EpiGRAPE: decoding histone acetylation in grapevine resistance to downy mildew

Abstract

Epigenetic mechanisms, particularly post-translational histone modifications, are pivotal regulators of phenotypic plasticity in perennial crops. In Vitis vinifera, histone acetylation acts as a dynamic molecular switch that modulates chromatin accessibility, governing the transcriptional reprogramming required to cope with biotic stress. This regulation is especially critical during the interaction withPlasmopara viticola, the causal agent of downy mildew, which severely impacts grapevine productivity. To understand these defensemechanisms, this study explores the epigenetic landscape of two contrasting genotypes upon inoculation with P. viticola: Chardonnay(highly susceptible) and C19 (a Portuguese Vitis vinifera selection with enhanced resilience). We aim to characterize the acetylation statusof Histone H3 and the transcriptional profile of its regulatory enzymes in these distinct genetic backgrounds. The experimental work followed a multi-level approach starting with the extraction of nuclear proteins from leaves to evaluate the levels of total versus acetylated Histone H3 via Western Blot, complemented by protein quantification using ImageJ. Simultaneously, transcriptional activity is assessed through RNAextraction and RT-qPCR to monitor the expression patterns of Histone Acetyltransferases (VvHATs) and Histone Deacetylases (VvHDACs) during the compatible and incompatible interaction.

The data obtained will be instrumental for subsequent large-scale analyses, including Transcriptomics, ChIP-seq, and ChIP-MS, aimed at mapping genome-wide histone modifications and identifying the specific proteins associated with chromatin remodeling. These insightsopen new frontiers for precision viticulture, potentially leading to the development of epigenetic biomarkers for early resistance screening and the use of epi-priming agents. Ultimately, EpiGRAPE aims to provide a molecular blueprint for breeding or gene-editing programsfocused on enhancing the natural defenses of Vitis vinifera against downy mildew, reducing the reliance on chemical fungicides.

Acknowledgements

This work was supported by funds through FCT – Fundação para a Ciência e a Tecnologia, I.P., under the project EpiGRAPE (Ref. 2024.16170.PEX), DOI: https://doi.org/10.54499/2024.16170.PEX. The authors also acknowledge the support of the research unit UID/04046/2025 – Biosystems and Integrative Sciences Institute Centre grant from FCT, Portugal.