https://flore.unifi.it/bitstream/2158/1073524/1/2016%20Pertot%20A%20critical%20review.pdf

A critical review of plant protection tools for reducing pesticide use on grapevine and new perspectives for the implementation of IPM in viticulture

Plant pathogenic fungi are the causal agents of the most detrimental diseases in plants, including economically important crops, provoking considerable yield losses worldwide. Fungal pathogens can infect a wide range of plant species or be restricted to one or few host species. Some of them are obligate parasites requiring the presence of the living host to grow and reproduce, but most of them are saprophytic and can survive without the presence of the living plant, in the soil, water or air. Isolates of a fungal species can be differentiated by morphological characteristics, host range (formae speciales), pathogenic aggressiveness (pathotypes or races) or their ability to form stable vegetative heterokaryons by fusion between genetically different strains (belonging to the same vegetative compatibility group, VCG).

/pdf/molecular-tools-for-detection-of-plant-pathogenic-fungi-and-4h6jrc5l9y.pdf

Molecular Tools for Detection of Plant Pathogenic Fungi and Fungicide Resistance

Many innovations in the development and use of air sampling devices have occurred in plant pathology since the first description of the Hirst spore trap. These include improvements in capture efficiency at relatively high air-volume collection rates, methods to enhance the ease of sample processing with downstream diagnostic methods and even full automation of sampling, diagnosis and wireless reporting of results. Other innovations have been to mount air samplers on mobile platforms such as UAVs and ground vehicles to allow sampling at different altitudes and locations in a short space of time to identify potential sources and population structure. Geographical Information Systems and the application to a network of samplers can allow a greater prediction of airborne inoculum and dispersal dynamics. This field of technology is now developing quickly as novel diagnostic methods allow increasingly rapid and accurate quantifications of airborne species and genetic traits. Sampling and interpretation of results, particularly action-thresholds, is improved by understanding components of air dispersal and dilution processes and can add greater precision in the application of crop protection products as part of integrated pest and disease management decisions. The applications of air samplers are likely to increase, with much greater adoption by growers or industry support workers to aid in crop protection decisions. The same devices are likely to improve information available for detection of allergens causing hay fever and asthma or provide valuable metadata for regional plant disease dynamics.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/aab.12191

Innovations in air sampling to detect plant pathogens.

Management of grape powdery mildew (Erysiphe necator) and other polycyclic diseases often relies on calendar-based pesticide application schedules that assume the presence of inoculum. An inexpensive, loop-mediated isothermal amplification (LAMP) assay was designed to quickly detect airborne inoculum of E. necator to determine when to initiate a fungicide application programme. Field efficacy was tested in 2010 and 2011 in several commercial and research vineyards in the Willamette Valley of Oregon from pre-bud break to veraison. In each vineyard, three impaction spore traps were placed adjacent to the trunk. One trap was maintained and used by the grower to conduct the LAMP assay (G-LAMP) on-site and the other two traps were used for laboratory-conducted LAMP (L-LAMP) and quantitative PCR assay (qPCR). Using the qPCR as a gold standard, L-LAMP was comparable with qPCR in both years, and G-LAMP was comparable to qPCR in 2011. Latent class analysis indicated that qPCR had a true positive proportion of 98% in 2010 and 89% in 2011 and true negative proportion of 96% in 2010 and 64% in 2011. An average of 3·3 fewer fungicide applications were used when they were initiated based on spore detection relative to the grower standard practice. There were no significant differences in berry or leaf incidence between plots with fungicides initiated at detection or grower standard practice plots, suggesting that growers using LAMP to initiate fungicide applications can use fewer fungicide applications to manage powdery mildew compared to standard practices.

/pdf/development-of-a-grower-conducted-inoculum-detection-assay-53isbg6y8u.pdf

Development of a grower-conducted inoculum detection assay for management of grape powdery mildew

Quantitative polymerase chain reaction (qPCR) is a versatile technique for the accurate, sensitive, reliable and high-throughput detection and quantification of target DNA in various environmental samples, and in recent years, it has greatly contributed to the advancement of knowledge in the plant pathology field. Indeed, this technique is ideal to evaluate inoculum threshold levels and to study the epidemiology, biology and ecology of phytopathogenic fungi and oomycetes, thus opening up new research opportunities to investigate host–pathogen interactions and to address tasks related to quarantine, eradication and biosecurity. Moreover, it can be a useful tool in breeding programs. The present review analyses the most relevant applications of qPCR for the detection and quantification of filamentous fungi and oomycetes within host tissues and in soil, air and water, along with brief paragraphs focusing on new application fields such as the detection and quantification of mycotoxigenic fungi and biocontrol agents. The high potentiality of qPCR for present and future applications is highlighted together with a critical analysis of major drawbacks that need to be corrected to definitively confirm it as a preferential routine quantitative detection method.

Use of Quantitative PCR Detection Methods to Study Biocontrol Agents and Phytopathogenic Fungi and Oomycetes in Environmental Samples

The use of a DNA-based method for quantifying airborne inoculum of Botrytis squamosa, a damaging pathogen of onion, was investigated. A method for purifying DNA from conidia collected using rotating-arm samplers and quantifying it using a TaqMan real-time quantitative polymerase chain reaction (qPCR) assay is described. The sensitivity of the qPCR assay was high, with a detection limit of 2 conidia/rod. A linear relationship between numbers of conidia counted with a compound microscope and those determined with the qPCR assay was obtained. Receiver operating characteristic curve analysis was used to evaluate the reliability of the two methods of conidia quantification (microscope examination and qPCR assay) to predict the risk of disease being below or above a damage threshold (D(th)). In total, 142 field samples from commercial onion fields were analyzed. At damage thresholds of 5 or 10 lesions/leaf, conidia quantification with the qPCR assay was more reliable at predicting disease risk than conidia quantification based on microscope counts. The proportion of decisions where the disease was present and predicted was higher for the qPCR assay than for the microscope counts, with values of 0.95 and 0.89 compared with 0.79 and 0.81 for D(th) of 5 and 10 lesions/leaf, respectively. The proportion of decisions where the disease was present but not predicted was lower for the qPCR assay than for microscope counts, with values of 0.05 and 0.11 compared with 0.20 and 0.19 for D(th) of 5 and 10 lesions/leaf, respectively. The results demonstrated that this new qPCR assay was reliable for quantifying B. squamosa airborne inoculum in commercial onion fields and that molecular conidia quantification could be used as a component of a risk management system for Botrytis leaf blight.

https://apsjournals.apsnet.org/doi/pdf/10.1094/PHYTO-99-11-1273

Development of a TaqMan real-time PCR assay for quantification of airborne conidia of Botrytis squamosa and management of Botrytis leaf blight of onion.

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Development of a TaqMan real-time PCR assay for quantification of airborne conidia of Botrytis squamosa and management of Botrytis leaf blight of onion.