Development of a reverse transcription-loop- mediated isothermal amplification (LAMP) assay for the rapid detection of onion yellow dwarf virus

•In this paper a LAMP based diagnostic method for OYDV detection was developed.•OYDV is the most limiting biotic stress in ‘Rossa di Tropea’ onion. (Italian IGP trademark).•The protocol was validated according European standard (EPPO guideline PM 7/98(2)).•The developed method results also easily appicable in laboratories with ho sophisticated facilities. Onion yellow dwarf virus (OYDV) is one of the most important viral pathogens of onion. In particular, on ‘Rossa di Tropea’ onion, granted with Protected Geographical Indication (PGI) trademarks, this pathogen represents the most limiting biotic stress in terms of spread, severity of symptoms and damage, and its detection is necessary to preserve high quality standards and avoid yield losses. A reverse transcription-loop mediated isothermal amplification (RT-LAMP) assay was developed for detection of OYDV. The specificity, sensitivity, repeatability and reproducibility of the assay were validated according to EPPO standard PM7/98 (2). Diagnostic specificity, diagnostic sensitivity and diagnostic accuracy were determined in both leaf and bulb tissues. To enhance the feasibility of a LAMP-based method for field diagnosis, several nucleic acid extraction methods were compared to simplify sample preparation. The results showed the reliability of the method for OYDV detection, with a limit of detection (LOD) comparable to real time reverse transcription polymerase chain reaction (RT-qPCR). The ease of sample preparation, and the more than acceptable LOD, indicated that the RT-LAMP assay could be used in plant pathology laboratories with limited facilities and resources, as well as directly in the field. This work was carried out in the frame of “SI.ORTO” project.