Probing cellular landscapes in plants via single-cell transcriptomics

Single-cell RNA sequencing (scRNA-seq) has brought a significant shift in our ability to dissect plant cellular heterogeneity and developmental processes with unprecedented resolution. However, its integration with functional genomics and spatial technologies in plant systems remains limited, leaving critical gaps in our understanding of gene regulation, stress responses, and cell fate decisions. In this review, we provide a comprehensive synthesis of scRNA-seq applications across diverse plant tissues, illustrating how these datasets have uncovered developmental trajectories, lineage dynamics, and cell-type-specific transcriptional programs, including cell identity transitions and developmental plasticity. We further highlight how scRNA-seq has revealed cell-layer-specific responses to abiotic and biotic stresses, and its emerging role in tracing the production of specialized metabolites and dissecting mutational effects at single-cell resolution. Notably, we highlight how scRNA-seq enables the precise identification of candidate genes, which have been functionally validated through CRISPR/Cas9-mediated genome editing to enhance specific traits. We also explore recent advances in spatial transcriptomics and emerging multi-omics approaches that combine transcriptomic data with chromatin accessibility or protein expression. Uniquely, our review integrates insights across plant species and tissue types, offering a cross-cutting perspective on plant development and adaptation. Finally, we critically evaluate key technical challenges, such as protoplast isolation, limited marker gene availability, and cell-type annotation, and propose potential solutions. Collectively, this review offers a timely overview of how single-cell and spatial transcriptomics have advanced gene discovery and trait improvement by enabling high-resolution insights into plant tissue development and stress responses.