Proteomic insights into early grapevine defense responses to downy and powdery mildew

Abstract

Grapevine is a globally significant crop whose productivity is constantly threatened by fungal and oomycete diseases. At the same time, increasing environmental and regulatory pressures demand a substantial reduction in pesticide use in viticulture¹. Achieving durable disease control under these constraints depends on improving our understanding of the molecular basis of grapevine tolerance, thereby enabling the development of more resilient cultivars and sustainable crop protection strategies.

Multi-omics approaches are particularly suitable to unravel the complex signalling networks underlying grapevine immunity². This is a central objective of the Horizon Europe SHIELD4GRAPE project, which combines multi-omics analyses with breeding and integrated pest management strategies to promote viticulture sustainability.

Within the multilayer framework of the Horizon Europe SHIELD4GRAPE project, we focused on early proteome reprogramming associated with grapevine responses to Plasmopara viticola and Erysiphe necator. Proteins play a fundamental role in grapevine development, stress responses, and immune regulation, acting as key effectors of metabolic pathways and defence signalling and their characterization can be particularly important in grapevine breeding programs facilitating the identification of tolerance-associated traits^3,4.

In this work, we selected tolerant minority genotypes from Mediterranean regions and compared them with the susceptible genotype ‘Chardonnay’ under controlled inoculation conditions. Leaf samples were collected at 24 hours post-inoculation, a critical stage for defence activation and pathogen establishment. Ashotgun proteomics LC-MS/MS approach allowed the analysis of differentially accumulated grapevine proteins 24h post inoculation. Tolerant genotypes displayed some overlap in protein accumulation tendencies, while simultaneously showing genotype-specific response, demonstrating the complexities of proteome remodelling upon pathogen challenge. Gene ontology enrichment analysis reflected this complex accumulation pattern, revealing a concerted effort at the proteome level with the biological goal of stress amelioration and response to disease.

Ongoing integration of proteomics with transcriptomic, epigenomic and metabolomic datasets generated within SHIELD4GRAPE will contribute to reconstructing regulatory networks underlying disease tolerance and to identify candidate molecular markers for breeding more resilient grapevine cultivars.

References

¹ Fouillet, E. et al. Reducing pesticide use in vineyards. Evidence from the analysis of the French DEPHY network. Eur. J. Agron., 136, 126503 (2022) doi.org/10.1016/j.eja.2022.126503.

² Kundu, B. K. & Tanti, B. Decoding plant physiology through systems biology: Integrative multi-omics and computational perspectives for next-generation crop design. Plant Commun., 101668 (2025) doi:10.1016/j.xplc.2025.101668.

³ Figueiredo, A. et al. Specific adjustments in grapevine leaf proteome discriminating resistant and susceptible grapevine genotypes to Plasmopara viticola. Journal of proteomics, Elsevier (2017) doi.org/10.1016/j.jprot.2016.10.012.

⁴ Santos, RB. et al. Grapevine – Downy Mildew Rendez-Vous: Proteome Analysis of the First Hours of an Incompatible Interaction. Plants (2020) https://doi.org/10.3390/plants9111498

Acknowledgements

This work was supported by the European Commission in the frame of the Horizon Europe program, project ‘Shield4Grape’ (grant agreement number 101135088). Views and opinions expressed are those of the authors only and do not necessarily reflect those of the European Union. Neither the European Union nor the granting authority can be held responsible for them. CPS was supported by a FCT PhD Studentship (reference 2025.02061.BD) and project UID/04046/2025–Instituto de Biossistemas e Ciências Integrativas grant from FCT, Portugal.