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

Dong, Liang, Sun, Yonghao, Kang, Lu, Li, Zichao, Liang, Yameng, Sheng, Huangjun, Tian, Feng, Jackson, David, Yang, Fang (March 2026) Dynamic and cell-type specific transcriptional reprogramming underlies the floral transition in the maize shoot apical meristem. Genome Biology, 27 (1). p. 143. ISSN 1474-7596

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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.

Item Type:	Paper
Subjects:	organism description > plant > maize organs, tissues, organelles, cell types and functions > tissues types and functions > apical meristem organs, tissues, organelles, cell types and functions > tissues types and functions > meristem organs, tissues, organelles, cell types and functions organism description > plant organs, tissues, organelles, cell types and functions > tissues types and functions
CSHL Authors:	Jackson, David P.
Communities:	CSHL labs > Jackson lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	18 March 2026
Date Deposited:	12 May 2026 14:20
Last Modified:	12 May 2026 14:20
PMCID:	PMC13112620
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/42199

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