Rapid Detection of Xanthomonas citri pv. fuscans and Xanthomonas phaseoli pv. phaseoli in Common Bean by Loop-Mediated Isothermal Amplification

Paiva, Bruna Alicia Rafael de; Wendland, A.; Teixeira, Nara Cristina; Ferreira, Maria Lurdes

doi:10.1094/pdis-02-19-0325-re

Cited by 13 publications

(7 citation statements)

References 35 publications

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“…The LAMP test resulted positive for samples numbered: 2, 3, 4, 5, 7, 10,11,12,15,16,18,20,40,41,45,46, 47 and 50. The others showed no color change, considered samples negative for the presence of the pathogen (Table 3 and Fig.…”

Section: Diversity and Contrast Test With Nested-pcrmentioning

confidence: 99%

Specific colorimetric LAMP assay for the detection of maize bushy stunt phytoplasma in corn through comparative genomics

Egito,

Alves,

Carvalho

et al. 2023

Preprint

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Brazil stands out for being the third largest corn producer in the world, in addition to having self-sufficiency in national supply. Even with the high production, the country has, throughout its extension, climatic conditions that favor the attack of several pathogens. Maize red stunt, caused by maize bushy stunt phytoplasma (MBSP), is one of the most harmful diseases to the crop, therefore, there is a demand for detection methods that are fast and accurate. Loop-mediated isothermal amplification (LAMP) is one of these methods, being fast, sensitive, with high specificity and can be used in field analysis. The goal of the present work was the development of a LAMP protocol, through comparative genomics, for MBSP in maize. To design the sets of primers, MBSP genome sequence and other sequences of other pathogens were used in the RUCS software to select only core unique sequences. Three sets of primers presented the desired criteria and were synthetized. The most promising primer set, MBSP-LP, was used to test the LAMP assay together with the Warmstart colorimetric LAMP 2X master mix (NEB) Kit. The collection of 51 samples of corn with and without symptoms was tested with a typical nested-PCR and compared with the proposed LAMP assay. Considering the presence and absence of symptoms, there was confirmation that the symptomatic plants were positive for LAMP in a greater proportion than for nested-PCR. The proposed LAMP assay proved to be sensitive, detecting up to 0.1 fg µL-1 of DNA. The use of plant material directly in the reaction was evaluated for changing the color of the master mix and also for inhibiting the reaction. It was identified that there are no inhibitors in the maize plant tissue, being possible to use this LAMP with plant tissue without the DNA extraction step.

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Section: Diversity and Contrast Test With Nested-pcrmentioning

confidence: 99%

Specific colorimetric LAMP assay for the detection of maize bushy stunt phytoplasma in corn through comparative genomics

Egito,

Alves,

Carvalho

et al. 2023

Preprint

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show abstract

“…However, at the point of symptom development, infection is already well established and consequently the effectiveness of control methods is limited. Currently, diagnostic methods are destructive, lab-based and time-consuming so there is a need for the development of rapid in-field diagnostics, e.g., loop-mediated isothermal amplification (LAMP) and Lateral Flow Tests (LFTs), which have been developed for Xanthomonas pathogens of other crops ( Hodgetts et al, 2015 ; López-Soriano et al, 2017 ; de Paiva et al, 2019 ).…”

Section: Black Rotmentioning

confidence: 99%

The current status, challenges, and future perspectives for managing diseases of brassicas

et al. 2023

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The Brassica genus comprises the greatest diversity of agriculturally important crops. Several species from this genus are grown as vegetable and oil crops for food, animal feed and industrial purposes. In particular, B. oleracea has been extensively bred to give rise to several familiar vegetables (cabbage, broccoli, cauliflower, kale and Brussels Sprouts, etc.) that are grouped under seven major cultivars. In 2020, 96.4 million tonnes of vegetable brassicas were produced globally with a 10.6% increase over the past decade. Yet, like other crops, the production of brassicas is challenged by diseases among which, black rot, clubroot, downy mildew and turnip yellows virus have been identified by growers as the most damaging to UK production. In some cases, yield losses can reach 90% depending upon the geographic location of cultivation. This review aims to provide an overview of the key diseases of brassicas and their management practices, with respect to the biology and lifecycle of the causal pathogens. In addition, the existing controls on the market as well as those that are currently in the research and development phases were critically reviewed. There is not one specific control method that is effective against all the diseases. Generally, cultural practices prevent disease rather than reduce or eliminate disease. Chemical controls are limited, have broad-spectrum activity, are damaging to the environment and are rapidly becoming ineffective due to the evolution of resistance mechanisms by the pathogens. It is therefore important to develop integrated pest management (IPM) strategies that are tailored to geographic locations. Several knowledge gaps have been identified and listed in this review along with the future recommendations to control these four major diseases of brassicas. As such, this review paper will act as a guide to sustainably tackle pre-harvest diseases in Brassica crops to reduce food loss.

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“…A developing yellow colour in a positive LAMP reaction is easily distinguishable from a pink negative sample [157][158][159][160]. The opposite colorization is also available [161][162][163]. There are commercial premixes containing pH indicators that can provide detection without opening the tube after the LAMP mix to prevent possible contamination.…”

Section: Colorimetric Detection Of Lamp Ampliconsmentioning

confidence: 99%

The Potential Use of Isothermal Amplification Assays for In-Field Diagnostics of Plant Pathogens

Иванов

Safenkova

Zherdev

et al. 2021

Plants

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Rapid, sensitive, and timely diagnostics are essential for protecting plants from pathogens. Commonly, PCR techniques are used in laboratories for highly sensitive detection of DNA/RNA from viral, viroid, bacterial, and fungal pathogens of plants. However, using PCR-based methods for in-field diagnostics is a challenge and sometimes nearly impossible. With the advent of isothermal amplification methods, which provide amplification of nucleic acids at a certain temperature and do not require thermocyclic equipment, going beyond the laboratory has become a reality for molecular diagnostics. The amplification stage ceases to be limited by time and instruments. Challenges to solve involve finding suitable approaches for rapid and user-friendly plant preparation and detection of amplicons after amplification. Here, we summarize approaches for in-field diagnostics of phytopathogens based on different types of isothermal amplification and discuss their advantages and disadvantages. In this review, we consider a combination of isothermal amplification methods with extraction and detection methods compatible with in-field phytodiagnostics. Molecular diagnostics in out-of-lab conditions are of particular importance for protecting against viral, bacterial, and fungal phytopathogens in order to quickly prevent and control the spread of disease. We believe that the development of rapid, sensitive, and equipment-free nucleic acid detection methods is the future of phytodiagnostics, and its benefits are already visible.

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Rapid Detection of Xanthomonas citri pv. fuscans and Xanthomonas phaseoli pv. phaseoli in Common Bean by Loop-Mediated Isothermal Amplification

Cited by 13 publications

References 35 publications

Specific colorimetric LAMP assay for the detection of maize bushy stunt phytoplasma in corn through comparative genomics

Specific colorimetric LAMP assay for the detection of maize bushy stunt phytoplasma in corn through comparative genomics

The current status, challenges, and future perspectives for managing diseases of brassicas

The Potential Use of Isothermal Amplification Assays for In-Field Diagnostics of Plant Pathogens

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