利用加权基因共表达网络分析(WGCNA)的方法挖掘番茄果实成熟相关的转录因子

Mining Fruit Ripening-related Transcription Factors in Tomato by Weighted Gene Co-expression Network Analyses(WGCNA)

为挖掘番茄果实成熟相关的转录因子,利用10个不同番茄组织RNA-Seq数据,通过加权基因共表达网络分析的方法构建网络。进一步将该网络划分为24个模块,并寻找到8个组织中共16个组织特异性模块。通过对3个番茄破色10 d的果实组织特异性模块分析,发现这些模块中含有大量果实品质形成所需的糖、脂、蛋白等相关的代谢过程,并存在类萝卜素合成、果实软化、芳香物质合成以及乙烯生物合成和信号转导所需的关键基因。此结果验证了网络和组织特异性模块的可靠性。通过对棕色模块中转录因子分析,发现在该模块中存在MADS-RIN、AP2a、FUL1(TDR4)、CNR、NAC4、ERF6、NAC-NOR等果实成熟相关的转录因子,以及大量MADS-RIN转录因子直接作用的靶基因。由此推断棕色模块中其它58个转录因子是潜在的果实成熟转录因子。此结果为番茄果实成熟机制的研究提供新思路。

In order to detect fruit ripening-related transcription factors in tomato, a network was constructed by weighted gene co-expression network analyses（WGCNA） using RNA-Seq data of 10 different tissues of tomato in this research. Then the network was divided into 24 modules, and 16 tissue-specific modules were identified in 8 tissues. In3 Breaker＋10（BK＋10） tissue-specific modules, there were a lot of biological processes about carbohydrate, lipid, protein metabolism and key genes in carotenoid synthesis, fruit softening, aromatic synthesis, ethylene synthesis and ethylene signal transduction. These results demonstrated that the network and the tissue-specific modules were reliable.Through analysis of transcription factors in brown module, there were many fruit ripening-related transcription factors,such as MADS-RIN, AP2 a, FUL1（TDR4）, CNR, NAC4, ERF6, NAC-NOR, and direct targets of MADS-RIN. So the other 58 transcription factors in brown module may be as potential transcription factors regulating fruit ripening, which provided a new research idea to explore the tomato fruit ripening mechanism.