Potato is the world’s fourth most important food crop, yet it remains highly vulnerable to late blight caused by the oomycete Phytophthora infestans, which results in billions of dollars in annual losses. Plant immunity relies on rapid transcriptional reprogramming, tightly regulated by epigenetic mechanisms such as DNA methylation. While transcriptomic responses of potato to late blight have been extensively studied, how DNA methylation dynamically changes during infection—and how it coordinates with gene expression—remains poorly understood. Given the critical role of epigenetic regulation in plant stress responses, deeper investigation is required to clarify how DNA methylation contributes to disease progression.
In a study published (DOI: 10.1093/hr/uhaf297) in Horticulture Research (2025), scientists from Northwest A&F University and Shenzhen University performed whole-genome bisulfite sequencing and RNA sequencing on the widely cultivated potato cultivar Qingshu No.9 following Phytophthora infestans infection. By integrating methylome and transcriptome analyses across multiple infection stages, the team uncovered dynamic DNA methylation shifts that correlate with large-scale transcriptional reprogramming and progressive immune suppression during late blight development.
Time-course transcriptome profiling identified over 18,000 differentially expressed genes, representing more than half of the annotated potato genome. As infection advanced from biotrophic to necrotrophic stages, down-regulated genes increasingly outnumbered up-regulated ones, indicating widespread immune suppression. Whole-genome methylation analysis revealed a striking two-phase pattern. At 12 hours post-infection, global hypomethylation occurred—primarily at CHH sites—followed by strong hypermethylation at 24 hours. These non-CG methylation changes were initially concentrated in transposable elements but later expanded toward gene regions, suggesting a shift from genome-wide stress response to targeted gene regulation. Importantly, methylation changes exhibited both positional and hysteretic effects. For example, CHG hypermethylation within gene bodies at 24 hours was associated with transcriptional down-regulation at 48 hours, particularly affecting chromatin remodeling genes such as INO80 and SWI/SNF complex components. Moreover, hypo-methylation at exons of NB-LRR resistance genes was significantly enriched, coinciding with their progressive transcriptional decline. Rather than immediately activating immunity, epigenetic remodeling appeared to precede and accompany defense suppression, highlighting a complex temporal coordination between methylation and gene expression.
“Our findings show that DNA methylation does not simply switch genes on or off,” the authors note. “Instead, methylation changes occur in specific genomic positions and exert delayed regulatory effects on transcription.” They emphasize that susceptibility is not a passive process; rather, host epigenetic reprogramming may create conditions that facilitate pathogen proliferation. Understanding these methylation dynamics provides new insight into how plants balance defense, metabolism, and chromatin organization under severe pathogen stress.
The study advances understanding of epigenetic regulation in crop–pathogen interactions and opens new avenues for disease management. By identifying methylation-associated repression of chromatin remodelers and resistance genes, the findings suggest that manipulating DNA methylation pathways could enhance late blight resistance. Epigenetic markers may also serve as early indicators of disease progression before visible symptoms emerge. Beyond potato, the work highlights the broader importance of dynamic non-CG methylation in shaping plant stress responses. Integrating epigenomic information into breeding strategies may ultimately support the development of more resilient cultivars and contribute to global food security under increasing pathogen pressure.
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References
DOI
10.1093/hr/uhaf297
Original Source URL
https://doi.org/10.1093/hr/uhaf297
Funding information
This project was supported by the National Key R&D Program of China (2023YFD2302100), the PhD Start-up Fund of Northwest A&F University (grant no. Z1090122063), the open fund of Guangdong Provincial Key Laboratory for Plant Epigenetics (GPKLPE202414), the China Agriculture Research System (CARS-09).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.