Microarray analysis of Fusarium graminearum‐induced wheat genes: identification of organ‐specific and differentially expressed genes
Identifieur interne : 001C55 ( Istex/Corpus ); précédent : 001C54; suivant : 001C56Microarray analysis of Fusarium graminearum‐induced wheat genes: identification of organ‐specific and differentially expressed genes
Auteurs : Saber Golkari ; Jeannie Gilbert ; Suvira Prashar ; J. Douglas ProcunierSource :
- Plant Biotechnology Journal [ 1467-7644 ] ; 2007-01.
English descriptors
- Teeft :
- Abiotic stress conditions, Accession, Accession number, Anther, Arabidopsis, Arabidopsis genome, Arabidopsis thaliana, Ascorbate peroxidase, Axon instruments, Biological replications, Biotechnology, Blackwell publishing, Blight, Bract tissues, Cap3 assembly program, Cdna, Cell rescue, Cellular transport, Clone, Control plants, Database, Default parameters, Different tissues, Differentially, Disease resistance protein class, East lansing, Elongation factor, Est, Expression data, Expression levels, Expression patterns, Expression profiles, Expression ratio, Expression ratio signal intensity ratio, False discovery rate, Functional catalogue, Functional class, Functional classes, Fungal, Fungal attack, Fungal inoculation, Fungus, Fusarium, Fusarium culmorum, Fusarium graminearum, Fusarium graminearum accession number, Fusarium graminearum infection, Fusarium head blight, Fusarium head blight resistance, Fusarium wheat genes, Genbank, Genbank accession number, Genbank accession numbers, Gene, Gene expression, Gene expression patterns, Genome, Glume, Graminearum, Graminearum infection, Graminearum interaction, Heat shock protein, Homology, Homology searches, Hybridization, Hybridization efficiency, Hypothetical protein, Inner surfaces, Inoculation, Large number, Linear correlations, Michigan state university, Microarray, Microarray analysis, Microarray data, Microarray techniques, Microarrays, Minimum score, Molecular chaperones, Monodehydroascorbate reductase, Munich information centre, National fusarium head blight forum, Northern blot analysis, Nucleic acids, Other organs, Ovary, Oxidative burst, Oxidative stress, Palea, Pathogen, Pathway, Phenylpropanoid, Phenylpropanoid metabolism, Phenylpropanoid pathway, Phosphatidylinositol synthase, Plant biotechnology journal, Plant cell, Plant cell walls, Plant pathol, Plant physiol, Polyphenol oxidase, Principal components analysis, Protein, Protein sequences, Protein synthesis, Rachis, Redundant ests, Responsive organ, Ribosomal, Ribosomal protein, Rrna band intensities, Saber, Saber golkari, Salmon sperm, Salt stress, Sequence tags, Signal intensity ratios, Signal transduction pathways, Significance analysis, Significant increase, Specific organs, Specific tissues, Spike, Stringent conditions, Supplementary material, Tissue type, Tissue types, Total number, Transcript, Transcript level, Transcription factors, Transcriptome, Transport facilitation, Transport routes, Trends plant, Trichothecene mycotoxins, Triticum aestivum, Unclassified proteins, Unigenes, Unknown function, Unknown protein, Water bath, Water control, Wheat, Wheat spike, Wheat spikes, Wheat tissues, Wrky superfamily, Yellow spots.
