ArticlePlant physiology2022
An in situ sequencing approach maps PLASTOCHRON1 at the boundary between indeterminate and determinate cells.
Article in Plant physiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 47 citations in OpenAlex.
- Unlocking the full potential of spatial omics in plants: practical challenges, solutions, and a path forward.The Plant cell · 2026Review
- Multimodal single cell analysis reveals a link between flowering and leaf initiation.bioRxiv : the preprint server for biology · 2026Article
- Serial Spatial Transcriptomes Reveal Regulatory Transitions in Maize Leaf Development.Plant biotechnology journal · 2026Article
- Imputation integrates single-cell and spatial gene expression data to resolve transcriptional networks in barley shoot meristem development.Nature plants · 2026Article
- Large-scale single-cell profiling of stem cells identifies redundant regulators of shoot development and yield trait variation.Developmental cell · 2025Article
- Unlocking grass leaf development: foundations for tunable cereal design.The New phytologist · 2025Review
- Exploring the untapped potential of single-cell and spatial omics in plant biology.The New phytologist · 2025Review
- Diverse roles of ethylene in maize growth and development, and its importance in shaping plant architecture.Journal of experimental botany · 2025Review
- Multiplexed transcriptomic analyzes of the plant embryonic hourglass.Nature communications · 2025Article
- Spatial-Omics Methods and Applications.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Harnessing Single-Cell and Spatial Transcriptomics for Crop Improvement.Plants (Basel, Switzerland) · 2024Review
- Multiplexed in situ hybridization reveals distinct lineage identities for major and minor vein initiation during maize leaf development.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics.The Plant cell · 2024Article
- The Shoot Apical Meristem: An Evolutionary Molding of Higher Plants.International journal of molecular sciences · 2024Review
- A rapid and sensitive, multiplex, whole mount RNA fluorescence in situ hybridization and immunohistochemistry protocol.Plant methods · 2023Article
- Exploring the identity of individual plant cells in space and time.The New phytologist · 2023Review
- Multiplexed single-cell 3D spatial gene expression analysis in plant tissue using PHYTOMap.Nature plants · 2023Article
- Characterization of Gene Regulatory Networks in Plants Using New Methods and Data Types.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Putting genes on the map: Spatial transcriptomics of the maize shoot apical meristem.Plant physiology · 2022Article
- Single-cell genomics revolutionizes plant development studies across scales.Development (Cambridge, England) · 2022Article
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Authors and funding
13 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The plant shoot apex houses the shoot apical meristem, a highly organized and active stem-cell tissue where molecular signaling in discrete cells determines when and where leaves are initiated. We optimized a spatial transcriptomics approach, in situ sequencing (ISS), to colocalize the transcripts of 90 genes simultaneously on the same section of tissue from the maize (Zea mays) shoot apex. The RNA ISS technology reported expression profiles that were highly comparable with those obtained by in situ hybridizations (ISHs) and allowed the discrimination between tissue domains. Furthermore, the application of spatial transcriptomics to the shoot apex, which inherently comprised phytomers that are in gradual developmental stages, provided a spatiotemporal sequence of transcriptional events. We illustrate the power of the technology through PLASTOCHRON1 (PLA1), which was specifically expressed at the boundary between indeterminate and determinate cells and partially overlapped with ROUGH SHEATH1 and OUTER CELL LAYER4 transcripts. Also, in the inflorescence, PLA1 transcripts localized in cells subtending the lateral primordia or bordering the newly established meristematic region, suggesting a more general role of PLA1 in signaling between indeterminate and determinate cells during the formation of lateral organs. Spatial transcriptomics builds on RNA ISH, which assays relatively few transcripts at a time and provides a powerful complement to single-cell transcriptomics that inherently removes cells from their native spatial context. Further improvements in resolution and sensitivity will greatly advance research in plant developmental biology.
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