ZmKTF1 promotes salt tolerance by mediating RNA-directed DNA methylation in maize

The epigenetic process of RNA-directed DNA methylation (RdDM) regulates the expression of genes and transposons. However, little is known about the involvement of RdDM in the response of maize (Zea mays) to salt stress. Here, we isolated a salt-sensitive maize mutant and cloned the underlying gene, which encodes KOW DOMAIN-CONTAINING TRANSCRIPTION FACTOR1 (KTF1), an essential component of the RdDM pathway. Evolutionary analysis identified two homologs of KTF1 (ZmKTF1A and ZmKTF1B) with highly similar expression patterns. Whole-genome bisulfite sequencing revealed that mutations in ZmKTF1 substantially decrease genome-wide CHH (H = A, C, or T) methylation levels. Moreover, our findings suggest that ZmKTF1-mediated DNA methylation regulates the expression of multiple key genes involved in oxidoreductase activity upon exposure to salt, concomitant with increased levels of reactive oxygen species. In addition, insertion-deletion mutations (InDels) in the promoter of ZmKTF1 affect its expression, thereby altering Na⁺ concentrations in seedlings in a natural maize population. Therefore, ZmKTF1 might represent an untapped epigenetic resource for improving salt tolerance in maize. Overall, our work demonstrates the critical role of ZmKTF1 involved in the RdDM pathway in maize salt tolerance.