Abstract
A wheat cDNA microarray consisting of 5739 expressed sequence tags (ESTs) was used to investigate the transcriptome patterns of the glume, lemma, palea, anther, ovary and rachis dissected from infected wheat spikes after inoculation with the fungus Fusarium graminearum, the causal agent of fusarium head blight (FHB) disease. Stringent conditions were employed to reduce the false discovery rate. The significance analysis of microarrays (SAM) was used to identify transcripts that showed a differential response between fungal‐challenged vs. control plants. To verify the microarray data, Northern blot analysis was carried out on randomly selected up‐regulated clones. We observed 185 (3.2%) up‐regulated and 16 (0.28%) down‐regulated ESTs in the six organs constituting the wheat spike. Many up‐regulated ESTs (46.67%) showed no homology with sequences of known functions, whereas others showed homology with genes involved in defence and stress responses, the oxidative burst of H2O2, regulatory functions, protein synthesis and the phenylpropanoid pathway. The monitoring of genes in specific organs avoided the averaging of expression values over multiple organs that occurs when using data from the whole spike. Our data allowed us to uncover new up‐regulated genes expressed in specific organs. The study revealed that each organ had a defined and distinctive transcriptome pattern in response to F. graminearum infection.
Url:
DOI: 10.1111/j.1467-7652.2006.00213.x
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ISTEX:3D429C0FBFA1E65A904AD90131E383B958B1D073Le document en format XML
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correlations</term><term>Michigan state university</term><term>Microarray</term><term>Microarray analysis</term><term>Microarray data</term><term>Microarray techniques</term><term>Microarrays</term><term>Minimum score</term><term>Molecular chaperones</term><term>Monodehydroascorbate reductase</term><term>Munich information centre</term><term>National fusarium head blight forum</term><term>Northern blot analysis</term><term>Nucleic acids</term><term>Other organs</term><term>Ovary</term><term>Oxidative burst</term><term>Oxidative stress</term><term>Palea</term><term>Pathogen</term><term>Pathway</term><term>Phenylpropanoid</term><term>Phenylpropanoid metabolism</term><term>Phenylpropanoid pathway</term><term>Phosphatidylinositol synthase</term><term>Plant biotechnology journal</term><term>Plant cell</term><term>Plant cell walls</term><term>Plant pathol</term><term>Plant physiol</term><term>Polyphenol oxidase</term><term>Principal components analysis</term><term>Protein</term><term>Protein sequences</term><term>Protein synthesis</term><term>Rachis</term><term>Redundant ests</term><term>Responsive organ</term><term>Ribosomal</term><term>Ribosomal protein</term><term>Rrna band intensities</term><term>Saber</term><term>Saber golkari</term><term>Salmon sperm</term><term>Salt stress</term><term>Sequence tags</term><term>Signal intensity ratios</term><term>Signal transduction pathways</term><term>Significance analysis</term><term>Significant increase</term><term>Specific organs</term><term>Specific tissues</term><term>Spike</term><term>Stringent conditions</term><term>Supplementary material</term><term>Tissue type</term><term>Tissue types</term><term>Total number</term><term>Transcript</term><term>Transcript level</term><term>Transcription factors</term><term>Transcriptome</term><term>Transport facilitation</term><term>Transport routes</term><term>Trends plant</term><term>Trichothecene mycotoxins</term><term>Triticum aestivum</term><term>Unclassified 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Stringent conditions were employed to reduce the false discovery rate. The significance analysis of microarrays (SAM) was used to identify transcripts that showed a differential response between fungal‐challenged vs. control plants. To verify the microarray data, Northern blot analysis was carried out on randomly selected up‐regulated clones. We observed 185 (3.2%) up‐regulated and 16 (0.28%) down‐regulated ESTs in the six organs constituting