ArticleNucleic acids research2023
Spatially resolved transcriptomic analysis of the germinating barley grain.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Unlocking the full potential of spatial omics in plants: practical challenges, solutions, and a path forward.The Plant cell · 2026Review
- A spatiotemporal atlas of giant-cell formation during Meloidogyne incognita infection in tomato roots.Molecular horticulture · 2026Article
- Single-Nucleus Transcriptome Analysis Provides New Insights Into B Chromosome Elimination in Sorghum.Plant biotechnology journal · 2026Article
- Single-cell insights into plant growth, adaptation, and evolution.Journal of integrative plant biology · 2026Review
- Germination as a Strategy to Enhance the Bioactivity of Whole Grains: Phytochemical Remodeling and Health Implications.Comprehensive reviews in food science and food safety · 2026Review
- Build me up to break me down: mapping grain development and germination in barley over time and space.The Plant cell · 2026Article
- A four-dimensional spatial transcriptome atlas of barley caryopsis development and germination.The Plant cell · 2026Article
- The potential of wheat spatial omics.Nature genetics · 2026Review
- Integrated Single-Cell and Spatial Transcriptomics Reveal Cell-Type-Specific Immune Regulatory Networks in Maize Responding to Southern Corn Rust.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Serial Spatial Transcriptomes Reveal Regulatory Transitions in Maize Leaf Development.Plant biotechnology journal · 2026Article
- Holistic overview of regulatory networks governing seed dormancy and germination in plants.Science China. Life sciences · 2026Review
- Spatial transcriptome analysis of the tea tender shoot sheds light on transcriptional regulation of characteristic metabolites.Horticulture research · 2026Article
- Advances in seed omics.Journal of experimental botany · 2026Review
- PreTSA: computationally efficient modeling of temporal and spatial gene expression patterns.Genome biology · 2026Article
- Towards a Holistic View of the Orchestration Between Sugar Transporters in Cereal Crops.Plants (Basel, Switzerland) · 2026Article
- Seed function in space and time: how spatial transcriptomics completes the picture.Frontiers in plant science · 2026Review
- Plant-Compatible Xenium In Situ Sequencing: Protocol for Spatial Transcriptomics in Medicago truncatula Roots and Nodules.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Why "Where" Matters as Much as "How Much": Single-Cell and Spatial Transcriptomics in Plants.International journal of molecular sciences · 2025Review
- Spatial Transcriptomics of Developing Wheat Seed Reveals Concentric Gene Expression Zones and Subgenome Biased Expression of Key Genes.Plant biotechnology journal · 2025Article
- Heterologous Expression of Bacterial Dehydrin Promotes Arabidopsis Tolerance to Cadmium and Arsenic Stress.Genes · 2025Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Seeds are a vital source of calories for humans and a unique stage in the life cycle of flowering plants. During seed germination, the embryo undergoes major developmental transitions to become a seedling. Studying gene expression in individual seed cell types has been challenging due to the lack of spatial information or low throughput of existing methods. To overcome these limitations, a spatial transcriptomics workflow was developed for germinating barley grain. This approach enabled high-throughput analysis of spatial gene expression, revealing specific spatial expression patterns of various functional gene categories at a sub-tissue level. This study revealed over 14 000 genes differentially regulated during the first 24 h after imbibition. Individual genes, such as the aquaporin gene family, starch degradation, cell wall modification, transport processes, ribosomal proteins and transcription factors, were found to have specific spatial expression patterns over time. Using spatial autocorrelation algorithms, we identified auxin transport genes that had increasingly focused expression within subdomains of the embryo over time, suggesting their role in establishing the embryo axis. Overall, our study provides an unprecedented spatially resolved cellular map for barley germination and identifies specific functional genomics targets to better understand cellular restricted processes during germination. The data can be viewed at https://spatial.latrobe.edu.au/.
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