Diagnostic qPCR Assay to Detect Fusarium brasiliense , a Causal Agent of Soybean Sudden Death Syndrome and Root Rot of Dry Bean
Species within clade 2 of the species complex (FSSC) are significant pathogens of dry bean ( ) and soybean ( ), causing root rot and/or sudden death syndrome (SDS). These species are morphologically difficult to distinguish and often require molecular tools for proper diagnosis to a species level. H...
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creator | Roth, Mitchell G Oudman, Kjersten A Griffin, Amanda Jacobs, Janette L Sang, Hyunkyu Chilvers, Martin I |
description | Species within clade 2 of the
species complex (FSSC) are significant pathogens of dry bean (
) and soybean (
), causing root rot and/or sudden death syndrome (SDS). These species are morphologically difficult to distinguish and often require molecular tools for proper diagnosis to a species level. Here, a TaqMan probe-based quantitative PCR (qPCR) assay was developed to distinguish
from other closely related species within clade 2 of the FSSC. The assay displays high specificity against close relatives and high sensitivity, with a detection limit of 100 fg. This assay was able to detect
from purified mycelia, infected dry bean roots, and soil samples throughout Michigan. When multiplexed with an existing qPCR assay specific to
, accurate quantification of both
and
was obtained, which can facilitate accurate diagnoses and identify coinfections with a single reaction. The assay is compatible with multiple qPCR thermal cycling platforms and will be helpful in providing accurate detection of
. Management of root rot and SDS pathogens in clade 2 of the FSSC is challenging and must be done proactively, because no midseason management strategies currently exist. However, accurate detection can facilitate management decisions for subsequent growing seasons to successfully manage these pathogens. |
doi_str_mv | 10.1094/PDIS-01-19-0016-RE |
format | Article |
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species complex (FSSC) are significant pathogens of dry bean (
) and soybean (
), causing root rot and/or sudden death syndrome (SDS). These species are morphologically difficult to distinguish and often require molecular tools for proper diagnosis to a species level. Here, a TaqMan probe-based quantitative PCR (qPCR) assay was developed to distinguish
from other closely related species within clade 2 of the FSSC. The assay displays high specificity against close relatives and high sensitivity, with a detection limit of 100 fg. This assay was able to detect
from purified mycelia, infected dry bean roots, and soil samples throughout Michigan. When multiplexed with an existing qPCR assay specific to
, accurate quantification of both
and
was obtained, which can facilitate accurate diagnoses and identify coinfections with a single reaction. The assay is compatible with multiple qPCR thermal cycling platforms and will be helpful in providing accurate detection of
. Management of root rot and SDS pathogens in clade 2 of the FSSC is challenging and must be done proactively, because no midseason management strategies currently exist. However, accurate detection can facilitate management decisions for subsequent growing seasons to successfully manage these pathogens.</description><identifier>ISSN: 0191-2917</identifier><identifier>EISSN: 1943-7692</identifier><identifier>DOI: 10.1094/PDIS-01-19-0016-RE</identifier><identifier>PMID: 31644390</identifier><language>eng</language><publisher>United States</publisher><subject>Fusarium - genetics ; Glycine max - microbiology ; Michigan ; Plant Diseases - microbiology ; Plant Roots - microbiology ; Polymerase Chain Reaction ; Soil Microbiology ; Species Specificity</subject><ispartof>Plant disease, 2020-01, Vol.104 (1), p.246-254</ispartof><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c347t-4bfa60a3d677f1b5d09ee460df55a0172df85fc048e235b070df0d074fafcdfa3</citedby><cites>FETCH-LOGICAL-c347t-4bfa60a3d677f1b5d09ee460df55a0172df85fc048e235b070df0d074fafcdfa3</cites><orcidid>0000-0002-0798-9312 ; 0000-0002-7459-5217 ; 0000-0001-8832-1666</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,3724,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31644390$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Roth, Mitchell G</creatorcontrib><creatorcontrib>Oudman, Kjersten A</creatorcontrib><creatorcontrib>Griffin, Amanda</creatorcontrib><creatorcontrib>Jacobs, Janette L</creatorcontrib><creatorcontrib>Sang, Hyunkyu</creatorcontrib><creatorcontrib>Chilvers, Martin I</creatorcontrib><title>Diagnostic qPCR Assay to Detect Fusarium brasiliense , a Causal Agent of Soybean Sudden Death Syndrome and Root Rot of Dry Bean</title><title>Plant disease</title><addtitle>Plant Dis</addtitle><description>Species within clade 2 of the
species complex (FSSC) are significant pathogens of dry bean (
) and soybean (
), causing root rot and/or sudden death syndrome (SDS). These species are morphologically difficult to distinguish and often require molecular tools for proper diagnosis to a species level. Here, a TaqMan probe-based quantitative PCR (qPCR) assay was developed to distinguish
from other closely related species within clade 2 of the FSSC. The assay displays high specificity against close relatives and high sensitivity, with a detection limit of 100 fg. This assay was able to detect
from purified mycelia, infected dry bean roots, and soil samples throughout Michigan. When multiplexed with an existing qPCR assay specific to
, accurate quantification of both
and
was obtained, which can facilitate accurate diagnoses and identify coinfections with a single reaction. The assay is compatible with multiple qPCR thermal cycling platforms and will be helpful in providing accurate detection of
