Use of LAMP for Assessing Botrytis cinerea Colonization of Bunch Trash and Latent Infection of Berries in Grapevines

Botrytis fruit rot management: What have we achieved so far?

Botrytis cinerea is a destructive necrotrophic phytopathogen causing overwhelming diseases in more than 1400 plant species, especially fruit crops, resulting in significant economic losses worldwide. The pathogen causes rotting of fruits at both pre-harvest and postharvest stages. Aside from causing gray mold of the mature fruits, the fungus infects leaves, flowers, and seeds, which makes it a notorious phytopathogen. Worldwide, in the majority of fruit crops, B. cinerea causes gray mold. In order to effectively control this pathogen, extensive research has been conducted due to its wide host range and the huge economic losses it causes. It is advantageous to explore detection and diagnosis techniques of B. cinerea to provide the fundamental basis for mitigation strategies. Botrytis cinerea has been identified and quantified in fruit/plant samples at pre- and post-infection levels using various detection techniques including DNA markers, volatile organic compounds, qPCR, chip-digital PCR, and PCR-based nucleic acid sensors. In addition, cultural, physical, chemical, biological, and botanical methods have all been used to combat Botrytis fruit rot. This review discusses research progress made on estimating economic losses, detection and diagnosis, as well as management strategies, including cultural, physical, chemical, and biological studies on B. cinerea along with knowledge gaps and potential areas for future research.

A Loop-Mediated Isothermal Amplification Assay for the Identification of Botrytis fragariae in Strawberry

Gray mold in strawberry is caused by multiple species of Botrytis, including Botrytis cinerea, B. pseudocinerea, B. fragariae, and B. mali. The species B. cinerea and B. fragariae are widespread in production regions of the eastern United States and Germany, and their distinction is important for disease management strategies. Currently, the only way to differentiate these species in field samples is by PCR, which is time consuming, labor intensive, and costly. In this study, a loop-mediated isothermal amplification (LAMP) technique was developed based on species-specific NEP2 gene nucleotide sequences. The designed primer set specifically amplified B. fragariae DNA and no other Botrytis spp. (B. cinerea, B. mali, and B. pseudocinerea) or plant pathogens. The LAMP assay was able to amplify fragments from DNA extracted from infected fruit using a rapid DNA extraction protocol, confirming its ability to detect low amounts of B. fragaria DNA from field-infected fruit. In addition, a blind test was performed to identify B. fragariae in 51 samples collected from strawberry fields in the eastern United States using the LAMP technique. The B. fragariae samples were identified with a reliability of 93.5% (29 of 32), and none of the B. cinerea, B. pseudocinerea, or B. mali samples included in the test were amplified in 10 min. Our results show that the LAMP technique is a specific and reliable method for the detection of B. fragariae from infected fruit tissue and can help to control this important disease in the field.

A Portable Nucleic Acid Sensor Based on PCR for Simple, Rapid, and Sensitive Testing of Botrytis cinerea in Ginseng

Botrytis cinerea is a ubiquitous pathogen that can infect at least 200 dicotyledonous plant species including many agriculturally and economically important crops. In Ginseng, the fungus may cause ginseng gray mold disease, causing great economic losses in the ginseng industry. Therefore, the early detection of B. cinerea in the process of ginseng production is necessary for the disease prevention and control of the pathogen's spread. In this study, a polymerase chain reaction-nucleic acid sensor (PCR-NAS) rapid detection technique was established, and it can be used for field detection of B. cinerea through antipollution design and portable integration. The present study showed that the sensitivity of PCR-NAS technology is 10 times higher than that of traditional PCR-electrophoresis, and there is no need for expensive detection equipment or professional technicians. The detection results of nucleic acid sensors can be read by the naked eye in under 3 min. Meanwhile, the technique has high specificity for the detection of B. cinerea. The testing of 50 field samples showed that the detection results of PCR-NAS were consistent with those of the real-time quantitative PCR (qPCR) method. The PCR-NAS technique established in this study can be used as a novel nucleic acid field detection technique, and it has a potential application in the field detection of B. cinerea to achieve early warning of the pathogen infection.

