Quick and accurate detection of Sclerotiniasclerotiorum and Phomopsis spp. in soybean seeds using qPCR and seed‐soaking method

Ramiro, Juliana; Ciampi‐Guillardi, Maisa; Caldas, Danielle Gregorio Gomes; Moraes, Maria Heloísa Duarte de; Barbieri, Marina Coan Goldoni; Pereira, Wagner Vicente; Júnior, Nelson Sidnei Massola

doi:10.1111/jph.12796

Cited by 7 publications

(4 citation statements)

References 27 publications

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“…Only higher numbers of tested seeds that also should be randomly chosen can guarantee reliability of the resulting values. A common number that is used is 400 seeds per seed lot [188,189]. In this context, however, it needs to be stated that while the PCR methods are much faster than classical seed plating, they are more labor intensive.…”

Section: Tests For Certification Purposes Often Require Large Samples...mentioning

confidence: 99%

Diagnosis of Soybean Diseases Caused by Fungal and Oomycete Pathogens: Existing Methods and New Developments

Hosseini

Voegele

Link

2023

JoF

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Soybean (Glycine max) acreage is increasing dramatically, together with the use of soybean as a source of vegetable protein and oil. However, soybean production is affected by several diseases, especially diseases caused by fungal seed-borne pathogens. As infected seeds often appear symptomless, diagnosis by applying accurate detection techniques is essential to prevent propagation of pathogens. Seed incubation on culture media is the traditional method to detect such pathogens. This method is simple, but fungi have to develop axenically and expert mycologists are required for species identification. Even experts may not be able to provide reliable type level identification because of close similarities between species. Other pathogens are soil-borne. Here, traditional methods for detection and identification pose even greater problems. Recently, molecular methods, based on analyzing DNA, have been developed for sensitive and specific identification. Here, we provide an overview of available molecular assays to identify species of the genera Diaporthe, Sclerotinia, Colletotrichum, Fusarium, Cercospora, Septoria, Macrophomina, Phialophora, Rhizoctonia, Phakopsora, Phytophthora, and Pythium, causing soybean diseases. We also describe the basic steps in establishing PCR-based detection methods, and we discuss potentials and challenges in using such assays.

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Section: Tests For Certification Purposes Often Require Large Samples...mentioning

confidence: 99%

Diagnosis of Soybean Diseases Caused by Fungal and Oomycete Pathogens: Existing Methods and New Developments

Hosseini

Voegele

Link

2023

JoF

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“…The correct identification of Colletotrichum spp. in seeds is essential for diagnostic laboratories and producers, avoiding the introduction and dissemination of the pathogen in soybean fields (Ramiro et al., 2019). To date, there are still no diagnostic tests for all Colletotrichum species associated with soybean.…”

Section: Identification and Molecular Diagnosticsmentioning

confidence: 99%

Soybean anthracnose caused by Colletotrichum species: Current status and future prospects

Boufleur

Ciampi‐Guillardi

Tikami

et al. 2021

Molecular Plant Pathology

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Soybean (Glycine max) is one of the most important cultivated plants worldwide as a source of protein‐rich foods and animal feeds. Anthracnose, caused by different lineages of the hemibiotrophic fungus Colletotrichum, is one of the main limiting factors to soybean production. Losses due to anthracnose have been neglected, but their impact may threaten up to 50% of the grain production. Taxonomy While C. truncatum is considered the main species associated with soybean anthracnose, recently other species have been reported as pathogenic on this host. Until now, it has not been clear whether the association of new Colletotrichum species with the disease is related to emerging species or whether it is due to the undergoing changes in the taxonomy of the genus. Disease symptoms Typical anthracnose symptoms are pre‐ and postemergence damping‐off; dark, depressed, and irregular spots on cotyledons, stems, petioles, and pods; and necrotic laminar veins on leaves that can result in premature defoliation. Symptoms may evolve to pod rot, immature opening of pods, and premature germination of grains. Challenges As accurate species identification of the causal agent is decisive for disease control and prevention, in this work we review the taxonomic designation of Colletotrichum isolated from soybean to understand which lineages are pathogenic on this host. We also present a comprehensive literature review of soybean anthracnose, focusing on distribution, symptomatology, epidemiology, disease management, identification, and diagnosis. We consider the knowledge emerging from population studies and comparative genomics of Colletotrichum spp. associated with soybean providing future perspectives in the identification of molecular factors involved in the pathogenicity process. Useful website Updates on Colletotrichum can be found at http://www.colletotrichum.org/. All available Colletotrichum genomes on GenBank can be viewed at http://www.colletotrichum.org/genomics/.

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“…It will be necessary to gather more data, to perform additional experiments studying disease progression, and to discuss with both seed companies and authorities involved in seed testing and certification to decide on the best sampling scheme and whether the pathogen load per seed should be considered in the decision on a seed lot. Seed soaking assays [27] could be an alternative to random sampling of seeds with DNA preparation from the seeds and will be considered in further tests of our assay.…”

Section: Plos Onementioning

confidence: 99%

Establishment of a quadruplex real-time PCR assay to distinguish the fungal pathogens Diaporthe longicolla, D. caulivora, D. eres, and D. novem on soybean

2021

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Diaporthe species are fungal plant pathogens of many important crops. Seed decay is one of the most important diseases on soybean. It is caused by various species of the genus Diaporthe and responsible for significant economic damage. In central Europe the four species D. longicolla, D. caulivora, D. eres, and D. novem are considered the principal species of Diaporthe on soybean. Fast and accurate detection of these pathogens is of utmost importance. In this study four species-specific TaqMan primer-probe sets that can be combined into a quadruplex assay were designed based on TEF sequences. The specificity and efficiency of the primer-probe sets were tested using PCR products and genomic DNA from pure cultures of the four Diaporthe species and other soybean fungal pathogens. Our results indicate that the primer-probe sets DPCL, DPCC, DPCE, and DPCN allow discrimination of D. longicolla, D. caulivora, D. eres, and D. novem, respectively, and can be used to detect and quantify these four Diaporthe species in parallel using quadruplex real-time PCR. In addition, the quadruplex real-time PCR assay was evaluated on different plant materials including healthy and infected soybean seeds or seed lots, soybean stems, and soybean leaves. This assay is a rapid and effective method to detect and quantify Diaporthe species from samples relevant for disease control.

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Quick and accurate detection of Sclerotiniasclerotiorum and Phomopsis spp. in soybean seeds using qPCR and seed‐soaking method

Cited by 7 publications

References 27 publications

Diagnosis of Soybean Diseases Caused by Fungal and Oomycete Pathogens: Existing Methods and New Developments

Diagnosis of Soybean Diseases Caused by Fungal and Oomycete Pathogens: Existing Methods and New Developments

Soybean anthracnose caused by Colletotrichum species: Current status and future prospects

Establishment of a quadruplex real-time PCR assay to distinguish the fungal pathogens Diaporthe longicolla, D. caulivora, D. eres, and D. novem on soybean

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