A structural variant of <i>Voltage‐Dependent Anion Channel 1/3a</i> confers cold tolerance in <i>Solanum habrochaites</i>

Cold stress is one of the major abiotic stresses affecting crop yield and quality in the context of global climate change. The cultivated tomato (Solanum lycopersicum) exhibits susceptibility to low temperature, while the wild relative tomato (Solanum habrochaites) can withstand chilling and even short-term frost. However, how wild tomato adapts to cold climate remains largely unclear. In this study, by analyzing microarray data and qRT-PCR validation, we observed that the transcript of Voltage-Dependent Anion Channel 1/3a (VDAC1/3a) was suppressed in cold-tolerant wild relative Solanum habrochaites LA1777 but was induced in cold-sensitive cultivated tomato LA4024 under cold stress. Knockout of VDAC1/3a enhanced cold tolerance in tomato. Additionally, there was no adverse effect on yield and fruit quality in the vdac1/3a lines. A 168 bp structural variation in the ShVDAC1/3a promoter confers enhanced cold tolerance in wild relative tomato by altering the binding site for CIGT transcription factor. Genetic and molecular evidence demonstrates that CIGT directly negatively regulates the expression of VDAC1/3a. Overexpression of CIGT positively regulates cold tolerance in tomato. Analysis of Non-invasive Micro-test Technique and methyl viologen treatment demonstrated that VDAC1/3a confers cold tolerance potentially by regulating Ca²⁺ influx and reactive oxygen species accumulation in tomato. RNA-seq reveals that VDAC1/3a is involved in integrating internal signal of phytohormone pathway and COR genes expression to response to cold stress. Our findings suggest that a naturally occurring structural variation is crucial for cold tolerance in Solanum habrochaites LA1777, providing valuable genetic resources for cold-tolerant tomato breeding.