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.

RNA指导的DNA甲基化（RNA-directed DNA methylation，RdDM）是一类可调控编码与非编码遗传元件表达的表观遗传过程。然而，目前学界对RdDM参与玉米（Zea mays）环境应答过程的认知仍较为匮乏。本研究分离并克隆了一个玉米盐敏感突变体，该突变体编码含KOW结构域的转录因子1（KOW DOMAIN-CONTAINING TRANSCRIPTION FACTOR1，KTF1）——RdDM通路的核心组分之一。通过进化分析，我们鉴定到两个KTF1的同源基因（分别命名为ZmKTF1A与ZmKTF1B），二者的表达模式与表达水平均高度相似。全基因组亚硫酸氢盐测序结果显示，ZmKTF1（此处指Zmktf1ab）的突变可显著降低全基因组范围内的CHH（H=A、C或T）甲基化水平。进一步研究发现，依赖于ZmKTF1的DNA甲基化可在盐胁迫条件下调控多种参与氧化还原酶过程的关键基因的表达，同时伴随活性氧（reactive oxygen species，ROS）水平的显著升高。此外，我们在天然玉米种群中观察到，启动子区域的插入缺失（Insertion-Deletion，InDel）可影响ZmKTF1的表达，进而改变幼苗体内的Na+浓度。ZmKTF1有望成为用于作物理想抗盐性状改良的未被充分发掘的表观遗传资源。综上，本研究证实了ZmKTF1通过介导RdDM依赖的DNA甲基化途径，在玉米盐胁迫应答过程中发挥关键调控作用。