Multiplex PCR assay for simultaneous detection of six major bacterial pathogens of rice
Aims The aim of this study was to develop a multiplex PCR (mPCR) assay for rapid, sensitive and simultaneous detection of six important rice pathogens: Xanthomonas oryzae pv. oryzae, X. oryzae pv. oryzicola, Pseudomonas fuscovaginae, Burkholderia glumae, Burkholderia gladioli and Acidovorax avenae s...
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| Veröffentlicht in: | Journal of applied microbiology 2016-05, Vol.120 (5), p.1357-1367 |
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| container_title | Journal of applied microbiology |
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| creator | Cui, Z. Ojaghian, M.R. Tao, Z. Kakar, K.U. Zeng, J. Zhao, W. Duan, Y. Vera Cruz, C.M. Li, B. Zhu, B. Xie, G. |
| description | Aims
The aim of this study was to develop a multiplex PCR (mPCR) assay for rapid, sensitive and simultaneous detection of six important rice pathogens: Xanthomonas oryzae pv. oryzae, X. oryzae pv. oryzicola, Pseudomonas fuscovaginae, Burkholderia glumae, Burkholderia gladioli and Acidovorax avenae subsp. avenae.
Methods and Results
Specific primers were designed through a bioinformatics pipeline. Sensitivity of detection was established using both traditional PCR and quantitative real‐time PCR on isolated DNA and on bacterial cells both in vitro and in simulated diseased seeds and the parameters were optimized for an mPCR assay. A total of 150 bacterial strains were tested for specificity. The mPCR assay accurately predicted the presence of pathogens among 44 symptomatic and asymptomatic rice seed, sheath and leaf samples.
Conclusions
This study confirmed that this mPCR assay is a rapid, reliable and simple tool for the simultaneous detection of six important rice bacterial pathogens.
Significance and Impact of the Study
This study is the first report of a method allowing simultaneous detection of six major rice pathogens. The ability to use crude extracts from plants without bacterial isolation or DNA extraction enhances the value of this mPCR technology for rapid detection and aetiological/epidemiological studies. |
| doi_str_mv | 10.1111/jam.13094 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_1785250076</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>1785250076</sourcerecordid><originalsourceid>FETCH-LOGICAL-c4214-c58c785bb78e3680c17d59d94e1110760609f363fad9c574d0b72ddacdd82da13</originalsourceid><addsrcrecordid>eNqN0U1LwzAcBvAgipvTg19ACl700C1J89bjGL6yoYjisaRJqi19mUmL27c3W6cHQTCXBPLjIf88AJwiOEZ-TQpZjVEEY7IHhihiNMSM4_3tmYQUcjwAR84VEHpE2SEYYCYYETEbgtdFV7b5sjSr4HH2FEjn5DrIGhu4vPI3sjZN5wJtWqPavKmDJvM3q6CShTepVK2xuSyDpWzfmzdTuw2wuTLH4CCTpTMnu30EXq6vnme34fzh5m42nYeKYERCRYXigqYpFyZiAirENY11TIyfC3IGGYyziEWZ1LGinGiYcqy1VFoLrCWKRuCiz13a5qMzrk2q3ClTlv3LE-TTMYU-6j8UIf9bjHt6_osWTWdrP8hGQSJQJKhXl71StnHOmixZ2rySdp0gmGyKSXwxybYYb892iV1aGf0jv5vwYNKDz7w067-Tkvvpoo_8AniJlfU</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1780481385</pqid></control><display><type>article</type><title>Multiplex PCR assay for simultaneous detection of six major bacterial pathogens of rice</title><source>MEDLINE</source><source>Access via Wiley Online Library</source><source>Oxford University Press Journals All Titles (1996-Current)</source><creator>Cui, Z. ; Ojaghian, M.R. ; Tao, Z. ; Kakar, K.U. ; Zeng, J. ; Zhao, W. ; Duan, Y. ; Vera Cruz, C.M. ; Li, B. ; Zhu, B. ; Xie, G.</creator><creatorcontrib>Cui, Z. ; Ojaghian, M.R. ; Tao, Z. ; Kakar, K.U. ; Zeng, J. ; Zhao, W. ; Duan, Y. ; Vera Cruz, C.M. ; Li, B. ; Zhu, B. ; Xie, G.</creatorcontrib><description>Aims
The aim of this study was to develop a multiplex PCR (mPCR) assay for rapid, sensitive and simultaneous detection of six important rice pathogens: Xanthomonas oryzae pv. oryzae, X. oryzae pv. oryzicola, Pseudomonas fuscovaginae, Burkholderia glumae, Burkholderia gladioli and Acidovorax avenae subsp. avenae.
