A blue light receptor CRY1 regulates de novo shoot regeneration

Tissue culture enables plant transformation and gene editing, yet inefficient regeneration remains a major bottleneck, and the downstream circuitry linking light perception to tissue culture has not been investigated. Here we demonstrate that the blue-light photoreceptor CRYPTOCHROME 1 (CRY1) enhances Arabidopsis thaliana shoot regeneration in a blue light dependent manner. In a two-step root-to-shoot tissue culture system, cry1 mutant exhibits reduced shoot regeneration. Transcriptomic analyses in the cry1 mutant reveal that CRY1 suppresses the expression of AUXIN RESPONSE TRANSCRIPTION FACTOR 3 (ARF3). Consistently, arf3 mutant exhibits enhanced shoot regeneration phenotype. Additionally, genetic and protein interaction assays show that ARF3 acts downstream of CRY1 at both transcriptional and post-translational levels. Furthermore, transcriptomic analyses in the arf3 mutant show that ARF3 activates salicylic acid (SA)-responsive genes that suppress shoot formation, and exogenous SA inhibits regeneration in arf3 calli. Integrating RNA-seq with cis-motif analysis identifies stress-responsive ARF3 targets within the CRY1 network. Our results establish a novel CRY1-ARF3 regulatory module that links blue-light perception to hormonal signaling during regeneration, revealing how plants integrate environmental cues with growth-defense trade-offs. SynopsisThe blue-light photoreceptor CRY1 promotes de novo shoot regeneration in Arabidopsis thaliana by restraining ARF3-mediated SA signaling. It reveals a fundamental trade-off between defense responses and regenerative growth in plants, coordinated by CRY1-ARF3 module. O_LICRY1-mediated blue light signaling enhances de novo shoot regeneration from callus. C_LIO_LIARF3 acts downstream of CRY1 and CRY1 physically interacts with ARF3. C_LIO_LIARF3-activated SA pathway represses shoot regeneration. C_LIO_LICRY1 enhances shoot regeneration by suppressing ARF3-activated stress responsive genes. C_LI