Polyploidization is a major driver of plant evolution and stress adaptation, yet its role in modulating biotic stress resistance through epigenetic mechanisms remains poorly understood. This study demonstrates that autotetraploidization in Chrysanthemum lavandulifolium significantly enhances resistance to Alternaria alternata, the cause of black spot disease. Whole-genome methylome and transcriptome analyses reveal that polyploidization induces locus-specific CHH hypomethylation in the promoters of a subset of WRKY transcription factors, leading to their transcriptional activation upon fungal infection. Functional characterization of CIWRKY103, a key hypomethylated WRKY gene, confirms its critical role in conferring disease resistance. Chemical inhibition of DNA methylation (5-azacytidine treatment) in diploid plants mimics the tetraploid phenotype by activating WRKY103 expression and enhancing resistance. This epigenetic regulatory mechanism is conserved across diverse chrysanthemum species, highlighting the potential of targeting DNA methylation to modulate fungal disease resistance in polyploid crops. Our findings unveil a novel link between polyploidy, epigenetic reprogramming, and pathogen defense, offering strategic insights for sustainable crop protection.

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