Methods and Results
Specific primers were designed through a bioinformatics pipeline. Sensitivity of detection was established using both traditional PCR and quantitative real‐time PCR on isolated DNA and on bacterial cells both in vitro and in simulated diseased seeds and the parameters were optimized for an mPCR assay. A total of 150 bacterial strains were tested for specificity. The mPCR assay accurately predicted the presence of pathogens among 44 symptomatic and asymptomatic rice seed, sheath and leaf samples.
Conclusions
This study confirmed that this mPCR assay is a rapid, reliable and simple tool for the simultaneous detection of six important rice bacterial pathogens.
Significance and Impact of the Study
This study is the first report of a method allowing simultaneous detection of six major rice pathogens. The ability to use crude extracts from plants without bacterial isolation or DNA extraction enhances the value of this mPCR technology for rapid detection and aetiological/epidemiological studies.</description><identifier>ISSN: 1364-5072</identifier><identifier>EISSN: 1365-2672</identifier><identifier>DOI: 10.1111/jam.13094</identifier><identifier>PMID: 26864896</identifier><identifier>CODEN: JAMIFK</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Acidovorax ; Bacteria ; Bacteriology ; Burkholderia - genetics ; Burkholderia gladioli ; Burkholderia glumae ; Comamonadaceae - genetics ; comparative genomics ; detection ; DNA, Bacterial - analysis ; multiplex PCR ; Multiplex Polymerase Chain Reaction - methods ; Oryza - microbiology ; Plant Diseases - microbiology ; Plant Leaves - microbiology ; Plant pathology ; Polymerase chain reaction ; Pseudomonas - genetics ; Pseudomonas fuscovaginae ; quantitative real‐time PCR ; Rice ; rice bacterial pathogens ; Seeds - microbiology ; Xanthomonas - genetics ; Xanthomonas oryzae</subject><ispartof>Journal of applied microbiology, 2016-05, Vol.120 (5), p.1357-1367</ispartof><rights>2016 The Society for Applied Microbiology</rights><rights>2016 The Society for Applied Microbiology.</rights><rights>Copyright © 2016 The Society for Applied Microbiology</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4214-c58c785bb78e3680c17d59d94e1110760609f363fad9c574d0b72ddacdd82da13</citedby><cites>FETCH-LOGICAL-c4214-c58c785bb78e3680c17d59d94e1110760609f363fad9c574d0b72ddacdd82da13</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fjam.13094$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fjam.13094$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1417,27924,27925,45574,45575</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26864896$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Cui, Z.</creatorcontrib><creatorcontrib>Ojaghian, M.R.</creatorcontrib><creatorcontrib>Tao, Z.</creatorcontrib><creatorcontrib>Kakar, K.U.</creatorcontrib><creatorcontrib>Zeng, J.</creatorcontrib><creatorcontrib>Zhao, W.</creatorcontrib><creatorcontrib>Duan, Y.</creatorcontrib><creatorcontrib>Vera Cruz, C.M.</creatorcontrib><creatorcontrib>Li, B.</creatorcontrib><creatorcontrib>Zhu, B.</creatorcontrib><creatorcontrib>Xie, G.</creatorcontrib><title>Multiplex PCR assay for simultaneous detection of six major bacterial pathogens of rice</title><title>Journal of applied microbiology</title><addtitle>J Appl Microbiol</addtitle><description>Aims
The aim of this study was to develop a multiplex PCR (mPCR) assay for rapid, sensitive and simultaneous detection of six important rice pathogens: Xanthomonas oryzae pv. oryzae, X. oryzae pv. oryzicola, Pseudomonas fuscovaginae, Burkholderia glumae, Burkholderia gladioli and Acidovorax avenae subsp. avenae.
Methods and Results
Specific primers were designed through a bioinformatics pipeline. Sensitivity of detection was established using both traditional PCR and quantitative real‐time PCR on isolated DNA and on bacterial cells both in vitro and in simulated diseased seeds and the parameters were optimized for an mPCR assay. A total of 150 bacterial strains were tested for specificity. The mPCR assay accurately predicted the presence of pathogens among 44 symptomatic and asymptomatic rice seed, sheath and leaf samples.
