Loop-mediated isothermal amplification for detection of plant pathogens in wheat (Triticum aestivum)

Authors: GOMEZ-GUTIERRIEZ, SANDRA - Purdue University; Goodwin, Stephen - Steve

Submitted to: Frontiers in Plant Science
Publication Type: Review Article
Publication Acceptance Date: 2/17/2022
Publication Date: 3/15/2022
Citation: Gomez-Gutierriez, S.V., Goodwin, S.B. 2022. Loop-mediated isothermal amplification for detection of plant pathogens in wheat (Triticum aestivum). Frontiers in Plant Science. 13. Article 857673. https://doi.org/10.3389/fpls.2022.857673.
DOI: https://doi.org/10.3389/fpls.2022.857673

Interpretive Summary: Wheat plants can be infected by a variety of pathogens that often cause similar symptoms making identification and diagnosis difficult. Accurate identification of wheat pathogens is essential in applying the most appropriate disease-management strategies yet the best method is not always clear. Loop-mediated isothermal amplification (LAMP) is a recent molecular technique that was rapidly adopted for plant pathogen detection and can be implemented easily for use in field conditions but has not been used extensively for pathogens of wheat. These results will be of interest to plant pathologists trying to manage diseases of wheat and other crops. A figure showing the LAMP process can be used by others to understand the technology and in educational materials to further adoption of this approach for detection of crop pathogens.

Technical Abstract: Wheat plants can be infected by a variety of pathogen species, with some of them causing similar symptoms. For example, Zymoseptoria tritici and Parastagonospora nodorum often occur together and form the Septoria leaf blotch complex. Accurate identification of wheat pathogens is essential in applying the most appropriate disease-management strategy. Loop-mediated isothermal amplification (LAMP) is a recent molecular technique that was rapidly adopted for plant pathogen detection and can be implemented easily for detection in field conditions. The specificity, sensitivity, and facility to conduct the reaction at a constant temperature are the main advantages of LAMP over immunological and nucleic acid-based methods. In plant pathogen detection studies, LAMP was able to differentiate related fungal species and non-target strains of virulent species with lower detection limits than those obtained with PCR. In this review, we explain the amplification process and elements of the LAMP reaction, and the variety of techniques for visualization of the amplified products, along with their advantages and disadvantages. Then, a compilation of analyses that show the application of LAMP for detection of fungal pathogens and viruses in wheat is presented. We also describe the modifications included in real-time and multiplex LAMP that reduce common errors from post-amplification detection in traditional LAMP assays and allow discrimination of targets in multi-sample analyses. Finally, we discuss the utility of LAMP for pathogen detection in wheat, its limitations, and current challenges of this technique. We provide prospects for application of real-time LAMP and multiplex LAMP in the field, using portable devices that measure fluorescence and turbidity, or facilitate colorimetric detection. New technologies for plant pathogen detection are discussed that can be integrated with LAMP to obtain elevated analytical sensitivity of detection. A CRISPR-related Cas protein system is one of the most promising technologies that has shown high sensitivity when applied with LAMP. This technology also gives new possibilities for rapid and portable detection of wheat pathogens in the field and was successfully applied for detection of the Magnaporthe oryzae Triticum pathotype.