Polyploidization enhances plant resistance to Alternaria alternata via DNA hypomethylation activated WRKYs

Abstract

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.

Acknowledgements

This work was supported by the Central Laboratory of the College of Horticulture and the high-performance computing platform of the Bioinformatics Center, Nanjing Agricultural University. This work was supported by grants from the National Key Research and Development Program of China (2024YFD1200503), the National Natural Science Foundation of China (32171854, 32371949, 32341048), the JBGS Project of Seed Industry Revitalization in Jiangsu Province (JBGS[2021]020), the China Agriculture Research System (CARS-23-A18), the Fundamental Research Funds for the Central Universities (QTPY2025005), and a project funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions.

Author contributions

F.C. and Z.W. conceived and supervised the project. Z.Y. performed the experiments and analysed the data, with help from H.C., R.J., Q.Y., J.H., and Y.L. Z.Y. wrote the manuscript with contributions from all the authors. J.J., H.W., and W.F. provided constructive suggestions and revised the manuscript. All the authors read and approved the final manuscript.

Data availability

All data supporting the findings of this study are available in the article and its supplementary figures and supplementary tables. The gene and protein sequences used in this study were derived from the published C. lavandulifolium genome [31]. The raw RNA-seq, WGBS, and DAP-seq data reported in this paper have been deposited in the Genome Sequence Archive (GSA) under project number PRJCA037346 and GSA accession number CRA023867 (https://ngdc.cncb.ac.cn/gsa). All other reasonable requests for data and research materials can be accommodated by reaching out to the authors.

Conflicts of interest statement

The authors declare that they have no financial or personal relationships with individuals or organizations that could inappropriately influence the work.

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