Temporal TOC1-CLV3-WUS cascade controls organogenesis and rhythmic stem development

Coordinated organogenesis and rhythmic stem development determine shoot morphogenesis, which governs distinct plant architecture and crop yield. The shoot apical meristem (SAM) drives organ initiation and stem growth, with its activity sustained by the spatially defined CLAVATA3 (CLV3)-WUSCHEL (WUS) feedback loop. However, how the temporal CLV3-WUS module modulates SAM activity remains elusive. Here, we demonstrate that both CLV3 and WUS are required for circadian stem elongation. The clock component TIMING OF CAB EXPRESSION1 (TOC1) directly activates and sustains the circadian expression of CLV3, and this regulatory process is controlled by the APETALA1-CIRCADIAN CLOCK-ASSOCIATED1 module. Notably, the rhythmic expression pattern of CLV3, rather than its transcript abundance, plays a more important role in regulating WUS expression and sustaining SAM activity, and CLV3 confers circadian rhythmicity to WUS protein accumulation. Transcriptome and ChIP seq analyses reveal that WUS modulates multiple developmental programs, including meristem homeostasis, phytohormone responses, and cell wall remodeling. Mechanistically, WUS directly activates PECTIN METHYLESTERASE5 expression to promote stem elongation. Collectively, our findings uncover a spatiotemporal regulatory cascade that fine-tunes SAM activity to coordinate rhythmic organogenesis and stem development, thereby establishing optimal phyllotactic patterning in plants.