Real-Time PCR Detection of the Onion Downy Mildew Pathogen <i>Peronospora destructor</i> From Symptomless Onion Seedlings and Soils

Fujiwara, Kazuki; Inoue, Hiroyoshi; Sonoda, R. M.; Iwamoto, Yutaka; Kusaba, Motoaki; Tashiro, Nobutada; Miyasaka, Atsushi

doi:10.1094/pdis-05-20-1095-re

Cited by 13 publications

(11 citation statements)

References 22 publications

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“…The regression line for predicting the number of oospores of P. destructor using purified DNA was obtained (R 2 = 0.98), and its minimum amplification threshold was 5 oospores/g soil. This result was more sensitive than the method of Fujiwara et al (2021).…”

Section: Discussionmentioning

confidence: 76%

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Monitoring of Peronospora destructor oospores from field samples using real‐time PCR

et al. 2022

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Onion downy mildew caused by Peronospora destructor has been widespread in Japan since 2016. Soil disinfection and use of fungicides have been implemented as control measures against oospores in the soil, which are the primary source of infection. Measurements of oospore density are needed to clarify the risk of disease development and inform disease management. In this study, an experimental system capable of detecting P. destructor DNA from field samples was developed. A TaqMan probe‐type primer was used to target the coxII (cytochrome c oxidase subunit II) region of the mitochondrial genome of P. destructor and no false positives were observed. Using this method, the detection limit was equivalent to 5 oospores of P. destructor/g soil in grey lowland soil and andosol. The correlation coefficient between oospore density and the primary infection rate was investigated by testing soil samples from 115 fields. Although no correlations between oospore density and the primary infection were observed in pesticide‐treated fields, significant correlations were observed in untreated fields. Continuous cropping of onions increased the oospore density. The correlation between primary and secondary infection was relatively weak, and the negative predictive value of primary infection was relatively high (89.0). These results suggest that the disease‐risk potential of onion downy mildew is very high, and thus it is necessary to set a low pathogen detection threshold. The system presented here provides a highly sensitive method for supporting decision‐making aimed at disease control.

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Section: Discussionmentioning

confidence: 76%

“…Therefore, oospores are an important inoculum source. To survey oospore density in the field, Fujiwara et al (2021) designed specific primers from the rDNA internal transcribed spacer (ITS) region of the P . destructor genome; however, they encountered issues with false positives and low detection sensitivity.…”

Section: Introductionmentioning

confidence: 99%

Monitoring of Peronospora destructor oospores from field samples using real‐time PCR

et al. 2022

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“…However, they are also capable of genetic recombination through sexual reproduction (homothallism and heterothallism), producing oospores, which are long‐term survival structures that can, like Peronospora destructor , survive up to 25 years in soils (McKay, 1957). Hence, given their abundant production of sporangia, their short infection–sporulation cycles, and their high host plant specificity, downy mildew pathogens are particularly destructive and of concern for several crops of economic importance, notably Plasmopara viticola in grapevine (Carisse et al, 2020), Bremia lactucae in lettuce (Dhar et al, 2019; Fall, Van der Heyden, Beaulieu, et al, 2015), Pseudoperonospora cubensis in cucurbits (Granke & Hausbeck, 2011; Granke et al, 2014; Summers, Adair, et al, 2015), Peronospora effusa in spinach (Klosterman et al, 2014), and P. destructor in onion (Fujiwara et al, 2021; Van der Heyden, Bilodeau, et al, 2020; Van der Heyden, Dutilleul, et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

“…Potential sources of inoculum are systemically infected plants (onion sets, volunteer plants, or waste piles), airborne sporangia, and oospores present in soil or plant debris (Hildebrand & Sutton, 1980; McKay, 1957; Palti, 1989). Real‐time quantitative PCR (qPCR) analysis of soil samples suggested the presence of quantifiable DNA in almost 11% of the soil samples analysed, especially samples taken from fields with a short crop rotation (Fujiwara et al, 2021; Van der Heyden, Bilodeau, et al, 2020). In addition, these results suggested local overwintering but did not provide information about population structures.…”

