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Background  Appropriate flowering time is very important to the success of modern agriculture. Maize ( Zea mays  L.) is a major cereal crop, originated in tropical areas, with photoperiod sensitivity. Which is an important obstacle to the utilization of tropical/subtropical germplasm resources in temperate regions. However, the study on the regulation mechanism of photoperiod sensitivity of maize is still in the early stage. Although it has been previously reported that  ZmCCT  is involved in the photoperiod response and delays maize flowering time under long-day conditions, the underlying mechanism remains unclear.    Results  Here, we showed that  ZmCCT  overexpression delays flowering time and confers maize drought tolerance under LD conditions. Implementing the Gal4-LexA/UAS system identified that  ZmCCT  has a transcriptional inhibitory activity, while the yeast system showed that  ZmCCT  has a transcriptional activation activity. DAP-Seq analysis and EMSA indicated that  ZmCCT  mainly binds to promoters containing the novel motifs CTC and AAATGGTC. DAP-Seq and RNA-Seq analysis showed that  ZmCCT  could directly repress the expression of  ZmPRR5  and  ZmCOL9 , and promote the expression of  ZmRVE6  to delay flowering under long-day conditions. Moreover, we also demonstrated that  ZmCCT  directly binds to the promoters of  ZmHY5 ,  ZmMPK3 ,  ZmVOZ1  and  ZmARR16  and promotes the expression of  ZmHY5  and  ZmMPK3 , but represses  ZmVOZ1  and  ZmARR16  to enhance stress resistance. Additionally,  ZmCCT  regulates a set of genes associated with plant development.    Conclusions    ZmCCT  has dual functions in regulating maize flowering time and stress response under LD conditions.  ZmCCT  negatively regulates flowering time and enhances maize drought tolerance under LD conditions.  ZmCCT  represses most flowering time genes to delay flowering while promotes most stress response genes to enhance stress tolerance. Our data contribute to a comprehensive understanding of the regulatory mechanism of  ZmCCT  in controlling maize flowering time and stress response.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-021-03231-y.

ZmCCT regulates photoperiod-dependent flowering and response to stresses in maize