Spatial transcriptomics reveals expression gradients in developing wheat inflorescences at cellular resolution

The diversity of plant inflorescence architecture is specified by gene expression patterns. In wheat (Triticum aestivum), the lanceolate-shaped inflorescence (spike) is defined by rudimentary spikelets at the base, which form as a result of delayed spikelet and floral development compared with central spikelets. While previous studies identified gene expression differences between central and basal inflorescence sections, gene expression patterns along the apical-basal axis remain poorly resolved due to bulk tissue-level techniques. Here, we optimize Multiplexed Error Robust Fluorescence In Situ Hybridization, a spatial transcriptomics technique, in wheat inflorescence tissue, enabling transcript localization for 200 genes to cellular resolution across 4 stages of development. Cell segmentation and clustering of 50,000 cells identified 18 expression domains and their enriched genes, revealing the spatio-temporal organization of spikelet and floral development, and characterizing tissue-level gene markers. Using these domain- and cell-level maps, we characterize expression patterns of genes differentially expressed across the apical-basal axis. We identify distinct, spatially coordinated expression patterns distinguishing axillary meristems and their subtending leaf ridges across the apical-basal axis before visible spikelet formation, highlighting factors patterning meristem identity and transition. To support the broader research community, all raw and processed data are publicly available, including through an interactive WebAtlas interface (www.wheat-spatial.com).

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Publication Details

Journal
The Plant Cell
Published
2025-12-12
DOI
https://doi.org/10.1093/plcell/koaf282
Citations
2
Primary Topic
Plant Molecular Biology Research
Type
article
Field-Weighted Citation Impact
3.50

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article

Spatial transcriptomics reveals expression gradients in developing wheat inflorescences at cellular resolution

Jun Ying Xiao, Wilfried Haerty, Maximillian R. W. Jones, Carole Chedid et al.
2 citations
The Plant Cell
Plant Molecular Biology Research
3.50
article

Spatial transcriptomics reveals expression gradients in developing wheat inflorescences at cellular resolution

Jun Ying Xiao, Wilfried Haerty, Maximillian R. W. Jones, Carole Chedid, Anna E. Backhaus, Ashleigh Lister, Iain C. Macaulay, Nikolai M. Adamski, Martin Vickers, Andrew Goldson, Yuanrong Pei, Gemy Kaithakottil, Cristóbal Uauy, Burkhard Steuernagel, Xuemei Liu, Vanda Knitlhoffer, Katie Long, Rob E. Ellis, Sophie J. Carpenter
article en
2 citations

Abstract

The diversity of plant inflorescence architecture is specified by gene expression patterns. In wheat (Triticum aestivum), the lanceolate-shaped inflorescence (spike) is defined by rudimentary spikelets at the base, which form as a result of delayed spikelet and floral development compared with central spikelets. While previous studies identified gene expression differences between central and basal inflorescence sections, gene expression patterns along the apical-basal axis remain poorly resolved due to bulk tissue-level techniques. Here, we optimize Multiplexed Error Robust Fluorescence In Situ Hybridization, a spatial transcriptomics technique, in wheat inflorescence tissue, enabling transcript localization for 200 genes to cellular resolution across 4 stages of development. Cell segmentation and clustering of 50,000 cells identified 18 expression domains and their enriched genes, revealing the spatio-temporal organization of spikelet and floral development, and characterizing tissue-level gene markers. Using these domain- and cell-level maps, we characterize expression patterns of genes differentially expressed across the apical-basal axis. We identify distinct, spatially coordinated expression patterns distinguishing axillary meristems and their subtending leaf ridges across the apical-basal axis before visible spikelet formation, highlighting factors patterning meristem identity and transition. To support the broader research community, all raw and processed data are publicly available, including through an interactive WebAtlas interface (www.wheat-spatial.com).

The Plant CellVol. 38(1)
John Innes Centre (GB), Biogen (United States) (US), International Center for Agricultural Research in the Dry Areas (LB), Chinese Academy of Sciences (CN), Norwich Research Park (GB), Earlham Institute (GB), Institut Supérieur du Génie Appliqué (MA), Institute of Genetics and Developmental Biology (CN), Repligen (United States) (US)
UK Research and Innovation, Directorate for Biological Sciences, Biotechnology and Biological Sciences Research Council
Openalex Percentile: Top 7%
Plant Molecular Biology Research
3.50
DOIOpen Access PDFOpenAlex
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