Loop-Mediated Isothermal Amplification for Detection of Plant Pathogens in Wheat (Triticum aestivum)

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 detection 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 detection of plant pathogens 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 alternative 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 compared with alternative isothermal approaches. 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 detection of pathogens 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 detection of plant pathogen are discussed that can be integrated with LAMP to obtain elevated analytical sensitivity of detection.

Fast and Sensitive Detection of Soil-Borne Cereal Mosaic Virus in Leaf Crude Extract of Durum Wheat

“…RT-LAMP technique has been used for the detection of several plant viruses with an RNA genome [ 25 ]. In particular, specific LAMP and RT-LAMP protocols have been described for the detection of some viruses in wheat [ 38 ]. Wheat yellow mosaic virus (WYMV) was also detected from total RNA extracts using a RT-LAMP protocol [ 39 ].…”

“…This indicates that sensitivity of LAMP is comparable to real-time PCR also when the virus was transmitted by the natural vector in infected soil. It is known that LAMP- and PCR-based assays reach similar levels of sensitivity [ 38 ].…”

The Novel ML Approaches on Wheat Disease by CLF and FOHF of Image Equalization Techniques

“…For four types of leaf diseases affecting tomato plants, it showed an average accuracy of 92.5%. Gomez et al [21] described a unique molecular approach based on loop-mediated isothermal amplification for identifying wheat pathogens. Although deep learning algorithms are capable of automatically extracting features, this is not always the case.…”

Lateral flow strip assay of a gene segment in the COVID-19 virus with combined dual readout mode and preliminary multisite hybrid chain reaction amplification

“…21 Compared to PCR, isothermal amplication technology has multiple advantages such as rapid response, miniaturization of detection equipment, and independence from temperature cycling instruments. As a point-of-care technique for the diagnosis of malaria, multicomplex loop-mediated isothermal amplication (m-LAMP), 22,23 multiplex RPA 24 and multicomplex HCR 25,26 have been reported. However, there has been no reported the integration of multicomplex HCR with LFTS.…”