Some crops inhibit shoot growth but maintain root growth under water−deficit conditions. Unraveling the molecular mechanisms of root plasticity under water deficit conditions in plants remains a major challenge. We developed an efficient platform for identifying core transcription factors (TFs) that collectively regulate each other and/or themselves in response to water stress,and exploring their interconnected regulatory circuitry involved in root growth maintenance under water deficit in

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... an. We performed multi−species phylogenetic footprinting combined with spatial−temporal transcriptome analysis of soybean (Glycine max) roots under water deficit to identify conserved motifs that function in the water−stress response. Using these functional conserved cis−motifs, we applied a new approach to trace back motifs−associated core TFs ingroup as signal mediators, which mediate signaling between abiotic and endogenous stimuli. We integrated a co−functional TF−TF network and conserved motif−centered TF−DNA networks to construct a core TF network defined by mutual cross−regulation among core TFs. We found that core TF ARG (Abscisic acid response element binding factor−like Root Growth regulator) represses BRG (Brassinosteroid enhanced expression−like Root Growth regulator) expression through binding to its promoter at a conserved binding site. ARG and BRG antagonistically regulate Phytochrome−interacting factor−like Root Growth regulator (PRG) and combinatorially regulate some other core TFs. These core TFs form complex regulatory circuits to integrate light and multiple hormone signaling pathways and maintain root growth in response to varying degrees of water stress. Our study provides valuable information to unravel the complicated mechanisms of molecular networks involved in the regulation of root growth under water deficit.