PREPRINT | Detection and quantification of Fusarium proliferatum in garlic using a specific droplet digital PCR assay

This article is a preprint and has not been certified by peer review

Edel-Hermann, V., Roux, A., Sarbach, A., Mondy, S., Leyronas, C. (2026) Detection and quantification of Fusarium proliferatum in garlic using a specific droplet digital PCR assay. SSRN, 2026

DOI : 10.2139/ssrn.7330516 

Abstract: Garlic (Allium sativum L.) is one of the most popular condiments worldwide. A new fungal disease has recently emerged – garlic dry rot – which affects crops during storage. The disease is mainly caused by fungi belonging to the genus Fusarium and Fusarium proliferatum is the predominant pathogen in several countries. The disease is not visible during cultivation, but only after harvest. It is essential to sow healthy cloves, but there is no way of guaranteeing that asymptomatic cloves are free from the pathogen. Controlling the disease therefore requires a tool for the early detection of the pathogen. The objective of this study was to propose an effective method for the early detection and quantification of F. proliferatum. To this end, we designed a TaqMan probe targeting the translation elongation factor 1-α gene and developed aspecific detection method based on droplet digital PCR (ddPCR). This method has enabled the detection of F. proliferatum DNA at levels as low as 100 fg. Forty garlic cloves collected during the storage period, whether symptomatic or asymptomatic, tested positive by ddPCR. By contrast, microbiological isolations detected F. proliferatum in nine symptomatic cloves but not in the 17 other symptomatic cloves or in the 14 asymptomatic cloves. The specific ddPCR method described in this study will provide a better understanding of dry rot caused by F. proliferatum. It will enable the pathogen to be detected at an early stage and throughout the growing cycle, and will help identify potential sources of inoculum.