| Summary: | In plants, light is an important environmental signal that induces meristem development and interacts with endogenous signals, including hormones. We found that treatment with 24 h of low-fluence red light (24 h R) or 24 h of darkness (24 h D) following root excision greatly increased the frequency of shoot generation, while continuous low-fluence red light in callus and shoot induction stages blocked the explants’ ability to generate shoots. Shoot generation ability was closely associated with <i>WUS</i> expression and distribution pattern. 1-N-naphthylphtalamic acid (NPA) disrupted the dynamic distribution of the <i>WUS</i> signal induced by early 24 h R treatment, and NPA plus 24 R treatment increased the average shoot number compared with early 24 h R alone. Transcriptome analysis revealed that differentially expressed genes involved in meristem development and hormone signal pathways were significantly enriched during 24 R or 24 D induced shoot regeneration, where early 24 h R or 24 h D treatment upregulated expression of <i>WOX5</i>, <i>LBD</i>16, <i>LBD</i>18 and <i>PLT</i>3 to promote callus initiation and formation of root primordia, and also activated <i>WUS</i>, <i>STM</i>, <i>CUC</i>1 and <i>CUC</i>2 expression, leading to initiation of the shoot apical meristem (SAM). This finding demonstrates that early exposure of explants to transient low-fluence red light or darkness modulates the expression of marker genes related with callus development and shoot regeneration, and dynamic distribution of <i>WUS</i>, leading to an increased ability to generate shoots.
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