Serial Spatial Transcriptomes Reveal Regulatory Transitions in Maize Leaf Development

Plant leaves originate from the shoot apical meristem (SAM) and undergo a developmental process of highly coordinated gene expression regulation. To date, only a few key regulators have been identified and characterised, so the gene expression cascades responsible for leaf cell specification and differentiation from SAM remain largely elusive. Here, we optimised a spatial transcriptomics protocol using the 10× Genomics Visium system and developed computational pipelines to reconstruct three-dimensional gene expression profiles of the SAM and sequentially developing leaves in maize seedlings. These enabled positional indexing of cells sampled from consecutive developmental stages, revealing dynamic transitions from undifferentiated stem cells in the SAM to functionally differentiated leaf structures. Through spatial-temporal transcriptome analysis, we identified distinct transcriptional programs and key regulatory genes involved in meristem maintenance, leaf primordia initiation, vascular tissue differentiation, and cellular heterogeneity. This approach outperforms the single-cell transcriptome profiling, which lacks temporal and spatial contexts. Our optimised experimental pipeline, which goes from section preparation to data processing, enables the spatial resolution and 3-dimensional mapping of gene expression profiles. The established pipeline is readily applicable to delineating molecular events underlying developmental transitions, cell type specifications, and differentiation in plants.