Lateral roots (LRs) are a major determinant of the root system architecture in plants, and thus developmental plasticity of LR formation is important for the survival of plants to changing environmental conditions. In Arabidopsis thaliana, the genetic pathways regulating LR branching in response to environmental cues such as some nutrients, salt and gravity have been identified. However, it is not known how genetic components are involved in LR adaptation response to cold. Here we demonstrate that CYTOKININ RESPONSE FACTOR2 (CRF2) and CRF3 encoding APETALA2 transcription factors play an important role in Arabidopsis LR initiation under cold stress. CRF2 was induced by cold via a subset of two-component signaling (TCS) pathways, whereas CRF3 was upregulated by cold via TCS-independent pathways. crf2 crf3 double mutants showed additively decreased LR densities of each single mutant, while CRF2 or CRF3 overexpression caused increased LR densities. Analysis of LR developmental kinetics demonstrated that both CRF2 and CRF3 regulate LR initiation. crf2 and crf3 single and double mutants exhibited additively decreased LR initiations under cold stress compared to wild-type. Our results suggest that CRF2 and CRF3 respond to cold via TCS-dependent and TCS-independent pathways and control LR initiation and development, contributing to LR adaptation response to cold stress.

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