Aug 2026· Plant Communications· pp.
102070
· 0 citations
Medicine
TL;DR
This review synthesizes recent progress across diverse plant species and tissues, showing that gene expression is not only cell-type specific but also tightly organized by position within organs and developmental niches, establishing spatial gene expression as a fundamental organizing principle of plant development and physiology.
Abstract
Spatial transcriptomics has transformed plant biology by restoring the spatial context lost in bulk and dissociation-based transcriptomic approaches. This review synthesizes recent progress across diverse plant species and tissues, showing that gene expression is not only cell-type specific but also tightly organized by position within organs and developmental niches. Studies of meristems, vascular tissues, and floral organs reveal spatially segregated developmental programs underlying growth and differentiation; seed and grain analyses uncover compartmentalized programs controlling nutrient transport, dormancy, and embryogenesis; plant-microbe and emerging plant-parasite studies show that symbiosis, immunity, and feeding-site development depend on sharply localized host responses; and work on photosynthesis, drought adaptation, and regeneration demonstrates that metabolic and stress-related processes are likewise spatially patterned. Together, these findings establish spatial gene expression as a fundamental organizing principle of plant development and physiology. At the same time, the plant spatial transcriptomics community faces important limitations, including restricted spatial resolution in standard array-based platforms, reliance on computational deconvolution, uneven taxonomic coverage, limited temporal resolution, and a persistent gap between correlation and causal validation. The next stage of plant spatial transcriptomics will require true single-cell spatial resolution, standardized computational pipelines, spatial multi-omics integration, improved benchmarking across platforms, and functional perturbation of spatially defined regulators. By connecting transcriptomic position to biological function, spatial transcriptomics is poised to move plant science from descriptive atlas-building toward mechanistic and predictive understanding with major implications for crop improvement and resilience.
Spatiotemporal gene expression is the underlying determinant of how living things grow and function, including the processes of seed development and germination. Understanding how these regulatory pathways work in space and time is critical to harnessing the functional diversity of the components of the seed and enhancing beneficial traits. The recent development of spatial transcriptomics technologies has greatly added to the knowledge of gene expression within plant and animal tissues but has only been applied in a handful of studies to seeds. Here we conduct a review of the literature on spatial omics research in developing and germinating seeds of wheat, barley, maize, rice, wild soybean and Arabidopsis, highlighting the major contributions to the field and the challenges faced. We outline how spatial transcriptomics has significantly improved the scale and resolution of gene expression analyses, revealing how the transcriptome explains the complete tissue architecture of the seed. This has resulted in the discovery of novel cell-subtypes, spatiotemporal gene expression gradients, and coordinated nutrient transport across tissues, completing the picture of seed composition in greater detail than could previously be achieved.
Tori Millsteed, Robert J Henry· Frontiers in Plant Science· 0 citations
Single-cell and spatial transcriptomics are transforming our ability to understand how crop roots respond to soil stress by resolving gene expression at cellular resolution within intact tissues. This is particularly important because roots grow in heterogeneous soil environments, where physical structure, mechanical impedance, water availability, and nutrient distribution vary at fine spatial and temporal scales. Such complexity generates dynamic and localized stress signals that cannot be captured by bulk transcriptomics. The logic of applying these approaches lies in linking soil structure and stress gradients to cell-specific transcriptional responses that ultimately regulate root growth. While recent advances have enabled single-cell atlases in several crop species and emerging spatial transcriptomic datasets, most studies have been conducted under simplified conditions (e.g. gels, hydroponics, artificial chemical treatments), only few studies are adopting soil stresses. Despite this progress, major gaps remain, including the need for true in-situ spatial maps in intact agriculture soil systems, integration with temporal dynamics of root growth, and coupling transcriptional data with local measurements of water status, mechanical stress, gaseous diffusion, microbial assembly and nutrient gradients. Addressing these challenges will be essential to capture the full complexity of root responses and to translate cell-level transcriptional dynamics under realistic soil stress conditions.
Grace Denis, Samuel Jamieson, Poonam Mehra et al.· Journal of Experimental Bota...· 0 citations
Plant immune responses are shaped by cellular identity and tissue context. During interactions with pathogenic microbes, different plant cell types activate distinct defense-associated transcriptional programs that are not readily resolved using whole-tissue analyses. As a result, bulk transcriptomic approaches have limited our ability to capture spatial and cellular heterogeneity during immune responses. Recent advances in single-cell RNA sequencing and spatial transcriptomics have enabled the analysis of plant immune responses at cellular resolution while preserving spatial information. Studies using these approaches have revealed heterogeneous and coordinated transcriptional responses across cell types and tissue regions during pathogen attacks. In this review, we summarize recent single-cell and spatial transcriptomic studies across diverse plant-pathogen systems, highlighting how these methods contribute to a more refined understanding of cell-type-specific immune responses, intercellular communication, and spatial organization of defense responses within plant tissues. We also discuss current technical limitations and future directions for applying spatially resolved transcriptomic approaches in plant-pathogen interaction research.