the wheat spike. Many up‐regulated ESTs (46.67%) showed no homology with sequences of known functions, whereas others showed homology with genes involved in defence and stress responses, the oxidative burst of H2O2, regulatory functions, protein synthesis and the phenylpropanoid pathway. The monitoring of genes in specific organs avoided the averaging of expression values over multiple organs that occurs when using data from the whole spike. Our data allowed us to uncover new up‐regulated genes expressed in specific organs. The study revealed that each organ had a defined and distinctive transcriptome pattern in response to F. graminearum infection.</div></front></TEI><istex><corpusName>wiley</corpusName><keywords><teeft><json:string>unknown protein</json:string><json:string>fusarium</json:string><json:string>graminearum</json:string><json:string>microarray</json:string><json:string>glume</json:string><json:string>cdna</json:string><json:string>palea</json:string><json:string>ovary</json:string><json:string>rachis</json:string><json:string>unigenes</json:string><json:string>anther</json:string><json:string>hybridization</json:string><json:string>arabidopsis</json:string><json:string>biotechnology</json:string><json:string>plant biotechnology journal</json:string><json:string>differentially</json:string><json:string>genome</json:string><json:string>database</json:string><json:string>accession</json:string><json:string>pathway</json:string><json:string>blackwell 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ratios</json:string><json:string>water bath</json:string><json:string>hybridization efficiency</json:string><json:string>axon instruments</json:string><json:string>expression levels</json:string><json:string>fusarium head blight resistance</json:string><json:string>microarray techniques</json:string><json:string>phosphatidylinositol synthase</json:string><json:string>significance analysis</json:string><json:string>wheat spike</json:string><json:string>fusarium culmorum</json:string><json:string>elongation factor</json:string><json:string>national fusarium head blight forum</json:string><json:string>arabidopsis thaliana</json:string><json:string>plant physiol</json:string><json:string>molecular chaperones</json:string><json:string>fusarium graminearum infection</json:string></teeft></keywords><author><json:item><name>Saber Golkari</name><affiliations><json:string>Cereal Research Centre, Agriculture & Agri‐Food Canada, 195 Dafoe Road, Winnipeg, MB, R3T 2M9, Canada</json:string></affiliations></json:item><json:item><name>Jeannie Gilbert</name><affiliations><json:string>Cereal Research Centre, Agriculture & Agri‐Food Canada, 195 Dafoe Road, Winnipeg, MB, R3T 2M9, Canada</json:string></affiliations></json:item><json:item><name>Suvira Prashar</name><affiliations><json:string>Cereal Research Centre, Agriculture & Agri‐Food Canada, 195 Dafoe Road, Winnipeg, MB, R3T 2M9, Canada</json:string></affiliations></json:item><json:item><name>J. Douglas Procunier</name><affiliations><json:string>E-mail: dprocunier@agr.gc.ca</json:string></affiliations></json:item></author><subject><json:item><lang><json:string>eng</json:string></lang><value>anther</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>expressed sequence tag microarray</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>fusarium head blight</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>glumes</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>lemmas</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>ovary</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>palea</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>rachis</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>wheat</value></json:item></subject><articleId><json:string>PBI213</json:string></articleId><arkIstex>ark:/67375/WNG-JLDBMH9C-B</arkIstex><language><json:string>eng</json:string></language><originalGenre><json:string>article</json:string></originalGenre><abstract>A wheat cDNA microarray consisting of 5739 expressed sequence tags (ESTs) was used to investigate the transcriptome patterns of the