A single-cell-resolution spatial transcriptomic atlas decodes wheat spike development and yield potential

The molecular regulatory mechanisms underlying spike development critically influence wheat (Triticum aestivum) grain yield but remain incompletely understood. Using spatial transcriptomic analysis at single-cell resolution, we comprehensively mapped the spatiotemporal transcriptomes across five key stages of wheat spike development. Our approach enabled the identification and annotation of nine distinct cell types, revealing the spatiotemporal distribution of hormonal and metabolic signaling pathways across multiple cell populations. Notably, we observed variations in biosynthesis and signaling responses among key phytohormones, particularly cytokinin and auxin. We demonstrated that the rachis cell population plays a crucial role in nutrient and energy supply during spike morphogenesis. The pseudotime and RNA velocity analyses revealed cell populations with distinct differentiation states, highlighting the potential influence of spikelet primordium base (SPB) cells on lateral organ development and grain number determination. By integrating single-nucleus RNA sequencing from the W3.5 stage, gene regulatory relationships, and GWAS data from public databases, we constructed a co-expression regulatory network for wheat spike development and identified a key gene module that regulates multiple spike-related traits. Subsequent investigations characterized heterogeneous subpopulations of SPB cells and identified a novel gene cluster that substantially regulates grain number per spike. Based on spatial transcriptomics data, we have developed a publicly accessible online platform that allows users to interactively query and visualize spatiotemporal gene expression patterns during wheat spike development. Collectively, our study provides a comprehensive molecular framework for early spike development in wheat, offering valuable genetic resources and public data for functional genomics research. These data and knowledge may have significant implications for breeding efforts to optimize spike architecture and enhance wheat's grain yield potential.