The interaction between BnaAIF1 and BnaICE1 enhances the low-temperature tolerance of Brassica napus

• A set of 11, 9 and 24 AIF genes were identified in B. rapa, B. oleracea , and B. napus , respectively. • BnaAIF1-C03 is highly induced under low-temperature. • Overexpression of BnaAIF1-C03 significantly improved the seed germination under cold stress (4 °C) and the survival rate of seedlings under freezing stress (−4 °C) in rapeseed. • BnaAIF1-C03, localized in the nucleus, interacts with BnaICE1 to activate the ICE1-CBF-COR pathway, thereby enhancing freezing tolerance. Rapeseed ( Brassica napus L.) is an important oilseed crop in the world, it’s often damaged by low-temperature (especially freezing) stress, which has the potential to cause significant yield losses. However, little is known about the molecular mechanisms for coping with low-temperature stress in rapeseed. In this study, a total of 24 atypical bHLH transcription factor AIF (ATBS1 INTERACTING FACTOR) gene family members were identified by systematically bioinformatics analysis in rapeseed, among which all six BnaAIF1 genes were strongly induced by low temperature stress, especially BnaAIF1-A03/C03 . Overexpression of BnaAIF1-C03 improved the seed germination under cold stress (4 °C) and the survival rate of seedlings under freezing stress (-4 °C) in rapeseed, with enhanced stability of light system II (Fv/Fm and NPQ_Lss increased) and reduced oxidative damage (decreased contents of H 2 O 2 and MDA). Further analysis revealed that BnaAIF1-C03 was localized in the nucleus and interacted with BnaICE1, activating the ICE1-CBF-COR pathway genes and thus participating in the low-temperature stress response of rapeseed. Overall, this study provides an important theoretical basis and new target gene for future breeding of low-temperature tolerant rapeseed.