glume, lemma, palea, anther, ovary and rachis dissected from infected wheat spikes after inoculation with the fungus Fusarium graminearum, the causal agent of fusarium head blight (FHB) disease. Stringent conditions were employed to reduce the false discovery rate. The significance analysis of microarrays (SAM) was used to identify transcripts that showed a differential response between fungal‐challenged vs. control plants. To verify the microarray data, Northern blot analysis was carried out on randomly selected up‐regulated clones. We observed 185 (3.2%) up‐regulated and 16 (0.28%) down‐regulated ESTs in the six organs constituting the wheat spike. Many up‐regulated ESTs (46.67%) showed no homology with sequences of known functions, whereas others showed homology with genes involved in defence and stress responses, the oxidative burst of H2O2, regulatory functions, protein synthesis and the phenylpropanoid pathway. The monitoring of genes in specific organs avoided the averaging of expression values over multiple organs that occurs when using data from the whole spike. Our data allowed us to uncover new up‐regulated genes expressed in specific organs. The study revealed that each organ had a defined and distinctive transcriptome pattern in response to F. graminearum infection.</abstract><qualityIndicators><score>9.484</score><pdfWordCount>6883</pdfWordCount><pdfCharCount>46838</pdfCharCount><pdfVersion>1.3</pdfVersion><pdfPageCount>12</pdfPageCount><pdfPageSize>595 x 782 pts</pdfPageSize><pdfWordsPerPage>574</pdfWordsPerPage><pdfText>true</pdfText><refBibsNative>true</refBibsNative><abstractWordCount>207</abstractWordCount><abstractCharCount>1431</abstractCharCount><keywordCount>9</keywordCount></qualityIndicators><title>Microarray analysis of Fusarium graminearum‐induced wheat genes: identification of organ‐specific and differentially expressed genes</title><pmid><json:string>17207255</json:string></pmid><genre><json:string>article</json:string></genre><host><title>Plant Biotechnology Journal</title><language><json:string>unknown</json:string></language><doi><json:string>10.1111/(ISSN)1467-7652</json:string></doi><issn><json:string>1467-7644</json:string></issn><eissn><json:string>1467-7652</json:string></eissn><publisherId><json:string>PBI</json:string></publisherId><volume>5</volume><issue>1</issue><pages><first>38</first><last>49</last><total>12</total></pages><genre><json:string>journal</json:string></genre></host><namedEntities><unitex><date><json:string>40S</json:string><json:string>25S</json:string><json:string>5739</json:string><json:string>2007</json:string><json:string>60S</json:string></date><geogName></geogName><orgName><json:string>Axon Instruments</json:string><json:string>UK Blackwell Publishing Journal Ltd Saber Golkari, Jeannie Gilbert, Suvira Prashar and J</json:string><json:string>Genomics Canada and CIMMYT, Mexico</json:string><json:string>Roche Diagnostics</json:string><json:string>Max Bell Research Centre, Toronto, ON, Canada</json:string><json:string>Corning Inc</json:string><json:string>Cereal Research Centre, Agriculture</json:string><json:string>Clontech, Palo Alto</json:string><json:string>Arabidopsis Biological Resource Center</json:string><json:string>Roche Diagnostics Canada, Laval, QC, Canada</json:string><json:string>Canada Received</json:string><json:string>Plant Biotechnology Journal</json:string><json:string>Blackwell Publishing Ltd</json:string><json:string>Biotech, UK</json:string><json:string>Agilent Technologies Canada, Mississauga, ON, Canada</json:string><json:string>Plant Article Publishing PBI Biotechnology</json:string><json:string>National Center for Biotechnology</json:string></orgName><orgName_funder></orgName_funder><orgName_provider></orgName_provider><persName><json:string>Nano LabChip</json:string><json:string>Travis Banks</json:string><json:string>Douglas Procunier</json:string><json:string>The</json:string><json:string>Thérèse Ouellet</json:string><json:string>Elmer Applied</json:string><json:string>La Jolla</json:string></persName><placeName><json:string>TX</json:string><json:string>Winnipeg</json:string><json:string>Foster