Spatiotemporal transcriptomic and metabolomic landscapes of wild soybean seed development reveal regulatory mechanisms of nutrient accumulation

Seed development is pivotal in soybean's lifecycle, directly determining yield and nutritional quality related to oil and protein contents. However, spatiotemporally resolved mechanisms underlying cell differentiation and nutrient accumulation during seed growth remain elusive, especially in wild soybean (Glycine soja Sieb. et Zucc.), which harbors rich genetic diversity for quality traits. Here, spatial transcriptomics and metabolomics were combined to dissect their dynamics in G. soja seeds at the mid-maturity stage. Differential expression analysis characterized the distinct accumulation patterns between adaxial and abaxial embryo parenchyma cells, revealing abaxial cells are enriched in protein metabolism pathways while adaxial cells focus on lipid metabolism pathways, which is consistent with previous studies reporting spatial nutrient accumulation in G. soja seeds. Meanwhile, pseudotemporal trajectory analyses briefly supported a sequential transcriptional regulation pattern for these differences. Cell-cell communication analysis further uncovered potential signaling interactions mediating cell-type-specific differences across seed cells. Key genetic regulators and differential metabolites were identified through spatial transcriptomics and metabolomics co-expression analysis, with GsMAPK23-4 screened as a core candidate linked to cotyledon nutrient metabolism. Functional validation confirmed GsMAPK23-4 modulates seed quality: knockout mutants had significantly higher amino acids and proteins. These findings elucidate the cellular characteristics and differentiation processes in G. soja seeds at the mid-maturity stage, providing a molecular basis for understanding this phase and generating targets to improve soybean yield and quality.