Multiomics Analysis Reveals Multiple Metabolic Processes, Phytohormone Signaling, and the Negative Regulatory Role of ZmPP2CA11 in Maize Seedling Water Deficit Responses

Abstract Water deficit limits maize establishment, but coordinated hormonal and metabolic responses remain incompletely understood. Physiological phenotyping, RNA sequencing, widely targeted metabolomics, and phytohormone profiling were integrated to characterize B73 seedlings during PEG-induced osmotic stress and early recovery. Stress reduced growth and leaf water status and increased the level of oxidative injury. The 266 differentially expressed genes (DEGs) and 47 differentially accumulated metabolites (DAMs) were associated with abscisic acid (ABA) and jasmonate (JA) signaling, amino acid (AA) metabolism, benzoxazinoid (BX) biosynthesis, and indole-derived metabolism. ABA, JA, and JA-Ile accumulated during stress and declined after PEG removal, whereas DIMBOA-Glc remained elevated during the recovery. Correlation and coexpression analyses identified ZmPP2CA11 as an ABA-associated hub gene. Two independent knockout lines showed reduced water loss, improved water status and growth under soil water deficit, and enhanced ABA-induced stomatal closure. These findings reveal coordinated hormonal and metabolic responses and identify ZmPP2CA11 as an ABA-associated negative regulator of water deficit adaptation.