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Spatial transcriptomics reveals expression gradients in developing wheat inflorescences at cellular resolution
Katie A Long1, Ashleigh Lister2, Maximillian R W Jones1
1John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom.
The Plant Cell
|December 13, 2025
Summary
Spatial transcriptomics in wheat reveals gene expression patterns shaping inflorescence development. This study maps gene activity at cellular resolution, uncovering factors controlling spikelet formation along the apical-basal axis.
Area of Science:
- Plant biology
- Developmental biology
- Genomics
Background:
- Plant inflorescence architecture diversity is driven by gene expression.
- Wheat spike development involves delayed basal spikelet formation.
- Previous studies lacked cellular resolution for apical-basal gene expression.
Purpose of the Study:
- To optimize spatial transcriptomics for wheat inflorescence.
- To map gene expression at cellular resolution across development.
- To identify gene expression patterns along the apical-basal axis.
Main Methods:
- Optimized Multiplexed Error Robust Fluorescence In Situ Hybridization (MERFISH).
- Analyzed 50,000 cells across 4 developmental stages.
- Performed cell segmentation and clustering to define expression domains.
Main Results:
- Identified 18 distinct gene expression domains and markers.
- Revealed spatio-temporal organization of spikelet and floral development.
- Characterized spatially coordinated expression patterns in meristems and leaf ridges.
Conclusions:
- Discovered novel insights into meristem identity and transition factors.
- Provided a cellular-resolution map of wheat inflorescence development.
- Made all data publicly available via an interactive WebAtlas interface.
