Comparative Evaluation of the LAMP Assay and PCR-Based Assays for the Rapid Detection of Alternaria solani

Frontiers in Microbiology
Mehran KhanQinghe Chen

Abstract

Early blight (EB), caused by the pathogen Alternaria solani, is a major threat to global potato and tomato production. Early and accurate diagnosis of this disease is therefore important. In this study, we conducted a loop-mediated isothermal amplification (LAMP) assay, as well as conventional polymerase chain reaction (PCR), nested PCR, and quantitative real-time PCR (RT-qPCR) assays to determine which of these techniques was less time consuming, more sensitive, and more accurate. We based our assays on sequence-characterized amplified regions of the histidine kinase gene with an accession number (FJ424058). The LAMP assay provided more rapid and accurate results, amplifying the target pathogen in less than 60 min at 63°C, with 10-fold greater sensitivity than conventional PCR. Nested PCR was 100-fold more sensitive than the LAMP assay and 1000-fold more sensitive than conventional PCR. qPCR was the most sensitive among the assays evaluated, being 10-fold more sensitive than nested PCR for the least detectable genomic DNA concentration (100 fg). The LAMP assay was more sensitive than conventional PCR, but less sensitive than nested PCR and qPCR; however, it was simpler and faster than the other assays evaluated. Despite of the...Continue Reading

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Citations

Mar 25, 2020·Microbial Biotechnology·Youming ShenHaifei Li
Sep 10, 2020·Journal of Plant Pathology : an International Journal of the Italian Phytopathological Society·Jugpreet SinghAwais Khan
Feb 16, 2021·ACS Omega·Marcelino Varona, Jared L Anderson
Mar 10, 2021·Sustainable Chemistry and Pharmacy·Sepideh AhmadiMichael R Hamblin
Oct 16, 2021·Scientific Reports·Chinbayar Bat-OchirHee Kyung Park

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Methods Mentioned

BETA
PCR
PCRs
Assay
electrophoresis
spore trap

Software Mentioned

Primer Premier
Beacon
Primer Explorer

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