摘要: Distinct Arabidopsis thaliana ecotypes differ in humidity adaptation, with Tibet ecotype adapted to arid habitats exhibiting lower submergence tolerance than humidity-adapted counterparts. Here, we identify a unique 332-bp transposable element (TE) insertion in the promoter of HYDROGEN-PEROXIDE-INDUCED Ca²⁺ INCREASES 1 (HPCA1) specific to the Tibet ecotype. This insertion upregulates HPCA1 expression by the recruitment of active histone modifications. HPCA1, in turn, negatively regulates submergence tolerance through its interaction with VOLTAGE-DEPENDENT ANION CHANNEL 3 (VDAC3), a voltage-dependent ionic channel localized in the mitochondrial outer membrane. Transcriptomic analyses indicate that the HPCA1–VDAC3 module modulates submergence tolerance, at least in part, by regulating RBOHD, WRKY46, and MYC2 to maintain reactive oxygen species (ROS) homeostasis. Additionally, HPCA1 facilitates VDAC3 phosphorylation and inhibits antioxidant enzyme activities, potentially disrupting ROS balance. A negative correlation between HPCA1 expression levels and precipitation is observed across global A. thaliana ecotypes. Together, our results suggest that the HPCA1–VDAC3 module integrates H₂O₂ signaling and ROS homeostasis via regulation of RBOHD, WRKY46, and MYC2, thereby mediating a trade-off in humidity adaptation in A. thaliana and providing insights for breeding flooding-tolerant crops.