Spatial and temporal dynamics of gene expression across wheat inflorescence development

Inflorescence architecture is central to reproductive success in grasses and strongly influences yield-related traits in crops such as wheat (Triticum aestivum L.). Inflorescence architecture is patterned by gene expression, which influences the initiation and arrangement of spikelets —the repeating units of the grass inflorescence. Characterising these expression patterns across space and time is essential to understanding inflorescence development. In this thesis, I apply spatial transcriptomics to characterise gene expression across wheat inflorescence development. Using Multiplexed Error-Robust Fluorescence In Situ Hybridisation (MERFISH), we mapped the expression patterns of 200 genes to cellular resolution across four developmental stages, within their native tissue context. Analysis 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 MERFISH, we investigated gene expression patterning along the apical–basal axis of the wheat spike. In wheat, the lanceolate-shaped inflorescence is defined by rudimentary spikelets at the base, which form as a result of delayed spikelet and floral development. Using domain- and cell-level maps, we identified distinct, spatially coordinated expression patterns that distinguish axillary meristems and their subtending leaf ridges across the apical-basal axis before visible spikelet formation, highlighting novel factors that pattern meristem identity and transition. Given the novelty of spatial transcriptomics techniques to plant sciences, I document the optimisation of both imaging-based and sequencing-based approaches. In addition to MERFISH, I present the first application of Spatio-Temporal Enhanced Resolution Omics sequencing (Stereo-seq) to wheat inflorescence tissue, critically assessing its performance and limitations. Together, this work establishes spatial transcriptomics as a powerful technique for characterising developmental programs in complex plant tissues and provides new insights into the genetic regulation of wheat inflorescence development.