. Management of root rot and SDS pathogens in clade 2 of the FSSC is challenging and must be done proactively, because no midseason management strategies currently exist. However, accurate detection can facilitate management decisions for subsequent growing seasons to successfully manage these pathogens.</description><subject>Fusarium - genetics</subject><subject>Glycine max - microbiology</subject><subject>Michigan</subject><subject>Plant Diseases - microbiology</subject><subject>Plant Roots - microbiology</subject><subject>Polymerase Chain Reaction</subject><subject>Soil Microbiology</subject><subject>Species Specificity</subject><issn>0191-2917</issn><issn>1943-7692</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNo9kEFv1DAQhS0Earelf4AD8pEDhnHsJOvjsruFSpWoduFsTeJxCUri1nYOOfHXm6WFy8zhfe8dPsbeSfgkwejPd7ubowAppBEAshKH_Su2kkYrUVemeM1WII0UhZH1ObtI6TcAaF2tz9i5kpXWysCK_dl1eD-GlLuWP95tD3yTEs48B76jTG3m11PC2E0DbyKmru9oTMQ_cuRbXJKeb-5pzDx4fgxzQzjy4-QcjUsd8y9-nEcXw0AcR8cPIeTl_KV3ceZfFvwte-OxT3T18i_Zz-v9j-03cfv96812cytapessdOOxAlSuqmsvm9KBIdIVOF-WCLIunF-XvgW9pkKVDdRLAg5q7dG3zqO6ZB-edx9ieJwoZTt0qaW-x5HClGyhYF0WRQl6QYtntI0hpUjePsRuwDhbCfYk3p7EW5BWGnsSbw_7pfT-ZX9qBnL_K_9MqyfDfn8f</recordid><startdate>202001</startdate><enddate>202001</enddate><creator>Roth, Mitchell G</creator><creator>Oudman, Kjersten A</creator><creator>Griffin, Amanda</creator><creator>Jacobs, Janette L</creator><creator>Sang, Hyunkyu</creator><creator>Chilvers, Martin I</creator><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-0798-9312</orcidid><orcidid>https://orcid.org/0000-0002-7459-5217</orcidid><orcidid>https://orcid.org/0000-0001-8832-1666</orcidid></search><sort><creationdate>202001</creationdate><title>Diagnostic qPCR Assay to Detect Fusarium brasiliense , a Causal Agent of Soybean Sudden Death Syndrome and Root Rot of Dry Bean</title><author>Roth, Mitchell G ; Oudman, Kjersten A ; Griffin, Amanda ; Jacobs, Janette L ; Sang, Hyunkyu ; Chilvers, Martin I</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c347t-4bfa60a3d677f1b5d09ee460df55a0172df85fc048e235b070df0d074fafcdfa3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Fusarium - genetics</topic><topic>Glycine max - microbiology</topic><topic>Michigan</topic><topic>Plant Diseases - microbiology</topic><topic>Plant Roots - microbiology</topic><topic>Polymerase Chain Reaction</topic><topic>Soil Microbiology</topic><topic>Species Specificity</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Roth, Mitchell G</creatorcontrib><creatorcontrib>Oudman, Kjersten A</creatorcontrib><creatorcontrib>Griffin, Amanda</creatorcontrib><creatorcontrib>Jacobs, Janette L</creatorcontrib><creatorcontrib>Sang, Hyunkyu</creatorcontrib><creatorcontrib>Chilvers, Martin I</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Plant disease</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Roth, Mitchell G</au><au>Oudman, Kjersten A</au><au>Griffin, Amanda</au><au>Jacobs, Janette L</au><au>Sang, Hyunkyu</au><au>Chilvers, Martin I</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Diagnostic qPCR Assay to Detect Fusarium brasiliense , a Causal Agent of Soybean Sudden Death Syndrome and Root Rot of Dry Bean</atitle><jtitle>Plant disease</jtitle><addtitle>Plant Dis</addtitle><date>2020-01</date><risdate>2020</risdate><volume>104</volume><issue>1</issue><spage>246</spage><epage>254</epage><pages>246-254</pages><issn>0191-2917</issn><eissn>1943-7692</eissn><abstract>Species within clade 2 of the
species complex (FSSC) are significant pathogens of dry bean (
) and soybean (
), causing root rot and/or sudden death syndrome (SDS). These species are morphologically difficult to distinguish and often require molecular tools for proper diagnosis to a species level. Here, a TaqMan probe-based quantitative PCR (qPCR) assay was developed to distinguish
from other closely related species within clade 2 of the FSSC. The assay displays high specificity against close relatives and high sensitivity, with a detection limit of 100 fg. This assay was able to detect
from purified mycelia, infected dry bean roots, and soil samples throughout Michigan. When multiplexed with an existing qPCR assay specific to
, accurate quantification of both
and
was obtained, which can facilitate accurate diagnoses and identify coinfections with a single reaction. The assay is compatible with multiple qPCR thermal cycling platforms and will be helpful in providing accurate detection of
. Management of root rot and SDS pathogens in clade 2 of the FSSC is challenging and must be done proactively, because no midseason management strategies currently exist. However, accurate detection can facilitate management decisions for subsequent growing seasons to successfully manage these pathogens.</abstract><cop>United States</cop><pmid>31644390</pmid><doi>10.1094/PDIS-01-19-0016-RE</doi><tpages>9</tpages><orcidid>https://orcid.org/0000-0002-0798-9312</orcidid><orcidid>https://orcid.org/0000-0002-7459-5217</orcidid><orcidid>https://orcid.org/0000-0001-8832-1666</orcidid><oa>free_for_read</oa></addata></record> |
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language | eng |
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source | MEDLINE; EZB-FREE-00999 freely available EZB journals; Alma/SFX Local Collection; American Phytopathological Society Journal Back Issues |
subjects | Fusarium - genetics Glycine max - microbiology Michigan Plant Diseases - microbiology Plant Roots - microbiology Polymerase Chain Reaction Soil Microbiology Species Specificity |
title | Diagnostic qPCR Assay to Detect Fusarium brasiliense , a Causal Agent of Soybean Sudden Death Syndrome and Root Rot of Dry Bean |
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