Dynamic and cell-type specific transcriptional reprogramming underlies the floral transition in the maize shoot apical meristem

Abstract Background The floral transition in maize represents a pivotal developmental switch that determines flowering time, environmental adaptation, and yield-related traits. However, the molecular mechanisms governing shoot apical meristem reprogramming and cell identity changes during this process remain poorly understood. Results By integrating time-course bulk RNA-seq, single-cell transcriptomics, chromatin accessibility, and transcription factor binding profiles, we construct a spatiotemporal molecular framework of the maize shoot apical meristem floral transition. Our analyses reveal global transcriptional reprogramming accompanied by pronounced cell type-specific regulation dynamics. At a global level, our transcriptional-level inference suggests that pathways associated with chromatin remodeling, environmental response, and reproductive development are sequentially activated. We further identify a ZmMADS69-ZmRap2.7-ZMM4 regulatory module that fine-tunes the floral transition within the shoot apical meristem. At single-cell resolution, we find that the floral transition is not driven by a uniform transcriptional switch, but instead emerges from the coordinated action of spatially distinct shoot apical meristem domains. Through differential expression, trajectory, and co-expression module analyses, we further identify previously unrecognized roles for the inflorescence regulators UNBRANCHED2 and UNBRANCHED3 in promoting the floral transition, suggesting that they coordinate floral induction with subsequent inflorescence development. Conclusions Our study establishes a comprehensive spatiotemporal regulatory framework for the maize floral transition, providing mechanistic insights into shoot apical meristem reprogramming and offering a foundation for identifying new regulators to improve maize adaptation and yield.