Early Low-Fluence Red Light or Darkness Modulates the Shoot Regeneration Capacity of Excised Arabidopsis Roots

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 WUS expression and distribution pattern. 1-N-naphthylphtalamic acid (NPA) disrupted the dynamic distribution of the WUS 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 WOX5, LBD16, LBD18 and PLT3 to promote callus initiation and formation of root primordia, and also activated WUS, STM, CUC1 and CUC2 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 WUS, leading to an increased ability to generate shoots.