和测试集,对训练集数据进行加权基因共表达网络分析(Weighted Gene Co‐expression Network Analysis,WGCNA),筛选与性状显著相关的基因模块,得到核心基因。[方法]通过GO和KEGG功能富集分析和共表达网络分析筛选模块的核心基因,采用随机森林方法通过测试集样本对核心基因进行验证,最终获得与性状显著相关的hub基因。[结果]WGCNA结果发现,2个品种7262条差异基因形成16个模块基因集,其中肌内脂肪含量与MEblack模块成极显著正相关,与MEsalmon模块显著负相关。肌纤维密度与MEblack模块和MElightgreen模块显著负相关。MEmagenta模块与肌纤维直径极显著正相关。对各模块共表达网络分析,根据基因连通度获得19条核心基因。随机森林法对19个核心基因进行监督学习,测试集样本预测准确率在87.50%以上。最终确定FAM131B、RIC8B、PLEKHA5、PARP6和CBX7是影响肌肉发育和肌内脂肪沉积的关键基因。[结论]本研究将WGCNA与随机森林深度学习方法相结合,确证了5条显著影响肌纤维发育和肌内脂肪沉积的hub基因,研究结果为解析猪肉质性状形成的分子机理提供理论参考。[Objective]Muscle fiber diameter and intramuscular fat(IMF)content are important factors affecting pork quality.There are big differences in muscle development and meat quality traits between Chinese pig breeds and foreign pig breeds.In the present study,the transcriptome data on porcine muscle development previously obtained by our research group were randomly divided into training and testing sets.We performed weighted gene co-expression network analysis(WGCNA)on the training set,and screen the gene modules that were significantly associated with meat-quality phenotypic traits,and got the hub genes.[Methods]The hub genes of the module were screened out by GO and KEGG functional enrichment analysis and co-expression network analysis.The hub genes were verified by the random forest method through the test set samples,and finally the hub genes that were significantly related to the traits were obtained.[Results]The WGCNA results showed that Mashen(MS)and Large White(LW)pigs had 7262 differentially expressed genes,divided into 16 gene modules.Intramuscular fat content was extremely significantly positively correlated with MEblack model,and significantly negatively correlated with MEsalmon module.There was a significant negative correlation between muscle fiber density and MEblack module and MElightgreen module,while MEmagenta module showed a significant positive correlation with muscle fiber diameter.By analyzing the co-expression network of each module,19 hub genes were obtained according to the connectivity degree of genes.Through the supervised learning of 19 hub genes by the random forest method,the prediction accuracy of the test set samples was above 87.50%.Finally,FAM131b,RIC8B,PLEKHA5,PARP6 and CBX7 were identified as key genes that affected muscle development and intramuscular fat deposition.[Conclusion]In this study,WGCNA was combined with random forest deep learning method to confirm five hub genes that significantly affect muscle fiber development and intramuscularly fat deposition.The results of this s

关 键 词：加权基因共表达网络分析 随机森林算法 肌肉特性相关性状 猪 

分 类 号：S826.2[农业科学—畜牧学]