Transcriptomic analysis reveals the gene regulatory networks involved in leaf and root response to osmotic stress in tomato

We performed a transcriptomic analysis on two tomato genotypes, M82 and Tondo, in response to a PEG-mediated osmotic treatment, mimicking water stress. The analysis was conducted separately on leaves and roots to characterize the specific response of these two organs. A total of 6,267 differentially expressed transcripts related to osmotic stress response was detected. The construction of gene co-expression networks defined the metabolic and signaling pathways of the common and specific responses of leaf and root. The common response was characterized by ABA-dependent and ABA-independent signaling pathways, and by the interconnection between ABA and JA signaling. The root specific response concerned genes involved in cell wall metabolism and remodeling, whereas the leaf specific response was principally related to leaf senescence and ethylene signaling. The transcription factors representing the hubs of these regulatory networks were identified. Some of them have not yet characterized and can represent novel candidates for tolerance. Finally, several genes showing a genotype-specific expression regulation in response to the treatment were detected. These genes may be involved in the different sensitivity to the osmotic treatment of the two tomato genotypes. In conclusion, this work shed new light on the regulatory networks occurring in tomato leaf and root under osmotic stress and set the base for an in-depth characterization of novel stress-related genes, that may represent potential candidates for improving tolerance to water stress in tomato. The study used 24 arrrays with RNA extracted from two tomato genotypes (Tondo and M82), two tissues (leaf and root), in control and under PEG conditions (2 genotypes x2 conditions x2 tissues x3 biological replicates= 24 arrays).

本研究针对两个番茄基因型（genotype）M82与Tondo，开展了聚乙二醇（PEG）介导的渗透处理模拟水分胁迫下的转录组分析。
本分析分别针对叶片与根系开展，以解析这两种器官的特异性胁迫响应。
共计检测到6267个与渗透胁迫响应相关的差异表达转录本（transcript）。
通过构建基因共表达网络，明确了叶片与根系共有的以及特异性响应所涉及的代谢通路与信号通路。
共有的响应以脱落酸（ABA）依赖型与ABA非依赖型信号通路，以及ABA与茉莉酸（JA）信号通路的互作为核心特征。
根系特异性响应涉及参与细胞壁代谢与重塑的基因，而叶片特异性响应则主要与叶片衰老及乙烯信号通路相关。
本研究鉴定出了构成这些调控网络枢纽的转录因子（transcription factor），其中部分尚未被功能表征，可作为渗透胁迫耐受的新型候选基因。
此外，本研究还检测到一批在处理后呈现基因型特异性表达调控的基因，这些基因或与两个番茄基因型对渗透处理的敏感性差异相关。
综上，本研究阐明了番茄叶片与根系在渗透胁迫下的调控网络特征，为深入解析新型胁迫相关基因，这些基因或可作为提升番茄水分胁迫耐受能力的潜在候选靶点，奠定了研究基础。
本研究共使用24张基因芯片（array），样本来自两个番茄基因型（Tondo与M82）、两种组织（叶片与根系），分别设置对照组与PEG胁迫组，实验设计为：2种基因型 × 2种处理条件 × 2种组织 × 3次生物学重复 = 24张芯片。