Chia-Yun Lee, Suchismita Ghosh, Kevin L. Cox· Journal of Experimental Bota...· 0 citations
Recent advances in single-cell and spatial omics technologies are transforming plant research by enabling cell-resolved analyses of gene expression, proteomics, chromatin organization, and metabolism at the level of individual cells and at spatial resolution. These approaches have revealed extensive cellular heterogeneity, rare and transient cell states, and previously unrecognized developmental and physiological programs. However, they also introduce conceptual, technical, and computational challenges related to data quality and integration, and biological interpretation. In this review, we summarize the emerging opportunities and key bottlenecks in plant single-cell and spatial biology. We discuss how embedding single-cell data within evolutionary developmental frameworks can accelerate the discovery of functionally relevant genes, and how spatial transcriptomics may enable comparative study designs, the study of cell-to-cell communication, and multi-organism spatial analyses. We also explore how integrating multiple datatypes and gene regulatory network inference can move the field from descriptive atlases toward mechanistic insights. Finally, we highlight the importance of visualization strategies across spatial, temporal, environmental, and evolutionary scales. Overall, we argue that careful experimental design, robust data integration, and a clear understanding of cell identity are essential to obtain the full potential of plant single-cell and spatial omics in basic research and crop improvement.
L. de Veylder, Maite Saura-Sánchez, B. De Rybel et al.· The Plant Cell· 0 citations
Plant development arises from the coordinated execution of gene regulatory programs across diverse cell types. While classical genetic and genomic approaches have revealed many of the genes required for plant growth and patterning, these methods often average signals across heterogeneous tissues, thereby obscuring how regulatory programs operate within individual cells. Resolving gene expression at cellular resolution is therefore essential for understanding how developmental decisions are made, integrated, and propagated during organ growth. The Arabidopsis root, with its simple anatomy and invariant cell lineages, provides an ideal system for addressing these questions. Recent advances in single-cell and single-nucleus transcriptomics have enabled the construction of comprehensive cellular atlases that capture gene expression dynamics across cell identities and developmental trajectories. In this Expert Views article, we highlight recent conceptual and technical developments that illustrate how single-cell atlases have transformed studies of root development. We emphasize how these atlases both serve as community resources to inform the interpretation of new datasets, including those generated from mutants and in response to perturbation, as well as provide a platform for meta-analysis to initiate new studies. Using auxin signaling as a meta-analysis case study, we demonstrate how legacy transcriptomic data can be reinterpreted within a cell lineage-resolved framework. Finally, we highlight how spatial transcriptomics and rigorous data-sharing practices will extend cellular atlases across tissues and species, thereby enabling increasingly precise strategies for understanding and engineering plant growth and resilience.
Min Chen, Saahithi Kari, Pablo Szekely et al.· Journal of Experimental Bota...· 0 citations
Single-cell RNA sequencing (scRNA-seq) has transformed transcriptomic studies by enabling gene expression profiling at the resolution of individual cells within and across a broad range of tissue types, revealing cellular heterogeneity that is obscured in bulk tissue transcriptomes. Over the past decade, improvements in microfluidics and library preparation have drastically increased throughput, allowing tens of thousands of cells to be assayed in a single experiment. Although initially developed in animal systems, scRNA-seq has rapidly emerged as a powerful and widely adopted approach in plant biology. Beyond transcriptomics, the integration of single-cell data with chromatin accessibility, proteomics, metabolomics, and spatial omics is enabling a system-level understanding of plant gene regulation and cellular organization. Network-based analytical frameworks further support the reconstruction of gene regulatory networks and the interpretation of complex single-cell data. In this review, we summarize the current technological landscape of plant single-cell studies, discuss key experimental and analytical challenges, and review emerging strategies for validating single-cell discoveries. We also discuss future directions in applying single-cell technologies to woody perennials plants and bioenergy-relevant crops, emphasizing their potential to accelerate the discovery of cell type-specific regulatory mechanisms underlying growth, stress resilience, and biomass production.
Miaomiao Li, Gabriela Madrid, Mallory Morgan et al.· Journal of Experimental Bota...· 0 citations
