利用WGCNA鉴定棉花抗黄萎病相关基因共表达网络  

Identification of co-expressed modules of cotton genes responding to Verticillium dahliae infection by WGCNA

作　　者：傅明川 李浩[1] 陈义珍 柳展基[1] 刘任重[1] 王立国[1] FU Ming-Chuan;LI Hao;CHEN Yi-Zhen;LIU Zhan-Ji;LIU Ren-Zhong;WANG Li-Guo(Cotton Research Center of Shandong Academy of Agricultural Sciences/Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain,Ministry of Agriculture,Jinan 250100,Shandong,China)

机构地区：[1]山东棉花研究中心/农业部黄淮海棉花遗传改良与栽培生理重点实验室,山东济南250100

出　　处：《作物学报》2020年第5期668-679,共12页Acta Agronomica Sinica

基　　金：山东省农业科学院农业科技创新工程(CXGC2018B01,CXGC2018E06)项目资助。

摘　　要：加权基因共表达网络分析(Weighted Gene Co-expression Network Analysis,WGCNA)作为一种典型的系统生物学方法,可用来鉴定协同表达的基因模块,探索模块与目标性状之间的生物学相关性,并挖掘网络中的核心基因。黄萎病(Verticillium wilt)可严重降低棉花(Gossypium spp.)的产量及品质,因此研究抗病基因及抗病机制,对于棉花抗病育种工作具有重要意义。本研究以黄萎病菌侵染不同时间点的海岛棉(Gossypium barbadense)幼苗根尖转录组数据为基础,分析其差异表达基因,并选取在不同样本之间表达水平变异最大的前50%基因(共35,647个)进行WGCNA。结果表明,在黄萎病菌侵染条件下,共有22,850个基因差异表达,其中4685个为所有侵染时间点共有的差异基因。共鉴定到18个基因共表达模块,其中5个为抗黄萎病相关特异性模块(black、mediumpurple3、darkolivegreen、plum3模块分别与侵染2 h、6 h、48 h、72 h时间点正相关;mediumpurple2与侵染2 h时间点负相关)。GO和KEGG富集分析表明,特异性模块可以富集到有生物学意义的富集结果,如刺激响应、钙离子结合、黄酮类化合物合成代谢等抗逆相关通路。通过计算模块内基因的连通性,挖掘出了网络中的核心基因,功能预测表明,这些基因可能在逆境胁迫响应中发挥重要作用。本研究为进一步理解棉花抗黄萎病的分子机制、选育棉花抗病新品种提供了理论指导。Weighted gene co-expression network analysis(WGCNA)is a classic systematic biological method,which can be used to identify co-expressed modules,investigate relationships between modules and specific traits,and screen hub genes in the networks.Verticillium wilt,caused by the fungal pathogen Verticillium dahliae,can cause severe fibre quality reduction and yield loss of cotton.Studying on cotton genes and molecular mechanisms related to defense responses against V.dahliae can shed light on cotton breeding.In this study,21 transcriptome data of Gossypium barbadense seedling roots infected by V.dahliae were used to investigate differentially expressed genes(DEGs).By filtering out the genes with low variation,35,647 genes were selected for WGCNA.In total,22,850 DEGs were identified under V.dahliae infection,with 4685 in common at all inoculated time points.Co-expression network analysis identified 18 modules,in which five modules significantly associated with V.dahliae infection(black,mediumpurple3,darkolivegreen,plum3 positively correlated with the 2 h,6 h,48 h,and 72 h inoculated time points,respectively;mediumpurple2 negatively correlated with the 2 h inoculated time point).GO and KEGG enrichment analysis were performed on these five specific modules,which could be enriched in GO terms and metabolic pathways,such as cellular response to stimulus,calcium ion binding and flavonoid biosynthesis.The hub genes were screened by calculating gene connectivity in the corresponding networks,and they may play important roles in the resistance against biotic/abiotic stresses.In summary,by WGCNA,a few defense-related co-expressed modules and hub genes were identified.The results of this study would be beneficial for further understanding of the molecular mechanisms of pathogen resistance in cotton,and provide new gene resources for cotton breeding in the future.

关 键 词：棉花 黄萎病 加权基因共表达网络分析 核心基因 

分 类 号：S435.621.2[农业科学—农业昆虫与害虫防治]