City</json:string><json:string>Munich</json:string><json:string>Columbus</json:string><json:string>Valencia</json:string><json:string>IN</json:string><json:string>Canada</json:string><json:string>Madison</json:string><json:string>Union City</json:string><json:string>Austin</json:string><json:string>USA</json:string><json:string>CA</json:string><json:string>Ottawa</json:string><json:string>WI</json:string><json:string>Indianapolis</json:string><json:string>OH</json:string></placeName><ref_url><json:string>http://www.maizegdb.org/</json:string><json:string>http://cogeme.ex.ac.uk/blast.html</json:string><json:string>http://www.broad.mit.edu/annotation/fungi/fusarium</json:string><json:string>http://www.ebi.ac.uk/arrayexpress</json:string><json:string>http://www.affymetrix.com</json:string><json:string>http://www.ncbi.nlm.nih.gov/</json:string><json:string>http://www-stat.stanford.edu/</json:string><json:string>http://signal.salk.edu/</json:string><json:string>http://mips.gsf.de</json:string></ref_url><ref_bibl><json:string>Procunier et al., 2000</json:string><json:string>Lee et al., 2002</json:string><json:string>Meyers et al., 1999</json:string><json:string>Di and Tumer (2004)</json:string><json:string>Lu et al., 2003</json:string><json:string>Mittler, 2002</json:string><json:string>Brandt, 2005</json:string><json:string>OriginalGolkari et al.</json:string><json:string>Gilbert and Tekauz, 2000</json:string><json:string>Ma et al., 2005</json:string><json:string>Pryor, 1997</json:string><json:string>Baldwin et al., 1999</json:string><json:string>van Montfort et al., 2002</json:string><json:string>van Eeuwijk et al., 1995</json:string><json:string>Ma et al. 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(2000)</json:string><json:string>Huang and Madan, 1999</json:string><json:string>Dixon and Paiva, 1995</json:string><json:string>Ruepp et al., 2004</json:string><json:string>Tusher et al., 2001</json:string><json:string>Hall and Van Sanford, 2003</json:string><json:string>Collinge et al., 1993</json:string></ref_bibl><bibl></bibl></unitex></namedEntities><ark><json:string>ark:/67375/WNG-JLDBMH9C-B</json:string></ark><categories><wos><json:string>1 - science</json:string><json:string>2 - plant sciences</json:string><json:string>2 - biotechnology & applied microbiology</json:string></wos><scienceMetrix><json:string>1 - applied sciences</json:string><json:string>2 - enabling & strategic technologies</json:string><json:string>3 - biotechnology</json:string></scienceMetrix><scopus><json:string>1 - Life Sciences</json:string><json:string>2 - Agricultural and Biological Sciences</json:string><json:string>3 - Plant Science</json:string><json:string>1 - Life Sciences</json:string><json:string>2 - Agricultural and Biological Sciences</json:string><json:string>3 - Agronomy and Crop Science</json:string><json:string>1 - Life Sciences</json:string><json:string>2 - Biochemistry, Genetics and Molecular Biology</json:string><json:string>3 - Biotechnology</json:string></scopus><inist><json:string>1 - sciences appliquees, technologies et medecines</json:string><json:string>2 - sciences biologiques et medicales</json:string><json:string>3 - sciences biologiques fondamentales et appliquees. psychologie</json:string></inist></categories><publicationDate>2007</publicationDate><copyrightDate>2007</copyrightDate><doi><json:string>10.1111/j.1467-7652.2006.00213.x</json:string></doi><id>3D429C0FBFA1E65A904AD90131E383B958B1D073</id><score>1</score><fulltext><json:item><extension>pdf</extension><original>true</original><mimetype>application/pdf</mimetype><uri>https://api.istex.fr/ark:/67375/WNG-JLDBMH9C-B/fulltext.pdf</uri></json:item><json:item><extension>zip</extension><original>false</original><mimetype>application/zip</mimetype><uri>https://api.istex.fr/ark:/67375/WNG-JLDBMH9C-B/bundle.zip</uri></json:item><istex:fulltextTEI uri="https://api.istex.fr/ark:/67375/WNG-JLDBMH9C-B/fulltext.tei"><teiHeader><fileDesc><titleStmt><title level="a" type="main">Microarray analysis of Fusarium graminearum‐induced wheat genes: identification of organ‐specific and differentially expressed