Towards dual-stage flood resilience: merging anaerobic germination and submergence tolerance in rice

Flooding threatens rice (Oryza sativa L.) during the germination/establishment and vegetative growth stages. Rice mitigates these hazards via two stage-specific strategies. Anaerobic germination (AG) enables escape-by-elongation, powered by starch mobilization through the CBL4-CIPK15-SnRK1A-MYBS1 cascade and trehalose-6-phosphate (Tre6P) tuning via Tre6P phosphatase 7 (TPP7/AG1); ABA inactivation and permissive ethylene/auxin cues sustain coleoptile growth. Vegetative submergence tolerance (SubTol) is regulated by the ERF transcription factor SUB1A, which stabilizes DELLA repressors to dampen gibberellin responsiveness, conserve carbohydrates, and coordinate recovery. SUB1A also modulates ABA and auxin pathways and enhances Tre6P synthase (TPS) expression, likely increasing Tre6P to inhibit SnRK1A-driven catabolism. Although AG and SubTol deploy opposite growth programs, they converge on shared control points-Tre6P/SnRK1A energy signaling, hormone crosstalk, fermentative capacity, and redox preparedness-enabling combination without antagonism. We synthesize recent mechanistic advances into design principles for breeding: enforcing stage-specific deployment of modules, tuning carbohydrate economy to developmental context, and minimizing pleiotropy. Conventional marker-assisted introgression (SUB1A; AG1/AG2), genomic selection to capture polygenic AG variation and background-dependent SubTol performance, and cis-regulatory genome editing for developmental specificity together provide a practical route to dual-stage, flood-resilient rice suited to direct seeding and increasingly variable climates.