Flavescence dorée phytoplasma infection represses the transcription of the lignin pathway in Vitis vinifera cv. Pinot noir without compromising monolignol accumulation.

Flavescence dorée phytoplasma (FDp) impairs shoot lignification in grapevines, but the underlying molecular mechanisms are unclear. This study examined how FDp infection affects the lignin/monolignol pathway in Vitis vinifera cv. Pinot Noir. Diseased (FDp positive) and healthy (FDp negative) shoots were sampled at three time points during the growing season. Metabolites were quantified by LC-MS/MS, key genes were analysed by RT-qPCR, and RNA sequencing was used to profile selected samples. FDp infection was found to reduce the expression of several lignin-biosynthetic genes and to broadly downregulate the phenylpropanoid pathway. Metabolomics revealed reduced levels of certain downstream intermediates, while shikimate and phenylalanine accumulated in infected shoots. However, the major monolignols coniferyl alcohol and sinapyl alcohol remained unchanged in mid- and late season. These results suggest that FDp represses transcription of the lignin pathway without substantially compromising monolignol accumulation, and that the lignification defect likely arises from downstream processes, such as precursor localisation or polymerisation.