genes</title><title level="a" type="short">Fusarium graminearum‐induced wheat genes</title></titleStmt><publicationStmt><authority>ISTEX</authority><publisher>Blackwell Publishing Ltd</publisher><pubPlace>Oxford, UK</pubPlace><date type="published" when="2007-01"></date></publicationStmt><notesStmt><note type="content-type" subtype="article" source="article" scheme="https://content-type.data.istex.fr/ark:/67375/XTP-6N5SZHKN-D">article</note><note type="publication-type" subtype="journal" scheme="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</note></notesStmt><sourceDesc><biblStruct type="article"><analytic><title level="a" type="main">Microarray analysis of Fusarium graminearum‐induced wheat genes: identification of organ‐specific and differentially expressed genes</title><title level="a" type="short">Fusarium graminearum‐induced wheat genes</title><author xml:id="author-0000"><persName><forename type="first">Saber</forename><surname>Golkari</surname></persName><affiliation><orgName type="laboratory">Cereal Research Centre</orgName><address><addrLine>Agriculture & Agri‐Food Canada</addrLine><addrLine>195 Dafoe Road, Winnipeg, MB, R3T 2M9, Canada</addrLine><country key="CA" xml:lang="en">CANADA</country></address></affiliation></author><author xml:id="author-0001"><persName><forename type="first">Jeannie</forename><surname>Gilbert</surname></persName><affiliation><orgName type="laboratory">Cereal Research Centre</orgName><address><addrLine>Agriculture & Agri‐Food Canada</addrLine><addrLine>195 Dafoe Road, Winnipeg, MB, R3T 2M9, Canada</addrLine><country key="CA" xml:lang="en">CANADA</country></address></affiliation></author><author xml:id="author-0002"><persName><forename type="first">Suvira</forename><surname>Prashar</surname></persName><affiliation><orgName type="laboratory">Cereal Research Centre</orgName><address><addrLine>Agriculture & Agri‐Food Canada</addrLine><addrLine>195 Dafoe Road, Winnipeg, MB, R3T 2M9, Canada</addrLine><country key="CA" xml:lang="en">CANADA</country></address></affiliation></author><author xml:id="author-0003" role="corresp"><persName><forename type="first">J. 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*
<i>Correspondence</i> (fax 204‐983‐4604; e‐mail <email>dprocunier@agr.gc.ca</email>)</correspondenceTo><linkGroup><link type="toTypesetVersion" href="file:PBI.PBI213.pdf"></link></linkGroup></publicationMeta><contentMeta><unparsedEditorialHistory>Received 17 March 2006; revised 13 July 2006; accepted 14 July 2006.</unparsedEditorialHistory><countGroup><count type="figureTotal" number="3"></count><count type="tableTotal" number="4"></count><count type="formulaTotal" number="0"></count><count type="referenceTotal" number="44"></count><count type="wordTotal" number="8474"></count></countGroup><titleGroup><title type="main">Microarray analysis of <i>Fusarium graminearum</i>‐induced wheat genes: identification of organ‐specific and differentially expressed genes</title><title type="shortAuthors"><i>Saber Golkari</i> et al.</title><title type="short"><i>Fusarium graminearum</i>‐induced wheat genes</title></titleGroup><creators><creator creatorRole="author" xml:id="cr1" affiliationRef="#aff-1-1"><personName><givenNames>Saber</givenNames><familyName>Golkari</familyName></personName></creator><creator creatorRole="author" xml:id="cr2" affiliationRef="#aff-1-1"><personName><givenNames>Jeannie</givenNames><familyName>Gilbert</familyName></personName></creator><creator creatorRole="author" xml:id="cr3" affiliationRef="#aff-1-1"><personName><givenNames>Suvira</givenNames><familyName>Prashar</familyName></personName></creator><creator creatorRole="author" xml:id="cr4" corresponding="yes"><personName><givenNames>J. Douglas</givenNames><familyName>Procunier</familyName></personName></creator></creators><affiliationGroup><affiliation xml:id="aff-1-1" countryCode="CA"><unparsedAffiliation>Cereal Research Centre, Agriculture & Agri‐Food Canada, 195 Dafoe Road, Winnipeg, MB, R3T 2M9, Canada</unparsedAffiliation></affiliation></affiliationGroup><keywordGroup xml:lang="en"><keyword xml:id="k1">anther</keyword><keyword xml:id="k2">expressed sequence tag microarray</keyword><keyword xml:id="k3">fusarium head blight</keyword><keyword xml:id="k4">glumes</keyword><keyword xml:id="k5">lemmas</keyword><keyword xml:id="k6">ovary</keyword><keyword xml:id="k7">palea</keyword><keyword xml:id="k8">rachis</keyword><keyword xml:id="k9">wheat</keyword></keywordGroup><supportingInformation><p><b>Figure S1</b> Northern blot validation of microarray data
