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 to 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 (MERFISH), a spatial transcriptomics technique, in wheat inflorescence tissue, enabling transcript localisation for 200 genes to cellular resolution across four stages of development. Cell segmentation and clustering of 50,000 cells identified 18 expression domains and their enriched genes, revealing the spatio-temporal organisation of spikelet and floral development, and characterising tissue-level gene markers. Using these domain- and cell-level maps, we characterise 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).
Long et al. (2025) studied this question.