H3K36 methyltransferase SDG102 enhances salt tolerance by altering the methylation level of genes in maize (Zea mays L.)

Chromatin modification governs plant abiotic stress responses, yet the regulatory interplay between H3K36 methylation-mediated transcriptome reprogramming and DNA methylation dynamics in maize salt tolerance remains elusive. This study identifies the maize-specific H3K36 methyltransferase SDG102 as a positive contributor of salt tolerance. Under salt stress, SDG102-overexpressing plants showed 10–21.3% higher antioxidant enzyme activities and reduced malondialdehyde content, confirming enhanced ROS scavenging and membrane integrity. Transcriptome sequencing of wild-type and SDG102-overexpressing plants revealed 614 differentially expressed genes predominantly enriched in ion homeostasis, antioxidant defense, and hormone signaling pathways. Genome-wide bisulfite sequencing detected about 45,817 differentially methylated regions, of which 5,896 DMRs located in the promoter region were anchored to 4,195 genes, and the DMRs with CHH background were anchored to the most genes CHH hypomethylation specifically overlaps with CHH hypomethylation specifically overlapped promoter regions of salt-tolerance genes ZmNHX16 and ZmNHX17. Integrated analysis supports a model wherein SDG102 orchestrates salt tolerance by modulating DNA methylation, specifically coregulating CHH methylation. Six key salt-tolerance genes were identified, advancing mechanistic understanding of salt adaptation and providing vital targets for crop improvement.