for a selected number of expressed sequence tags (ESTs) upregulated
in response to <i>Fusarium graminearum</i> infection. The first
five lanes contained total RNA (10 µg) blotted from
the water controls: glumes (G), lemma (L), palea (P), ovary (O) and
rachis (R). The following five lanes contained RNA from <i>Fusarium
graminearum</i>‐challenged organs. The selected clones were as
follows: (A) clone BQ901699, β‐1‐3‐glucanase; (B) clone
DV799683, leucine‐rich repeat (LRR) protein; (C) clone DV799622,
metallothionein (MT); (D) clone DV799628, unknown; (E) clone
DV799757, unknown. Loading controls (F) show the rRNA band
intensities of RNA samples loaded on to gels and visualized on the
Agilent 2100 Bioanalyser.
<b>Table S1</b> Complete list of expressed sequence tags (ESTs)
that were identified as differentially regulated in response to
Fusarium graminearum infection, together with the average
expression ratio derived from five replications for each
organ.</p><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:14677644:media:pbi213:pbi213_fS1"></mediaResource><caption>Supporting info item</caption></supportingInfoItem><supportingInfoItem><mediaResource alt="supporting info item" href="urn-x:wiley:14677644:media:pbi213:PBI213_TableS1"></mediaResource><caption>Supporting info item</caption></supportingInfoItem></supportingInformation><abstractGroup><abstract type="main" xml:lang="en"><title type="main">Summary</title><p>A wheat cDNA microarray consisting of 5739 expressed sequence tags (ESTs) was used to investigate the transcriptome patterns of the glume, lemma, palea, anther, ovary and rachis dissected from infected wheat spikes after inoculation with the fungus <i>Fusarium graminearum</i>, the causal agent of fusarium head blight (FHB) disease. Stringent conditions were employed to reduce the false discovery rate. The significance analysis of microarrays (SAM) was used to identify transcripts that showed a differential response between fungal‐challenged vs. control plants. To verify the microarray data, Northern blot analysis was carried out on randomly selected up‐regulated clones. We observed 185 (3.2%) up‐regulated and 16 (0.28%) down‐regulated ESTs in the six organs constituting the wheat spike. Many up‐regulated ESTs (46.67%) showed no homology with sequences of known functions, whereas others showed homology with genes involved in defence and stress responses, the oxidative burst of H<sub>2</sub>O<sub>2</sub>, regulatory functions, protein synthesis and the phenylpropanoid pathway. The monitoring of genes in specific organs avoided the averaging of expression values over multiple organs that occurs when using data from the whole spike. Our data allowed us to uncover new up‐regulated genes expressed in specific organs. The study revealed that each organ had a defined and distinctive transcriptome pattern in response to <i>F. graminearum</i> infection.</p></abstract></abstractGroup></contentMeta></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Microarray analysis of Fusarium graminearum‐induced wheat genes: identification of organ‐specific and differentially expressed genes</title></titleInfo><titleInfo type="abbreviated" lang="en"><title>Fusarium graminearum‐induced wheat genes</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>Microarray analysis of Fusarium graminearum‐induced wheat genes: identification of organ‐specific and differentially expressed genes</title></titleInfo><name type="personal"><namePart type="given">Saber</namePart><namePart type="family">Golkari</namePart><affiliation>Cereal Research Centre, Agriculture & Agri‐Food Canada, 195 Dafoe Road, Winnipeg, MB, R3T 2M9, Canada</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Jeannie</namePart><namePart