Multi-Omics Integrated Analysis Unravels the Pivotal Role of Lipid Mobilization in Wheat Embryos During Seed Germination Under Drought Stress

Drought stress during germination impairs seed germination and seedling development in wheat. Seed germination depends on embryo lipid mobilization for energy supply; however, the molecular mechanisms underlying lipid mobilization in drought stress germination remain unclear. Two wheat cultivars with significant differences in drought resistance, Shannong 28 (SN28) and Xinmai 296 (XM296), were subjected to integrated transcriptomic, metabolomic, and lipidomic analyses to reveal molecular response differences. SN28 exhibited increased root length (RL), while XM296 showed significant decreases in germination energy (GE), vigor index (VI), and single seedling dry weight (SSDW). Multi-omics integration revealed that SN28 maintained efficient lipid mobilization under drought through a distinctive regulatory strategy: suppressing jasmonic acid synthesis to prevent excessive growth inhibition, activating α-DOX1 signaling to maintain defense function, and coordinating these with low expression of ABA signaling factors MYB96 and ABI4 to relieve lipid mobilization suppression. Upregulated lipase and nsLTP genes (TaLTPIe.1, TaLTPIg.1) promoted lipid mobilization, while coordinated activation of arginine–proline metabolism, zeatin biosynthesis, and antioxidant defense pathways provided metabolic support. In contrast, XM296’s extensive inhibition of lipoxygenase enzymes and insufficient lipid mobilization capacity directly underlies its drought susceptibility. These findings indicate that cultivar-specific lipid metabolism patterns are key determinants of germination-stage drought resistance, providing candidate genes for wheat breeding.