ZmKTF1 is essential for regulating the gene expression through DNA methylation, ensuring the development of maize seedlings under salinity

RNA-directed DNA methylation (RdDM) is an epigenetic process that can regulate the expression of coding and non-coding genetic elements. However, little is known about the involvement of RdDM in response to environmental cues in maize. Here, we isolated and cloned a salt-sensitive mutant in maize (Zea mays), which encodes KOW DOMAIN-CONTAINING TRANSCRIPTION FACTOR1 (KTF1), an essential component of RdDM pathway. Through evolutionary analysis, we identified two homologs of KTF1 (namely ZmKTF1A and ZmKTF1B) that exhibited highly similar expression patterns and levels. Whole-genome bisulfite sequencing revealed that mutation in ZmKTF1 (refers to Zmktf1ab) consequently substantially decreased genome-wide CHH (H = A, C, or T) methylation. Moreover, we discovered that ZmKTF1-dependent DNA methylation may regulate the expression of multiple key genes involved in oxidoreductase upon exposure to the salt, concomitant with greater levels of reactive oxygen species (ROS). In addition, we observed that an InDel of promoter affected the expression of ZmKTF1, thereby changing seedlings Na+ concentration in natural maize population. ZmKTF1 may be an untapped epigenetic resource for ideal plant salt resistance improvement. Overall, our work demonstrated the critical roles of ZmKTF1 in response to salt via RdDM mediated DNA methylation in maize.