利用WGCNA进行棉花果枝节间伸长相关基因共表达模块鉴定

Identification of Co-expression Modules of Genes Related to Internode Elongation of Cotton Fruiting Branches by WGCNA

【目的】旨在进行棉花果枝节间伸长相关基因的共表达模块鉴定,研究基因整体表达规律,挖掘目标基因及候选基因。【方法】以两个株型结构差异显著的棉花品种(新陆中77和鲁棉研28)的18份不同长度果枝节间样本的转录组数据作为分析对象,通过权重基因共表达网络分析(Weighted gene co-expression network analysis,WGCNA)进行模块的划分,根据模块功能富集分析及基因表达模式进行特异性模块的筛选及枢纽基因的鉴定,利用Cytoscape_3.3.0进行加权基因共表达网络图的绘制。【结果】利用34 559个有效基因创建了共表达网络,划分为13个共表达模块,筛选得到Cyan模块为与棉花果枝节间伸长相关的特异性模块,并发现植物激素信号转导通路中的JAZ(Jasmonate-zim-domain protein)基因为该模块的枢纽基因,挖掘到80个潜在的候选基因,并用其构建了基因互作调控网络。【结论】JAZ类基因在抑制棉花果枝节间伸长生长过程中发挥着重要的作用,本研究结果可为棉花果枝节间伸长的调控机理研究提供数据支持,为进一步调控棉花株型结构奠定理论基础。

[Objective]The aims of this study were to identify the co-expression modules of genes related to the internode elongation of fruiting branches in cotton and to identify the associated hub and candidate genes.[Method]The transcriptome data of 18 fruiting branch internodes from two cotton cultivars(XLZ77 and L28)having significant differences in plant architecture were analyzed.The modules were divided using a weighted gene co-expression network analysis.The selection of specific modules and identification of hub genes were based on a functional enrichment analysis and the gene expression pattern of each module.The weighted co-expression gene network was constructed using Cytoscape_3.3.0.[Result]In total,34 559 effective genes were screened to construct a co-expression network,and 13 co-expression modules were obtained.Using gene ontology and a Kyoto Encyclopedia of Genes and Genomes enrichment analysis of each module,along with the gene expression patterns in the module,the Cyan module was selected as being related to internode elongation of cotton fruiting branches.Jasmonate-zim-domain protein(JAZ)genes in the plant hormone signal transduction pathway were identified as hub genes in this module.In total,80 potential candidate genes were identified using the JAZ hub genes,and a gene interaction regulatory network was constructed.[Conclusion]JAZ genes play important roles in inhibiting the internode elongation of fruiting branches in cotton. This study provides supporting data for studies on regulatory mechanisms of cotton fruiting branch elongation and lays a theoretical foundation for the future regulation of cotton plant architecture.