Single-cell network analysis reveals gene expression programs for Arabidopsis epidermis development and metabolism

The epidermis plays essential physiological roles in plants, yet its underlying gene regulatory programs remain poorly defined. To address this gap, we integrated 11 public single-cell RNA-seq datasets of Arabidopsis shoots and leaves, extracted 30 247 epidermal cells, and constructed a single-cell gene co-expression network, AtEpidermisGGM, using the SingleCellGGM algorithm. From this network, we identified 120 co-expression modules, termed gene expression programs (GEPs), that delineate key developmental and metabolism processes of epidermal lineages. Spatial-temporal analysis revealed GEPs associated with L1-layer epidermis in the shoot apical meristem, asymmetric and symmetric cell divisions during early stomatal development, and subsequent guard cell initiation, maturation, and functioning. Leveraging these GEPs, we discovered and validated the roles of DMS1/2-expressed during the symmetric cell division stage of stomatal development-in regulating stomatal density, and of DGC1/2/3-specifically expressed in mature stomata-in controlling stomatal movement. Overall, AtEpidermisGGM provides a comprehensive map of epidermal gene programs, uncovering molecular modules that coordinate epidermal development and metabolism, and offering a valuable resource for advancing plant epidermal biology.