# High-resolution SNP genotyping provides insight into the introduction and dissemination of Grapevine flavescence dorée phytoplasma in Switzerland

## TL;DR

This study uses high-resolution SNP genotyping to track the spread of a grapevine disease in Switzerland and identifies new tools for monitoring its dissemination.

## Contribution

The study introduces novel SNP markers that enhance genotyping resolution for tracking phytoplasma spread in grapevines.

## Key findings

- FDp was introduced through infected planting material, as indicated by shared genotypes across samples.
- Combining established and novel SNP markers revealed nine distinct multilocus genotypes, improving understanding of FDp population structure.
- The study highlights the roles of both planting material and local dissemination in FDp epidemic dynamics in Swiss vineyards.

## Abstract

Flavescence dorée is a quarantine grapevine disease transmitted by Scaphoideus titanus that was first detected north of the Swiss Alps in 2015 and has since progressively spread in western Switzerland, while its introduction routes and local dissemination dynamics remained poorly understood. To clarify these processes, we applied a molecular epidemiology approach combining MLST based on established markers (map, dnaK, vmpA, malG) with high-resolution SNP genotyping using newly developed loci to investigate FDp spatiotemporal dynamics and genetic diversity. Between 2015 and 2022, 4,212 symptomatic grapevines were sampled across Vaud, Valais, and Geneva, of which 26.3% tested positive for FDp. Established markers revealed highly homogeneous profiles, with all samples sharing the same genotypes (map M54, dnaK1, vmpA group II), supporting introduction through infected planting material. The malG locus alone distinguished only three profiles, but when combined with eight novel SNP markers, nine multilocus genotypes were identified, providing a finer resolution of FDp population structure. Our results provide the first genome-informed overview of FDp epidemiology in Swiss vineyards north of the Alps, highlighting the combined roles of planting material and local dissemination in shaping epidemic dynamics. The newly identified SNP markers enhance genotyping resolution and provide valuable tools for investigating phytoplasma spread and improving future surveillance strategies.