Single-nucleus and spatial transcriptomics reveal dynamic cell differentiation and storage product accumulation in rice endosperm

Rice (Oryza sativa) endosperm, a major food source worldwide, accumulates starch, proteins, and lipids. Understanding the cellular and molecular mechanisms that govern endosperm development and storage product accumulation is crucial for improving grain yield and quality. Through single-nucleus and spatial transcriptomic analyses of 177,820 nuclei and 60,003 spatial spots across four developmental stages of the rice caryopsis, we identified 12 distinct cell types and delineated seven precise anatomical regions, thereby establishing a spatially resolved single-cell transcriptomic atlas of the developing rice endosperm. Using these cell type annotations, we inferred the developmental trajectories of endosperm cells, uncovered gene regulatory networks underlying cell differentiation, and identified three key transcription factors that regulate aleurone cell-fate determination. Furthermore, we observed cellular heterogeneity in the aleurone layer and the starchy endosperm and showed how this heterogeneity coordinates nutrient transport and storage product biosynthesis during rice grain filling. This study establishes a comprehensive cellular foundation and genetic regulatory network for understanding rice endosperm formation and storage product accumulation.