Year and Flavescence dorée phytoplasma infection: impact on gene expression in two grapevine varieties

• Differences in gene expression exist between two cultivars, one highly susceptible and the other poorly susceptible to Flavescence dorée, independently of year and health status. • Year has an influence on grapevine transcripts, but varietal markers and potential markers of Flavescence dorée phytoplasma-infection have been identified. • A difference in metabolic function between the two varieties could explain the lower susceptibility of Merlot. Flavescence dorée (FD) is a severe phytoplasma disease affecting grapevine ( Vitis vinifera ) in Europe, significantly impacting plant gene expression. This study aimed to (i) identify in natura gene expression differences between a highly susceptible cultivar (Cabernet Sauvignon) and a less susceptible one (Merlot), (ii) understand plant responses to FD phytoplasma (FDp) infection, and (iii) possibly identify molecular markers associated with lower susceptibility to FD. The expression of 95 grapevine genes was analysed by high-throughput RT-qPCR on symptomatic, non-symptomatic, and healthy branches collected in vineyards over two consecutive years. Comparative analysis revealed cultivar-specific responses to FDp infection, year-specific expression patterns, and commonly modulated genes that could serve as markers of infection, health status, or varietal identity. Three genes were consistently down-regulated in Merlot compared to Cabernet Sauvignon, supporting the existence of varietal markers linked to genetic background. Several genes were specifically modulated in infected Merlot plants, including those related to defense and cell wall reinforcement, potentially contributing to restricted FDp movement. Non-symptomatic branches from infected vines showed intermediate expression profiles, suggesting systemic signaling or early responses. These findings highlight the complex interaction between grapevine genotype, environmental conditions, and pathogen infection, providing a basis for identifying molecular markers and improving strategies to manage FD in vineyards.