Loop-mediated isothermal amplification assay for rapid diagnosis soybean damping-off disease caused by Globisporangium intermedium

TL;DR

This study develops a fast and specific LAMP test to detect a new soybean pathogen in China, helping prevent crop losses.

Contribution

First report of Globisporangium intermedium as a soybean pathogen in China and a novel LAMP assay using the rpb1 gene for detection.

Findings

The LAMP assay using rpb1 gene is highly specific to Globisporangium intermedium.

The method can detect G. intermedium at low DNA concentrations (10 pg/μL).

The LAMP assay successfully detected G. intermedium in soybean tissues and field soil samples.

Abstract

Damping-off has caused huge losses in soybean production areas of China. Based on multi-locus phylogenetic analysis and Koch’s Postulates, the causal agent of soybean damping-off was identified as Globisporangium intermedium. Given the potential danger of G. intermedium, early and precise detection methods are needed for both disease management and prevention. In this study, a LAMP assay utilizing a new target gene rpb1 was developed and evaluated for the detection of G. intermedium. This rpb1 LAMP assay was found highly specific to G. intermedium. All nine tested isolates of G. intermedium yielded positive results, whereas 30 non-target isolates belonging to Globisporangium spp., Pythium spp., Phytophthora spp., Phytopythium spp., and soil-borne fungi lacked detection. The LAMP method can identify G. intermedium at DNA concentrations as low as 10 pg/μL. In terms of on-site disease diagnosis, the LAMP assay could detect G. intermedium from artificially inoculated soybean tissues and naturally infested rhizosphere soil collected from fields in soybean production regions. Consequently, this study not only stands as the first record of G. intermedium as a new soybean pathogen in China, but also provides an efficient LAMP field detection method that could significantly contribute to the management and prevention of soybean damping-off.

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