Potato cyst nematodes, Globodera pallida and G. rostochiensis, are economically important and difficult to manage pests of the potato crop. The cyst of both the species looks similar and it is difficult to differentiate once it turns brown upon maturity. Early detection of the PCN at the species level is crucial to avoid its further spread and for adopting the appropriate management strategies. Therefore, in the present study, highly specific and sensitive loop-mediated isothermal amplification (LAMP) assay was developed to amplify mitochondrial-Sequence Characterized Amplified Region (SCAR) sequence of potato cyst nematode, G. pallida. The LAMP assay was completed within a shorter incubation period of 60 min at 60 °C followed by the reaction termination at 80 °C for 5 min. The developed LAMP assay exhibited high specificity for G. pallida and did not detect any other species including its sibling species, G. rostochiensis. In sensitivity tests, the assay detected G. pallida at 1000 times less DNA concentration (10 fg/µl) as compared to conventional PCR (10 pg/µl). In addition to this, the developed LAMP assay was tested for the detection of G. pallida directly from the soil samples, and even a single cyst mixed with soil was successfully detected by the developed assay. Moreover, the utility of low-cost instruments like hot water bath was also demonstrated for the detection of G. pallida from the soil. The developed LAMP is a rapid, highly specific, sensitive, and cost-effective technique for the species-specific detection of G. pallida. The developed assay will facilitate the rapid detection of G. pallida at quarantine stations as well as from the fields which will help to stop its further spread in new areas and also to devise effective management strategies for sustainable potato production.
Supplementary information: The online version contains supplementary material available at 10.1007/s13205-023-03542-x.
Keywords: Detection; Globodera pallida; LAMP; Management; Mitochondrial-SCAR; Potato.
© King Abdulaziz City for Science and Technology 2023, Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.