A review of recent advances in plant-pathogen detection systems

Patel, Rhea; Mitra, Bappa; Vinchurkar, Madhuri; Adami, Andrea; Patkar, Rajul; Giacomozzi, F.; Lorenzelli, Leandro; Baghini, Maryam Shojaei

doi:10.1016/j.heliyon.2022.e11855

Cited by 30 publications

(22 citation statements)

References 81 publications

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“…Lateral flow immunoassays (LFIAs) are yet another popular technique for the on-site detection of a wide variety of compounds including pathogens [ 176 ]. These are immunochromatographic assays comprised of metal nanoparticles, antibodies against the pathogen, and signal amplification probes functionalized in a test strip.…”

Section: Existing Optical Sensing Technologies To Monitor Plant-micro...mentioning

confidence: 99%

Optical Sensing Technologies to Elucidate the Interplay between Plant and Microbes

Neelam

Tabassum

2023

Micromachines

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Plant-microbe interactions are critical for ecosystem functioning and driving rhizosphere processes. To fully understand the communication pathways between plants and rhizosphere microbes, it is crucial to measure the numerous processes that occur in the plant and the rhizosphere. The present review first provides an overview of how plants interact with their surrounding microbial communities, and in turn, are affected by them. Next, different optical biosensing technologies that elucidate the plant-microbe interactions and provide pathogenic detection are summarized. Currently, most of the biosensors used for detecting plant parameters or microbial communities in soil are centered around genetically encoded optical and electrochemical biosensors that are often not suitable for field applications. Such sensors require substantial effort and cost to develop and have their limitations. With a particular focus on the detection of root exudates and phytohormones under biotic and abiotic stress conditions, novel low-cost and in-situ biosensors must become available to plant scientists.

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Section: Existing Optical Sensing Technologies To Monitor Plant-micro...mentioning

confidence: 99%

Optical Sensing Technologies to Elucidate the Interplay between Plant and Microbes

Neelam

Tabassum

2023

Micromachines

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“…12,35 Among these, LAMP is particularly significant, as its set of primers enhances sensitivity, and intube colorimetric and fluorescent signals improve field applicability. 12,40 Isothermal amplification technologies do not require complex thermocyclers and can be integrated into simple hand-held devices, increasing their portability. 41 However, complex primer design, expensive reagents, and the need for instrumental product visualization introduce complexities in most of these methods compared to the CRISPR/Cas system.…”

Section: Current Molecular Diagnostic Tools For Plant Pathogensmentioning

confidence: 99%

CRISPR/Cas-Based Diagnostics in Agricultural Applications

Tanny

Sallam

Soda

et al. 2023

J. Agric. Food Chem.

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Pests and disease-causing pathogens frequently impede agricultural production. An early and efficient diagnostic tool is crucial for effective disease management. Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPRassociated protein (Cas) have recently been harnessed to develop diagnostic tools. The CRISPR/Cas system, composed of the Cas endonuclease and guide RNA, enables precise identification and cleavage of the target nucleic acids. The inherent sensitivity, high specificity, and rapid assay time of the CRISPR/Cas system make it an effective alternative for diagnosing plant pathogens and identifying genetically modified crops. Furthermore, its potential for multiplexing and suitability for point-of-care testing at the field level provide advantages over traditional diagnostic systems such as RT-PCR, LAMP, and NGS. In this review, we discuss the recent developments in CRISPR/Cas based diagnostics and their implications in various agricultural applications. We have also emphasized the major challenges with possible solutions and provided insights into future perspectives and potential applications of the CRISPR/Cas system in agriculture.

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“…For example, it is impossible to diagnose CLR on the stage of the masking of symptom using naked eye; and, it needs personal experiences using naked eye to identify the suspected symptoms to CLR in the coffee leaves, and sometimes, it is prone to misdiagnosis when symptoms and/or signs are not characteristic enough. Using molecular assays to detect plant pathogens is an effective way to accurately diagnose plant diseases at the early stages (Patel et al 2022;Salcedo et al 2021). Currently, several methods of molecular diagnostics have been developed for detection of H. vastatrix in coffee, including PCR using universal primers (White et al 1990) or specific primers (Wang et al 2017), and single-tube PCR (Wu et al 2022).…”

Section: Introductionmentioning

confidence: 99%

“…Currently, several methods of molecular diagnostics have been developed for detection of H. vastatrix in coffee, including PCR using universal primers (White et al 1990) or specific primers (Wang et al 2017), and single-tube PCR (Wu et al 2022). However, the disadvantages of these methods are time-consuming, laborious, high costs for reagents, specialized personnel and sophisticated equipment requirements; moreover, their sensitivity is still not enough to detect some low titer phytopathogens (Patel et al 2022;Salcedo et al 2021).…”

Section: Introductionmentioning

confidence: 99%

Development of a Loop-Mediated Isothermal Amplification Assay for Rapid and sensitive Detection of Hemileia vastatrix in Coffee

Wang²,

Han³

et al. 2023

Preprint

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Coffee leaf rust (CLR) caused by Hemileia vastatrix is a worldwide devastating disease. Early monitoring is crucial for controlling CLR quickly and efficiently. However, it is difficult to accurately identify CLR at the early stage via naked eye; and the detection of H. vastatrix using PCR-based methods were time-consuming, laborious, and sometimes low- sensitivity. LAMP technology is known for its speed, specificity, and sensitivity to accurately identify many different pathogens. Therefore, in this study, by comparing ITS sequences of H. vastatrix with other H. vastatrix and Uredinales strains using National Center for Biotec- hnology Information (NCBI) by BLASTn, we designed specific primers targeting the unique region and its flanking regions of ITS sequences for H. vastatrix. Using SYBR Green I dye, we established a LAMP technique for rapid and sensitive detection of H. vastatrix. Furthermore, we optimized the LAMP protocol was to enhance both sensitivity and specificity for H. vastatrix detection. Under the optimized condition, the establised LAMP protocol could detect as low as 1pg/μl of H. vastatrix DNA in 60min at 63℃, which is ~100 times more sensitive than conventional PCR. This method can successfully detect H. vastatrix in the early CLR symptom on the coffee leaves in the field.

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A review of recent advances in plant-pathogen detection systems

Cited by 30 publications

References 81 publications

Optical Sensing Technologies to Elucidate the Interplay between Plant and Microbes

Optical Sensing Technologies to Elucidate the Interplay between Plant and Microbes

CRISPR/Cas-Based Diagnostics in Agricultural Applications

Development of a Loop-Mediated Isothermal Amplification Assay for Rapid and sensitive Detection of Hemileia vastatrix in Coffee

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