Major crops are generally sensitive to waterlogging, but our limited understanding of the waterlogging gene regulatory network hinders the efforts to develop waterlogging-tolerant cultivars. We generated high-resolution temporal transcriptome data from root of two contrasting sesame genotypes over a 48 h period waterlogging and drainage treatments. Three distinct chronological transcriptional phases were identified, including the early-waterlogging, late-waterlogging and drainage responses. We identified 47 genes representing the core waterlogging-responsive genes. Waterlogging/drainage-induced transcriptional changes were mainly driven by ERF and WRKY transcription factors (TF). The major difference between the two genotypes resides in the early transcriptional phase. A chronological transcriptional network model predicting putative causal regulations between TFs and downstream waterlogging-responsive genes was constructed and some interactions were validated through yeast one-hybrid assay. Overall, this study unveils the architecture and dynamic regulation of the waterlogging/drainage response in a non-model crop and helps formulate new hypotheses on stress sensing, signaling and sophisticated adaptive responses.

主要作物通常对涝渍敏感，但我们对涝渍基因调控网络的了解有限，阻碍了开发耐涝品种的努力。我们在 48 小时的涝渍和排水处理过程中，从两种不同芝麻基因型的根中生成了高分辨率的时间转录组数据。确定了三个不同的按时间顺序转录的阶段，包括早期涝渍、晚期涝渍和排水反应。我们确定了 47 个代表核心涝渍反应基因的基因。涝渍/排水诱导的转录变化主要由 ERF 和 WRKY 转录因子 (TF) 驱动。两种基因型之间的主要区别在于早期转录阶段。构建了一个时序转录网络模型，预测 TF 与下游涝渍响应基因之间的假定因果关系，并通过酵母单杂交试验验证了一些相互作用。总体而言，这项研究揭示了非模式作物中涝/排水响应的结构和动态调节，并有助于形成关于压力感应、信号传导和复杂适应性响应的新假设。