基于WGCNA的棉花子叶抗冷相关共表达模块鉴定

Identification of Cold-related Co-expression Modules in Cotton Cotyledon by WGCNA

权重基因共表达网络分析(weighted gene co-expression network analysis,WGCNA)是系统生物学的一种研究方法,在多样本转录组数据中挖掘与目标性状相关的基因模块应用较广泛。为深入探究棉花应对冷害胁迫的分子机制,以4℃低温处理不同时间点的2个棉花品种(新陆中16和新陆中32)幼苗子叶转录组数据为基础,过滤低表达量基因,最终利用筛选的22083个表达的基因来构建共表达矩阵,得到9个共表达模块,其中2个为抗冷相关特异性模块(Blue模块与低温处理0、1和3 h时间点正相关,Brown模块与低温处理9和12 h时间点正相关)。GO和KEGG富集分析表明,特异性模块可以富集到对刺激反应的调节(GO:0048583)、对胁迫反应的调节(GO:0080134)、对油菜素类固醇的反应(GO:0009741)等抗逆相关通路。通过计算模块内基因的连通性挖掘网络中的核心基因,功能注释表明这些基因可能在棉花抗冷过程中发挥着重要作用。该结果为进一步研究棉花抗冷调控机理提供数据支持。

Weighted gene co-expression network analysis(WGCNA)is substantially used to identify gene modules related to the trait of interest in multi-sample transcriptome data.Transcriptome data of Xinluzhong 16 and Xinluzhong 32 were assessed to prospect molecular mechanisms under 4℃stress to study the mechnism of cotton’s response to cold stress.Ultimately,the co-expression matrix containing 22083 expressed genes was fabricated after the genes of low expression level were filtered.And them WGCNA identified 9 modules,among them 2 modules remarkably linked with cold resistance such as brown positively associated with 9 and 12 h,while blue positively associated with 0,1 and 3 h.KEGG and GO enrichment perusal were evaluated on these 2 modules which could be enriched with GO terms,i.e.modulation of stress response.Hub genes were screened by estimating gene connectivity in their corresponding networks which might play key roles in abiotic stress resistance.Above results would assist in understanding the regulatory mechanism of cold tolerance in cotton.