Improved Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) for the Rapid and Sensitive Detection of Yam mosaic virus

Yam (Dioscorea spp.) productivity is constrained significantly by the lack of a formal seed system. Vegetative propagation, through tuber setts as 'seed' yams, encourages the recycling of virus-infected planting materials, contributing to high virus incidence and yield losses. Efforts are ongoing to increase the production of high-quality seed yams in a formal seed system to reduce virus-induced yield losses and enhance the crop's productivity and food security. Specific and sensitive diagnostic tests are imperative to prevent the multiplication of virus-infected materials contributing to a sustainable seed yam certification system. During routine indexing of yam accessions, discrepancies were observed between the results obtained from the reverse transcription loop-mediated isothermal amplification (RT-LAMP) test and those from reverse transcription polymerase chain reaction (RT-PCR); RT-LAMP failed to detect Yam mosaic virus (YMV) in some samples that tested positive by RT-PCR. This prompted the design of a new set of LAMP primers, YMV1-OPT primers. These primers detected as little as 0.1 fg/µL of purified RNA obtained from a YMV-infected plant, a sensitivity equivalent to that obtained with RT-PCR. RT-LAMP using YMV1-OPT primers is recommended for all future virus-indexing of seed yams for YMV, offering a rapid, sensitive, and cost-effective approach.

A Review of Cultural Practices for Botrytis Bunch Rot Management in New Zealand Vineyards

Botrytis bunch rot of grapes (BBR) causes substantial crop and wine quality issues globally. Past and present foundations for BBR control are based upon synthetic fungicides and varying forms of canopy management. Many authors regard the continued dependence on fungicides as unsustainable and have urged greater deployment of cultural, biological and nutritional strategies. However, in contrast to organic wine production, the uptake of alternative strategies in conventional vineyards has been slow based on cost and perceived reliability issues. This review summarises research from many different wine growing regions in New Zealand with the aim of demonstrating how traditional and newly developed cultural control practices have cost-effectively reduced BBR. In addition to reviewing traditional cultural practices (e.g., leaf removal), mechanical tools are described that remove floral trash and mechanically shake the vines. Multi-omics has improved our knowledge of the underlying changes to grape berries after mechanical shaking. Exogenous applications of calcium may correct calcium deficiencies in the berry skin and reduce BBR but the outcome varies between cultivar and regions. Nitrogen aids in grapevine defence against BBR but remains a complex and difficult nutrient to manage. The sustainable growth of organics and The European Green Deal will stimulate researchers to evaluate new combinations of non-chemical BBR strategies in the next decade.

Fast Electrochemical Measurement of Laccase Activity for Monitoring Grapes’ Infection with Botrytis cinerea

Grapes’ infection with the fungi Botrytis cinerea is one of the major causes of economic loss in the winemaking sector worldwide. The laccase activity of grapes is considered an appropriate indicator of this type of fungal infection, and enzymatic activity higher than 3 U/mL indicates a high risk of irreversibly damaged grape must due to enzymatic browning. This work describes a fast test for the measurement of laccase activity based on a dual optical and electrochemical detection method. A paper sensor impregnated with the enzymatic substrate dye 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) provides a semi-quantitative optical measurement. While the paper sensor can be used independently, when combined with a screen-printed electrode and amperometry measurements, it enables the quantitative detection of laccase activities down to 0.4 U/mL in only 5 min. The method was applied for monitoring the artificial infection of white, rosé, and red grapes with different strains of Botrytis cinerea. The results were confirmed by parallel analysis using the spectrophotometric method of laccase activity determination based on syringaldazine. The influence of the fungal strain and type of grape on laccase activity levels is reported. The demonstrated robustness, simplicity, and versatility of the developed method make it ideal for application on-site in the vineyard or at grape processing points.