Conclusions
This study confirmed that this mPCR assay is a rapid, reliable and simple tool for the simultaneous detection of six important rice bacterial pathogens.
Significance and Impact of the Study
This study is the first report of a method allowing simultaneous detection of six major rice pathogens. The ability to use crude extracts from plants without bacterial isolation or DNA extraction enhances the value of this mPCR technology for rapid detection and aetiological/epidemiological studies.</description><subject>Acidovorax</subject><subject>Bacteria</subject><subject>Bacteriology</subject><subject>Burkholderia - genetics</subject><subject>Burkholderia gladioli</subject><subject>Burkholderia glumae</subject><subject>Comamonadaceae - genetics</subject><subject>comparative genomics</subject><subject>detection</subject><subject>DNA, Bacterial - analysis</subject><subject>multiplex PCR</subject><subject>Multiplex Polymerase Chain Reaction - methods</subject><subject>Oryza - microbiology</subject><subject>Plant Diseases - microbiology</subject><subject>Plant Leaves - microbiology</subject><subject>Plant pathology</subject><subject>Polymerase chain reaction</subject><subject>Pseudomonas - genetics</subject><subject>Pseudomonas fuscovaginae</subject><subject>quantitative real‐time PCR</subject><subject>Rice</subject><subject>rice bacterial pathogens</subject><subject>Seeds - microbiology</subject><subject>Xanthomonas - genetics</subject><subject>Xanthomonas oryzae</subject><issn>1364-5072</issn><issn>1365-2672</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqN0U1LwzAcBvAgipvTg19ACl700C1J89bjGL6yoYjisaRJqi19mUmL27c3W6cHQTCXBPLjIf88AJwiOEZ-TQpZjVEEY7IHhihiNMSM4_3tmYQUcjwAR84VEHpE2SEYYCYYETEbgtdFV7b5sjSr4HH2FEjn5DrIGhu4vPI3sjZN5wJtWqPavKmDJvM3q6CShTepVK2xuSyDpWzfmzdTuw2wuTLH4CCTpTMnu30EXq6vnme34fzh5m42nYeKYERCRYXigqYpFyZiAirENY11TIyfC3IGGYyziEWZ1LGinGiYcqy1VFoLrCWKRuCiz13a5qMzrk2q3ClTlv3LE-TTMYU-6j8UIf9bjHt6_osWTWdrP8hGQSJQJKhXl71StnHOmixZ2rySdp0gmGyKSXwxybYYb892iV1aGf0jv5vwYNKDz7w067-Tkvvpoo_8AniJlfU</recordid><startdate>201605</startdate><enddate>201605</enddate><creator>Cui, Z.</creator><creator>Ojaghian, M.R.</creator><creator>Tao, Z.</creator><creator>Kakar, K.U.</creator><creator>Zeng, J.</creator><creator>Zhao, W.</creator><creator>Duan, Y.</creator><creator>Vera Cruz, C.M.</creator><creator>Li, B.</creator><creator>Zhu, B.</creator><creator>Xie, G.</creator><general>Oxford University Press</general><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>7QL</scope><scope>7QO</scope><scope>7T7</scope><scope>7TM</scope><scope>7U7</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>7ST</scope><scope>SOI</scope></search><sort><creationdate>201605</creationdate><title>Multiplex PCR assay for simultaneous detection of six major bacterial pathogens of rice</title><author>Cui, Z. ; Ojaghian, M.R. ; Tao, Z. ; Kakar, K.U. ; Zeng, J. ; Zhao, W. ; Duan, Y. ; Vera Cruz, C.M. ; Li, B. ; Zhu, B. ; Xie, G.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4214-c58c785bb78e3680c17d59d94e1110760609f363fad9c574d0b72ddacdd82da13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Acidovorax</topic><topic>Bacteria</topic><topic>Bacteriology</topic><topic>Burkholderia - genetics</topic><topic>Burkholderia gladioli</topic><topic>Burkholderia glumae</topic><topic>Comamonadaceae - genetics</topic><topic>comparative genomics</topic><topic>detection</topic><topic>DNA, Bacterial - analysis</topic><topic>multiplex PCR</topic><topic>Multiplex Polymerase Chain Reaction - methods</topic><topic>Oryza - microbiology</topic><topic>Plant Diseases - microbiology</topic><topic>Plant Leaves - microbiology</topic><topic>Plant pathology</topic><topic>Polymerase chain reaction</topic><topic>Pseudomonas - genetics</topic><topic>Pseudomonas fuscovaginae</topic><topic>quantitative real‐time PCR</topic><topic>Rice</topic><topic>rice bacterial pathogens</topic><topic>Seeds - microbiology</topic><topic>Xanthomonas - genetics</topic><topic>Xanthomonas oryzae</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Cui, Z.