A cellular view of seed development and germination

Seeds are fundamental to global food security, yet their encapsulated structure, dense storage compounds, and spatial heterogeneity have created a "hidden box" problem, often restricting research to bulk and tissue approaches that mask cell type-specific regulatory programs. Advances in single-cell and spatial transcriptomics now enable systematic dissection of seed biology at cellular resolution. This review provides a cellular view spanning the developmental continuum from fertilization to seedling establishment by synthesizing single-cell and spatial transcriptomic studies in Arabidopsis thaliana and major crops (Oryza sativa-rice, Zea mays-maize, Hordeum vulgare-barley, Glycine max-soybean, Triticum aestivum-wheat). These technologies reveal previously undetected cellular complexity and heterogeneity: distinct transcriptional subpopulations within morphologically uniform tissues, specialized endosperm microdomains mediating nutrient transfer and metabolic polarity, cell type-specific genomic imprinting patterns, and spatially segregated hormone signaling hubs controlling dormancy and germination. Integration of transcriptional profiling with chromatin accessibility and transcription factor binding data has enabled construction of cell type-specific gene regulatory networks for seeds, advancing from correlation to causal inference and identifying master regulators of developmental transitions. These approaches illuminate how early embryonic patterning establishes transcriptional identities, how metabolic zonation coordinates storage compound accumulation and mobilization, how chromatin states maintain dormancy and license germination competence, and how spatiotemporal coordination integrates hormone signaling with energy metabolism across tissues. Single-cell and spatial approaches are establishing seeds not as opaque structures but as assemblies of coordinated cellular programs amenable to systematic analysis and targeted manipulation for crop improvement.