Piecing the puzzle together: Analyses in plants at the single-cell resolution

In recent years, single-cell and single-nuclei-omic technologies have advanced rapidly in plant research, with RNA sequencing being widely adopted, and chromatin accessibility profiling through assay for transposase-accessible chromatin with sequencing steadily expanding. These approaches have provided unprecedented insight into plant development, cell identity, and stress responses. Integrating transcriptomic and chromatin accessibility data has made it possible to link regulatory elements with gene expression across diverse plant tissues. The goal of this review is to provide a practical guide synthetizing current methods, bioinformatic tools, and applications for a clear perspective on the opportunities and challenges of implementing these technologies in plants. We place particular emphasis on the technical aspects of single-cell/single-nuclei methods, with the aim of enabling informed decisions regarding the choice of protocol. We also highlight emerging multi-omic strategies, the bioinformatic frameworks that enable their analysis, and applications across diverse plant species. In light of the current progress, we discuss that expanding the use of these technologies in plants will advance fundamental biology and generate actionable insights for crop improvement, driving the translation of single-cell discoveries into agricultural innovation.