Spatiotemporal transcriptomics reveals key gene regulation for grain yield and quality in wheat

Cereal grain size and quality are critical agronomic traits in crop production. Wheat grain development is governed by intricate regulatory networks that require precise spatiotemporal coordination of gene expression to establish functional compartments in different cell types. Here, we perform a spatial transcriptomics study covering the early stages of wheat grain development, from 4 to 12 days after pollination. We classify the grain into 10 distinct cell types and identify 192 marker genes associated with them. WGCNA analysis reveals that highly expressed genes in different cell types exhibit distinct enrichment patterns, significantly influencing grain development and filling. Through co-expression and motif analyses, we identify a specific group of genes that may regulate wheat grain development, including TaABI3-B1, a transcription factor specifically expressed in the embryo and surrounding endosperm, which negatively affects embryo and grain size. This study presents a comprehensive spatiotemporal transcriptional dataset for understanding wheat grain development. Additionally, it identifies key genetic resources with potential applications for improving wheat yield.