</creatorcontrib><creatorcontrib>Ojaghian, M.R.</creatorcontrib><creatorcontrib>Tao, Z.</creatorcontrib><creatorcontrib>Kakar, K.U.</creatorcontrib><creatorcontrib>Zeng, J.</creatorcontrib><creatorcontrib>Zhao, W.</creatorcontrib><creatorcontrib>Duan, Y.</creatorcontrib><creatorcontrib>Vera Cruz, C.M.</creatorcontrib><creatorcontrib>Li, B.</creatorcontrib><creatorcontrib>Zhu, B.</creatorcontrib><creatorcontrib>Xie, G.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Nucleic Acids Abstracts</collection><collection>Toxicology Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>Environment Abstracts</collection><collection>Environment Abstracts</collection><jtitle>Journal of applied microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Cui, Z.</au><au>Ojaghian, M.R.</au><au>Tao, Z.</au><au>Kakar, K.U.</au><au>Zeng, J.</au><au>Zhao, W.</au><au>Duan, Y.</au><au>Vera Cruz, C.M.</au><au>Li, B.</au><au>Zhu, B.</au><au>Xie, G.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Multiplex PCR assay for simultaneous detection of six major bacterial pathogens of rice</atitle><jtitle>Journal of applied microbiology</jtitle><addtitle>J Appl Microbiol</addtitle><date>2016-05</date><risdate>2016</risdate><volume>120</volume><issue>5</issue><spage>1357</spage><epage>1367</epage><pages>1357-1367</pages><issn>1364-5072</issn><eissn>1365-2672</eissn><coden>JAMIFK</coden><abstract>Aims
The aim of this study was to develop a multiplex PCR (mPCR) assay for rapid, sensitive and simultaneous detection of six important rice pathogens: Xanthomonas oryzae pv. oryzae, X. oryzae pv. oryzicola, Pseudomonas fuscovaginae, Burkholderia glumae, Burkholderia gladioli and Acidovorax avenae subsp. avenae.
Methods and Results
Specific primers were designed through a bioinformatics pipeline. Sensitivity of detection was established using both traditional PCR and quantitative real‐time PCR on isolated DNA and on bacterial cells both in vitro and in simulated diseased seeds and the parameters were optimized for an mPCR assay. A total of 150 bacterial strains were tested for specificity. The mPCR assay accurately predicted the presence of pathogens among 44 symptomatic and asymptomatic rice seed, sheath and leaf samples.
Conclusions
This study confirmed that this mPCR assay is a rapid, reliable and simple tool for the simultaneous detection of six important rice bacterial pathogens.
Significance and Impact of the Study
This study is the first report of a method allowing simultaneous detection of six major rice pathogens. The ability to use crude extracts from plants without bacterial isolation or DNA extraction enhances the value of this mPCR technology for rapid detection and aetiological/epidemiological studies.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>26864896</pmid><doi>10.1111/jam.13094</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 1364-5072 |
| ispartof | Journal of applied microbiology, 2016-05, Vol.120 (5), p.1357-1367 |
| issn | 1364-5072 1365-2672 |
| language | eng |
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| source | MEDLINE; Access via Wiley Online Library; Oxford University Press Journals All Titles (1996-Current) |
| subjects | Acidovorax Bacteria Bacteriology Burkholderia - genetics Burkholderia gladioli Burkholderia glumae Comamonadaceae - genetics comparative genomics detection DNA, Bacterial - analysis multiplex PCR Multiplex Polymerase Chain Reaction - methods Oryza - microbiology Plant Diseases - microbiology Plant Leaves - microbiology Plant pathology Polymerase chain reaction Pseudomonas - genetics Pseudomonas fuscovaginae quantitative real‐time PCR Rice rice bacterial pathogens Seeds - microbiology Xanthomonas - genetics Xanthomonas oryzae |
| title | Multiplex PCR assay for simultaneous detection of six major bacterial pathogens of rice |
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