Section: Introductionmentioning

confidence: 99%

Genotyping by sequencing suggests overwintering of Peronospora destructor in southwestern Québec, Canada

Heyden

Dutilleul

Duceppe

et al. 2021

Molecular Plant Pathology

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Several Peronospora species are carried by wind over short and long distances, from warmer climates where they survive on living plants to cooler climates. In eastern Canada, this annual flow of sporangia was thought to be the main source of Peronospora destructor responsible for onion downy mildew. However, the results of a recent study showed that the increasing frequency of onion downy mildew epidemics in eastern Canada is associated with warmer autumns, milder winters, and previous year disease severity, suggesting overwintering of the inoculum in an area where the pathogen is not known to be endogenous. In this study, genotyping by sequencing was used to investigate the population structure of P. destructor at the landscape scale. The study focused on a particular region of southwestern Québec—Les Jardins de Napierville—to determine if the populations were clonal and regionally differentiated. The data were characterized by a high level of linkage disequilibrium, characteristic of clonal organisms. Consequently, the null hypothesis of random mating was rejected when tested on predefined or nonpredefined populations, indicating that linkage disequilibrium was not a function of population structure and suggesting a mixed reproduction mode. Discriminant analysis of principal components performed with predefined population assignment allowed grouping P. destructor isolates by geographical regions, while analysis of molecular variance confirmed that this genetic differentiation was significant at the regional level. Without using a priori population assignment, isolates were clustered into four genetic clusters. These results represent a baseline estimate of the genetic diversity and population structure of P. destructor.

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“…The application of molecular tools to soilborne pathogens has become common in recent years (Bilodeau, 2011). Nonetheless, to date there have been only a few studies on quantitative real-time PCR detection of onion soil pathogens, such as Sclerotium cepivorum (white rot;Woodhall et al, 2012), Peronospora destructor (downy mildew; Fujiwara et al, 2021), and Rhizoctonia solani AG-3 (Salamone & Okubara, 2020). In this study, a PCR-based detection method specific to the pink root fungus, S. terrestris, from soils was developed.…”

Section: Introductionmentioning

confidence: 99%

Seasonal dynamics of the pink root fungus (Setophoma terrestris) in rhizosphere soil: Effect of crop species and rotation

Yoshida

2021

Plant Pathology

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Pink root rot of onion (Allium cepa) caused by Setophoma terrestris is a common disease in warm climates and can be severe in monoculture (Hess, 1962;Sumner, 2002). The primary symptoms are characterized by pale pinkening on root tips and branching points of roots, followed by root shrivelling with red to deep purple discolouration, and eventually decay. Generally, losses owing to the disease remain low; however, a period of drought and high temperature after planting may result in serious plant damage accompanied by withering of aerial parts and a subsequent decrease in the number of leaves, leading to bulb size reduction (Gorenz et al., 1949;Sumner, 2002).The causal agent was first named as Phoma terrestris based on aetiological studies (Hansen, 1926, 1929), and Gorenz et al. (1948 proposed a transfer to Pyrenochaeta owing to septa on their pycnidia. Recently, de Gruyter et al. (2010) arranged the Phoma section based on both morphological and genetic properties and reclassified it into the genus Setophoma.S. terrestris has a broad host range, including wild and crop plants in families such as Amaranthaceae, Amaryllidaceae, Apiaceae,

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Real-Time PCR Detection of the Onion Downy Mildew Pathogen Peronospora destructor From Symptomless Onion Seedlings and Soils

Cited by 13 publications

References 22 publications

Monitoring of Peronospora destructor oospores from field samples using real‐time PCR

Monitoring of Peronospora destructor oospores from field samples using real‐time PCR

Genotyping by sequencing suggests overwintering of Peronospora destructor in southwestern Québec, Canada

Seasonal dynamics of the pink root fungus (Setophoma terrestris) in rhizosphere soil: Effect of crop species and rotation

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