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首页> 外文期刊>BMC Plant Biology >Co-expression network analysis of the transcriptomes of rice roots exposed to various cadmium stresses reveals universal cadmium-responsive genes
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Co-expression network analysis of the transcriptomes of rice roots exposed to various cadmium stresses reveals universal cadmium-responsive genes

机译：暴露于各种镉胁迫下的水稻根转录组的共表达网络分析揭示了通用的镉响应基因

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The migration of cadmium (Cd) from contaminated soil to rice is a cause for concern. However, the molecular mechanism underlying the response of rice roots to various Cd stresses remains to be clarified from the viewpoint of the co-expression network at a system-wide scale. We employed a comparative RNAseq-based approach to identify early Cd-responsive differentially expressed genes (DEGs) in rice ‘Nipponbare’ seedling roots after 1?h of high-Cd treatment. A multiplicity of the identified 1772 DEGs were implicated in hormone signaling and transcriptional regulation, particularly NACs and WRKYs were all upregulated under Cd stress. All of the 6 Cd-upregulated ABC transporters were pleiotropic drug resistance proteins (PDRs), whereas all of the 6 ZRT/IRT-like proteins (ZIPs) were consistently downregulated by Cd treatment. To further confirm our results of this early transcriptomic response to Cd exposure, we then conducted weighted gene co-expression network analysis (WGCNA) to re-analyze our RNAseq data in combination with other 11 previously published RNAseq datasets for rice roots exposed to diverse concentrations of Cd for extended treatment periods. This integrative approach identified 271 transcripts as universal Cd-regulated DEGs that are key components of the Cd treatment coupled co-expression module. A global view of the 164 transcripts with annotated functions in pathway networks revealed several Cd-upregulated key functional genes, including transporter ABCG36/OsPDR9, 12-oxo-phytodienoic acid reductases (OPRs) for JA synthesis, and ZIM domain proteins JAZs in JA signaling, as well as OsWRKY10, NAC, and ZFP transcription factors. More importantly, 104 of these, including ABCG36/OsPDR9, OsNAC3, as well as several orthologs in group metalloendoproteinase, plastocyanin-like domain containing proteins and pectin methylesterase inhibitor, may respond specifically to various Cd pressures, after subtracting the 60 general stress-responsive genes reported to be commonly upregulated following multiple stresses. An integrative approach was implemented to identify DEGs and co-expression network modules in response to various Cd pressures, and 104 of the 164 annotatable universal Cd-responsive DEGs may specifically respond to various Cd pressures. These results provide insight into the universal molecular mechanisms beneath the Cd response in rice roots, and suggest many promising targets for improving the rice acclimation process against Cd toxicity.
机译：镉（Cd）从受污染的土壤向水稻的迁移令人担忧。然而，从系统范围内的共表达网络的角度来看，水稻根对各种镉胁迫响应的分子机制仍有待阐明。我们采用基于RNAseq的比较方法，在高Cd处理1小时后，鉴定了水稻“ Nipponbare”幼苗根中的早期Cd响应差异表达基因（DEG）。鉴定出的1772个DEGs与激素信号传导和转录调控有关，尤其是NACs和WRKYs在镉胁迫下均被上调。所有6个Cd上调的ABC转运蛋白都是多效性耐药蛋白（PDR），而所有6个ZRT / IRT样蛋白（ZIP）始终通过Cd处理而下调。为了进一步证实我们对Cd暴露的早期转录组反应的结果，我们随后进行了加权基因共表达网络分析（WGCNA）以结合其他11种先前发表的针对不同浓度水稻根系的RNAseq数据集重新分析我们的RNAseq数据Cd延长治疗时间。这种综合方法将271个转录物鉴定为通用的Cd调节DEG，它们是Cd治疗耦合共表达模块的关键组成部分。在通路网络中具有注释功能的164个转录本的全局视图揭示了几个Cd上调的关键功能基因，包括JA信号传导中的转运蛋白ABCG36 / OsPDR9，用于JA合成的12-氧-植物二烯酸还原酶（OPR）和ZIM中的ZIM域蛋白JAZ以及OsWRKY10，NAC和ZFP转录因子。更重要的是，其中的104种，包括ABCG36 / OsPDR9，OsNAC3，以及金属内切蛋白酶组中的几个直系同源物，含有质体蓝素样结构域的蛋白和果胶甲基酯酶抑制剂，在减去60种一般应激反应后，可能对多种Cd压力有特殊反应。据报道，在多个压力下，这些基因通常被上调。已实施一种集成方法来识别DEG和共表达网络模块以响应各种Cd压力，并且164个可注释的通用Cd响应DEG中的104个可以专门响应各种Cd压力。这些结果提供了对水稻根部Cd响应下普遍的分子机制的见解，并提出了许多有希望的目标来改善水稻对Cd毒性的适应过程。

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