Genetic Study Reveals How Biocontrol Agents Help Grapevines Resist Fungal Disease

Researchers from an international team have used advanced genetic analysis to study how grapevines respond to biological control agents when facing Neofusicoccum parvum, a fungus linked to Botryosphaeria dieback. This disease is a major threat to vineyards worldwide, especially as climate change increases plant stress and disease pressure. The study, recently accepted in the journal Phytopathology, focused on two grapevine cultivars, Chardonnay and Tempranillo, and examined how they react at the molecular level when protected by two different biocontrol agents: Bacillus subtilis PTA-271 and Trichoderma atroviride SC1.

The research was conducted as part of the BIOVIGNE program, with support from French regional authorities and industry partners. Scientists applied the biocontrol agents to grapevines, then inoculated them with N. parvum. Leaf samples were collected a few days after treatment for RNA sequencing (RNA-seq), a method that allows researchers to see which genes are active in the plant under different conditions. The results were validated using quantitative real-time PCR (qRT-PCR), a technique that confirms changes in gene expression.

The bioinformatics analysis included quality control of the genetic data, trimming of sequences, alignment to the Vitis vinifera genome, and identification of genes that were expressed differently depending on treatment. Researchers also performed functional enrichment analysis to understand which biological processes were affected.

The findings show that Chardonnay and Tempranillo activate different sets of genes when exposed to N. parvum and protected by biocontrol agents. In Chardonnay, the main changes involved pathways related to terpenes and carotenoids—compounds often linked to plant defense and aroma. In Tempranillo, the response was more focused on amino acid transport and photosynthesis. When protected by Bacillus subtilis PTA-271, Chardonnay showed increased activity in phenylpropanoid pathways and other secondary metabolic processes known for their role in plant defense. In contrast, Trichoderma atroviride SC1 triggered broader metabolic changes in Tempranillo.

Importantly, the study identified potential molecular markers in grapevine leaves that could help distinguish between healthy plants protected by biocontrol agents and those infected by N. parvum. These markers could be used for early detection of disease or monitoring plant health in nurseries and vineyards, offering a practical tool for growers.

Currently, there are no effective chemical treatments for grapevine trunk diseases like Botryosphaeria dieback. The use of biocontrol agents is seen as a promising alternative for sustainable vineyard management. By understanding how these agents work at the genetic level in different grape varieties, researchers hope to develop better strategies for disease prevention and control.

The RNA-seq and qRT-PCR analyses were carried out at specialized platforms associated with the project partners. The work provides new evidence supporting non-chemical approaches to managing grapevine trunk diseases and highlights the importance of early detection tools based on molecular biomarkers.

The study was led by Catarina Leal, Larissa Heck, Idir Saber, Dina Aggad, Nicolas Richet, David Gramaje, Josep Armengol, Florence Fontaine, and Patricia Trotel-Aziz. Their research offers new insights into how grapevines can be protected from serious fungal threats using biological methods rather than traditional chemical treatments.