Table_8_Abiotic Stress-Responsive miRNA and Transcription Factor-Mediated Gene Regulatory Network in Oryza sativa: Construction and Structural Measure Study.XLSX

Climate changes and environmental stresses have a consequential association with crop plant growth and yield, meaning it is necessary to cultivate crops that have tolerance toward the changing climate and environmental disturbances such as water stress, temperature fluctuation, and salt toxicity. Recent studies have shown that trans-acting regulatory elements, including microRNAs (miRNAs) and transcription factors (TFs), are emerging as promising tools for engineering naive improved crop varieties with tolerance for multiple environmental stresses and enhanced quality as well as yield. However, the interwoven complex regulatory function of TFs and miRNAs at transcriptional and post-transcriptional levels is unexplored in Oryza sativa. To this end, we have constructed a multiple abiotic stress responsive TF-miRNA-gene regulatory network for O. sativa using a transcriptome and degradome sequencing data meta-analysis approach. The theoretical network approach has shown the networks to be dense, scale-free, and small-world, which makes the network stable. They are also invariant to scale change where an efficient, quick transmission of biological signals occurs within the network on extrinsic hindrance. The analysis also deciphered the existence of communities (cluster of TF, miRNA, and genes) working together to help plants in acclimatizing to multiple stresses. It highlighted that genes, TFs, and miRNAs shared by multiple stress conditions that work as hubs or bottlenecks for signal propagation, for example, during the interaction between stress-responsive genes (TFs/miRNAs/other genes) and genes involved in floral development pathways under multiple environmental stresses. This study further highlights how the fine-tuning feedback mechanism works for balancing stress tolerance and how timely flowering enable crops to survive in adverse conditions. This study developed the abiotic stress-responsive regulatory network, APRegNet database (http://lms.snu.edu.in/APRegNet), which may help researchers studying the roles of miRNAs and TFs. Furthermore, it advances current understanding of multiple abiotic stress tolerance mechanisms.

气候变化和环境压力与作物植物的生长与产量之间存在显著的关联性，意即有必要培育出对气候变化和环境扰动（如水分胁迫、温度波动和盐毒性）具有耐受性的作物。近期研究显示，转录调控元件，包括微RNA（miRNA）和转录因子（TFs），正成为构建对多种环境压力具有耐受性、品质提升及产量增加的原始改良作物品种的极具潜力的工具。然而，在水稻（Oryza sativa）中，TFs和miRNA在转录及转录后水平上的错综复杂的调控功能尚未得到充分探索。为此，我们采用转录组和降解组测序数据的元分析方法，构建了一个针对O. sativa的多重非生物胁迫响应TF-miRNA-基因调控网络。理论网络分析表明，该网络具有密集、无标度和小世界特性，从而使得网络稳定。网络对尺度变化具有不变性，在遭遇外源阻碍时，网络内部仍能高效、迅速地传递生物信号。分析还揭示了存在社区（TF、miRNA和基因的簇）共同协作以帮助植物适应多种胁迫的现象。研究突出了在多种环境压力下，共享的基因、TFs和miRNAs作为信号传播的枢纽或瓶颈的作用，例如，在胁迫响应基因（TFs/miRNAs/其他基因）与在多种环境压力下参与花发育途径的基因相互作用时。本研究进一步阐明了精细调节反馈机制如何实现压力耐受性的平衡，以及适时开花如何使作物在恶劣条件下得以生存。本研究开发了非生物胁迫响应调控网络APRegNet数据库（http://lms.snu.edu.in/APRegNet），该数据库可能有助于研究miRNA和TFs的作用。此外，它也推进了对多种非生物胁迫耐受机制的当前理解。