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Phytoplasmas are phytopathogenic bacteria that cause serious damage to agriculture. A quarantine pathogen, the flavescence dorée phytoplasma (FDp), often associated with grapevine yellows disease, affects viticultural production across Europe. However, the mechanisms of FDp pathogenicity are not still elucidated. In this study, symptomatic and asymptomatic grapevine (Vitis vinifera L. var. ‘Pinot gris’) leaves were sampled. Two different FDp genotypes (M38 and M54) were identified, and genotype-dependent changes to grapevine physiological responses through the development of FDp infection were analysed. Correlation analyses established a potential link between measured physiological parameters and relative FDp DNA abundance. Increased malondialdehyde levels pointed to the oxidative stress in infected leaves, and highly correlated with the activation of L-ascorbic acid synthesis. Levels of hydrogen peroxide were reduced in infected leaves, possibly as an FDp mechanism to avoid plant-derived oxidative damage. Genotype M54 was associated with a lower accumulation of soluble sugars and lower damage to photosynthetic pigments while retaining a higher titre than M38. Therefore, pronounced phytoplasma genotype-dependent changes in grapevine physiology, potentially caused by the differences between M54 and M38 on the level of the efficiency of their effectors should be further investigated. Altogether, results provide data on certain targets of FDp in grapevine and could assist in the identification of potential specific effectors of this phytoplasma to aid the efforts of FDp management in European vineyards. [ABSTRACT FROM AUTHOR]