Plants respond to abiotic stressors through a suite of strategies including differential regulation of stress-responsive genes. Hence, characterizing the influences of the relevant global regulators or on stress-related transcription factors is critical to understand plant stress response. Rice seed development is highly sensitive to elevated temperatures. To elucidate the extent and directional hierarchy of gene regulation in rice seeds under heat stress, we developed and implemented a robust multi-level optimization-based algorithm called Minimal Regulatory Network identifier (MiReN). MiReN could predict the minimal regulatory relationship between a gene and its potential regulators from our temporal transcriptomic dataset. MiReN predictions for global regulators including stress-responsive gene Slender Rice 1 (SLR1) and disease resistance gene XA21 were validated with published literature. It also predicted novel regulatory influences of other major regulators such as Kinesin-like proteins KIN12C and STD1, and WD repeat-containing protein WD40. Out of the 228 stress-responsive transcription factors identified, we predicted de novo regulatory influences on three major groups (MADS-box M-type, MYB, and bZIP) and investigated their physiological impacts during stress. Overall, MiReN results can facilitate new experimental studies to enhance our understanding of global regulatory mechanisms triggered during heat stress, which can potentially accelerate the development of stress-tolerant cultivars.

植物通过一系列策略应对非生物胁迫，包括胁迫响应基因的差异调控。因此，表征相关全球调控因素或对逆境相关转录因子的影响对于了解植物逆境响应至关重要。水稻种子发育对高温高度敏感。为了阐明热胁迫下水稻种子中基因调控的程度和方向层次，我们开发并实现了一种稳健的基于多级优化的算法，称为最小调控网络标识符（MiReN）。MiReN可以从我们的时间转录组数据集中预测基因与其潜在调控因子之间的最小调控关系。MiReN对包括压力响应基因Slender Rice 1在内的全球监管机构的预测（SLR1）和抗病基因XA21已通过公开文献验证。它还预测了其他主要调控因子（如驱动蛋白样蛋白KIN12C和STD1，以及含有WD重复序列的蛋白WD40）的新调控作用。在确定的228种压力响应转录因子中，我们预测了从头对三个主要组（MADS-box M型，MYB和bZIP）的调节作用，并研究了它们在压力下的生理影响。总体而言，MiReN的结果可以促进新的实验研究，以加深我们对热胁迫期间触发的全球调控机制的了解，这可能会加速耐胁迫品种的发展。