22 January 2026
How do just a few cells give rise to the complex floral structures of crops such as barley? An international research team from the CEPLAS Cluster of Excellence has now answered this question at cellular resolution. In a study recently published in the journal Nature Plants, the researchers present the first detailed cell map of barley ear development. Scientists from the Institute of Bio- and Geosciences – Bioinformatics (IBG-4) at Forschungszentrum Jülich contributed key expertise to the project.
The team focused on the shoot meristem – a specialised tissue at the tip of young plants from which flowers, and ultimately grains, are formed. Which type of cell emerges in this region depends strongly on its position within the tissue and on which genes are active at a given time.
To capture these processes in detail, the researchers combined two state-of-the-art approaches. Single-cell transcriptomics was used to determine which genes are active in individual cells, while a spatial gene expression method revealed the precise location of these cells within the tissue. The challenge lay in the fact that the two datasets provide complementary information and cannot easily be integrated.
This is where expertise from Forschungszentrum Jülich proved crucial. Hannah Dörpholz from IBG-4 developed a computational gene expression imputation method that allows missing information to be inferred. Using this approach, the team was able to integrate both datasets and generate expression profiles for more than 40,000 genes at single-cell resolution.
With the help of a web-based visualisation tool, the researchers then traced how undifferentiated cells gradually develop into specialised floral organs. They identified marker genes that define specific cell types, as well as genes whose activity changes along the developmental axis of the barley ear. At later stages, particular attention was drawn to genes from the MADS transcription factor family. These genes act as central regulatory switches, controlling how and when individual floral organs form – processes that ultimately influence grain formation and yield.
Beyond providing new insights into the development of barley – one of the world’s most important crops – the study establishes a transferable analytical framework that can be applied to other plant species. Existing datasets can be re-analysed using this approach, reducing the need for costly and time-intensive experiments.
All data generated in the project, as well as the BARVISTA visualisation platform developed at Forschungszentrum Jülich, are publicly available. They adhere to the FAIR principles, meaning the data are findable, accessible, interoperable and reusable by the scientific community. The project therefore lays an important foundation for future research in plant and agricultural sciences.
Demesa-Arevalo, E., Dӧrpholz, H., Vardanega, I. et al. Imputation integrates single-cell and spatial gene expression data to resolve transcriptional networks in barley shoot meristem development. Nat. Plants (2026). https://doi.org/10.1038/s41477-025-02176-6
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