Single-cell RNA sequencing (scRNA-seq) analyses map transcriptional networks during plant development, but rare cell populations or expression values for several genes are often missing. As the origin or position of cells correlates with specific gene expression markers, we spatially resolved gene expression during barley meristem development by integrating a scRNA-seq dataset from cells with unknown position with spatial transcriptomics. This dataset is publicly available through the online web-based BARVISTA application.
This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$32.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 digital issues and online access to articles
$119.00 per year
only $9.92 per issue
Buy this article
- Purchase on SpringerLink
- Instant access to the full article PDF.
USD 39.95
Prices may be subject to local taxes which are calculated during checkout
References
Kellogg, E. A. Genetic control of branching patterns in grass inflorescences. Plant Cell 34, 2518–2533 (2022). A review article that discusses the molecular mechanisms controlling branching of grass inflorescences.
Lohoff, T. et al. Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis. Nat. Biotechnol. 40, 74–85 (2022). This paper reports gene expression imputation in mouse brain.
Poursarebani, N. et al. COMPOSITUM 1 contributes to the architectural simplification of barley inflorescence via meristem identity signals. Nat. Commun. 11, 5138 (2020). This paper reports the cloning and phenotypic characterization of com1a;com2g.
Guillotin, B. et al. A pan-grass transcriptome reveals patterns of cellular divergence in crops. Nature 617, 785–791 (2023). This paper reports a scRNA-seq-based pan-transcriptome using roots from multiple grass species.
Xu, X. et al. Large-scale single-cell profiling of stem cells identifies redundant regulators of shoot development and yield trait variation. Dev. Cell 60, 3514–3526.e7 (2025). This paper reports the use of adapted protocols and mutants to efficiently capture stem cells in maize for scRNA-seq.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
This is a summary of: Demesa-Arevalo, E. et al. Imputation integrates single-cell and spatial gene expression data to resolve transcriptional networks in barley shoot meristem development. Nat. Plants https://doi.org/10.1038/s41477-025-02176-6 (2026).
Rights and permissions
About this article
Cite this article
Gene expression imputation spatially resolves transcriptional programs in barley spike development. Nat. Plants 12, 12–13 (2026). https://doi.org/10.1038/s41477-025-02177-5
Published:
Version of record:
Issue date:
DOI: https://doi.org/10.1038/s41477-025-02177-5