type="family">Gilbert</namePart><affiliation>Cereal Research Centre, Agriculture & Agri‐Food Canada, 195 Dafoe Road, Winnipeg, MB, R3T 2M9, Canada</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Suvira</namePart><namePart type="family">Prashar</namePart><affiliation>Cereal Research Centre, Agriculture & Agri‐Food Canada, 195 Dafoe Road, Winnipeg, MB, R3T 2M9, Canada</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">J. Douglas</namePart><namePart type="family">Procunier</namePart><affiliation>E-mail: dprocunier@agr.gc.ca</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="article" displayLabel="article" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-6N5SZHKN-D">article</genre><originInfo><publisher>Blackwell Publishing Ltd</publisher><place><placeTerm type="text">Oxford, UK</placeTerm></place><dateIssued encoding="w3cdtf">2007-01</dateIssued><edition>Received 17 March 2006; revised 13 July 2006; accepted 14 July 2006.</edition><copyrightDate encoding="w3cdtf">2007</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><physicalDescription><extent unit="figures">3</extent><extent unit="tables">4</extent><extent unit="formulas">0</extent><extent unit="references">44</extent><extent unit="words">8474</extent></physicalDescription><abstract lang="en">A wheat cDNA microarray consisting of 5739 expressed sequence tags (ESTs) was used to investigate the transcriptome patterns of the glume, lemma, palea, anther, ovary and rachis dissected from infected wheat spikes after inoculation with the fungus Fusarium graminearum, the causal agent of fusarium head blight (FHB) disease. Stringent conditions were employed to reduce the false discovery rate. The significance analysis of microarrays (SAM) was used to identify transcripts that showed a differential response between fungal‐challenged vs. control plants. To verify the microarray data, Northern blot analysis was carried out on randomly selected up‐regulated clones. We observed 185 (3.2%) up‐regulated and 16 (0.28%) down‐regulated ESTs in the six organs constituting the wheat spike. Many up‐regulated ESTs (46.67%) showed no homology with sequences of known functions, whereas others showed homology with genes involved in defence and stress responses, the oxidative burst of H2O2, regulatory functions, protein synthesis and the phenylpropanoid pathway. The monitoring of genes in specific organs avoided the averaging of expression values over multiple organs that occurs when using data from the whole spike. Our data allowed us to uncover new up‐regulated genes expressed in specific organs. The study revealed that each organ had a defined and distinctive transcriptome pattern in response to F. graminearum infection.</abstract><subject lang="en"><genre>keywords</genre><topic>anther</topic><topic>expressed sequence tag microarray</topic><topic>fusarium head blight</topic><topic>glumes</topic><topic>lemmas</topic><topic>ovary</topic><topic>palea</topic><topic>rachis</topic><topic>wheat</topic></subject><relatedItem type="host"><titleInfo><title>Plant Biotechnology Journal</title></titleInfo><genre type="journal" authority="ISTEX" authorityURI="https://publication-type.data.istex.fr" valueURI="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</genre><note type="content"> Figure S1 Northern blot validation of microarray data for a selected number of expressed sequence tags (ESTs) upregulated in response to Fusarium graminearum infection. The first five lanes contained total RNA (10 µg) blotted from the water controls: glumes (G), lemma (L), palea (P), ovary (O) and rachis (R). The following five lanes contained RNA from Fusarium graminearum‐challenged organs. The selected clones were as follows: (A) clone BQ901699, β‐1‐3‐glucanase; (B) clone DV799683, leucine‐rich repeat (LRR) protein; (C) clone DV799622, metallothionein (MT); (D) clone DV799628, unknown; (E) clone DV799757, unknown. Loading controls (F) show the rRNA band intensities of RNA samples loaded on to gels and visualized on the Agilent 2100 Bioanalyser.
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