30Some crops inhibit shoot growth but maintain root growth under water-deficit conditions. 31Unraveling the molecular mechanisms of root plasticity under water deficit conditions in plants 32 remains a major challenge. We developed an efficient platform for identifying core transcription 33 factors (TFs) that collectively regulate each other and/or themselves in response to water stress, 34 and exploring their interconnected regulatory circuitry involved in root growth maintenance under 35 water deficit in soybean. We performed multi-species phylogenetic footprinting combined with 36 spatial-temporal transcriptome analysis of soybean (Glycine max) roots under water deficit to 37 identify conserved motifs that function in the water-stress response. Using these functional 38 conserved cis-motifs, we applied a new approach to trace back motifs-associated core TFs ingroup 39 2 as signal mediators, which mediate signaling between abiotic and endogenous stimuli. We 40 integrated a co-functional TF-TF network and conserved motif-centered TF-DNA networks to 41 construct a core TF network defined by mutual cross-regulation among core TFs. We found that 42 core TF ARG (Abscisic acid response element binding factor-like Root Growth regulator) 43represses BRG (Brassinosteroid enhanced expression-like Root Growth regulator) expression 44 through binding to its promoter at a conserved binding site. ARG and BRG antagonistically 45 regulate Phytochrome-interacting factor-like Root Growth regulator (PRG) and combinatorially 46 regulate some other core TFs. These core TFs form complex regulatory circuits to integrate light 47 and multiple hormone signaling pathways and maintain root growth in response to varying degrees 48 of water stress. Our study provides valuable information to unravel the complicated mechanisms 49 of molecular networks involved in the regulation of root growth under water deficit. 50 51
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