Use of a custom array to study differentially expressed genes during blood orange (Citrus sinensis L. Osbeck) ripening.
Identifieur interne : 000874 ( PubMed/Curation ); précédent : 000873; suivant : 000875Use of a custom array to study differentially expressed genes during blood orange (Citrus sinensis L. Osbeck) ripening.
Auteurs : Jamila Bernardi [Italie] ; Concetta Licciardello ; Maria Patrizia Russo ; Maria Luisa Chiusano ; Giorgia Carletti ; Giuseppe Reforgiato Recupero ; Adriano MaroccoSource :
- Journal of plant physiology [ 1618-1328 ] ; 2010.
English descriptors
- KwdEn :
- Citrus sinensis (genetics), Citrus sinensis (growth & development), Cluster Analysis, Expressed Sequence Tags, Fruit (genetics), Fruit (growth & development), Gene Expression Profiling (methods), Gene Expression Regulation, Plant, Oligonucleotide Array Sequence Analysis (methods), Pigmentation (genetics), Reverse Transcriptase Polymerase Chain Reaction, Solubility.
- MESH :
- genetics : Citrus sinensis, Fruit, Pigmentation.
- growth & development : Citrus sinensis, Fruit.
- methods : Gene Expression Profiling, Oligonucleotide Array Sequence Analysis.
- Cluster Analysis, Expressed Sequence Tags, Gene Expression Regulation, Plant, Reverse Transcriptase Polymerase Chain Reaction, Solubility.
Abstract
A flesh-specific oligonucleotide custom array was designed to study gene expression during blood orange ripening. The array included 301 probes derived from a subtracted SSH library, a cDNA-AFLP collection, and a set of regulatory genes from the Harvest citrus database. The custom array was hybridized using samples of Moro, a pigmented cultivar, and Cadenera, a common cultivar, at three different ripening stages: the immature phase, the halfway point of maturation (corresponding to the start of Moro pigmentation) and the full ripening. Of the 301 probes, 27 in total, corresponding to 20 different transcripts, indicated differential expression in stage-to-stage and/or cultivar-to-cultivar comparisons. Transcripts encoding for anthocyanin biosynthesis represented most of the total over-expressed probes. The remaining differentially expressed transcripts were functionally associated with primary metabolism as flavor biosynthesis, defense and signal transduction. The expressed products associated with probes indicating differential expression were confirmed by qRT-PCR. The microarray was designed considering a small collection of sequences useful for monitoring specific pathways and regulatory genes related to fruit ripening and anthocyanin pigmentation. The main novelty of this customization is the use of expressed sequences specifically derived from blood orange flesh to study different cultivars and ripening stages, and the provision of further information about processes related to anthocyanin pigmentation in citrus fruit flesh.
DOI: 10.1016/j.jplph.2009.09.009
PubMed: 19864041
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Osbeck) ripening.</title><author><name sortKey="Bernardi, Jamila" sort="Bernardi, Jamila" uniqKey="Bernardi J" first="Jamila" last="Bernardi">Jamila Bernardi</name><affiliation wicri:level="1"><nlm:affiliation>Istituto di Agronomia, Genetica e Coltivazioni erbacee, Università Cattolica del Sacro Cuore, via Emilia Parmense 84, 29100 Piacenza, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Istituto di Agronomia, Genetica e Coltivazioni erbacee, Università Cattolica del Sacro Cuore, via Emilia Parmense 84, 29100 Piacenza</wicri:regionArea></affiliation></author><author><name sortKey="Licciardello, Concetta" sort="Licciardello, Concetta" uniqKey="Licciardello C" first="Concetta" last="Licciardello">Concetta Licciardello</name></author><author><name sortKey="Russo, Maria Patrizia" sort="Russo, Maria Patrizia" uniqKey="Russo M" first="Maria Patrizia" last="Russo">Maria Patrizia Russo</name></author><author><name sortKey="Luisa Chiusano, Maria" sort="Luisa Chiusano, Maria" uniqKey="Luisa Chiusano M" first="Maria" last="Luisa Chiusano">Maria Luisa Chiusano</name></author><author><name sortKey="Carletti, Giorgia" sort="Carletti, Giorgia" uniqKey="Carletti G" first="Giorgia" last="Carletti">Giorgia Carletti</name></author><author><name sortKey="Recupero, Giuseppe Reforgiato" sort="Recupero, Giuseppe Reforgiato" uniqKey="Recupero G" first="Giuseppe Reforgiato" last="Recupero">Giuseppe Reforgiato Recupero</name></author><author><name sortKey="Marocco, Adriano" sort="Marocco, Adriano" uniqKey="Marocco A" first="Adriano" last="Marocco">Adriano Marocco</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2010">2010</date><idno type="RBID">pubmed:19864041</idno><idno type="pmid">19864041</idno><idno type="doi">10.1016/j.jplph.2009.09.009</idno><idno type="wicri:Area/PubMed/Corpus">000874</idno><idno type="wicri:Area/PubMed/Curation">000874</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Use of a custom array to study differentially expressed genes during blood orange (Citrus sinensis L. Osbeck) ripening.</title><author><name sortKey="Bernardi, Jamila" sort="Bernardi, Jamila" uniqKey="Bernardi J" first="Jamila" last="Bernardi">Jamila Bernardi</name><affiliation wicri:level="1"><nlm:affiliation>Istituto di Agronomia, Genetica e Coltivazioni erbacee, Università Cattolica del Sacro Cuore, via Emilia Parmense 84, 29100 Piacenza, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Istituto di Agronomia, Genetica e Coltivazioni erbacee, Università Cattolica del Sacro Cuore, via Emilia Parmense 84, 29100 Piacenza</wicri:regionArea></affiliation></author><author><name sortKey="Licciardello, Concetta" sort="Licciardello, Concetta" uniqKey="Licciardello C" first="Concetta" last="Licciardello">Concetta Licciardello</name></author><author><name sortKey="Russo, Maria Patrizia" sort="Russo, Maria Patrizia" uniqKey="Russo M" first="Maria Patrizia" last="Russo">Maria Patrizia Russo</name></author><author><name sortKey="Luisa Chiusano, Maria" sort="Luisa Chiusano, Maria" uniqKey="Luisa Chiusano M" first="Maria" last="Luisa Chiusano">Maria Luisa Chiusano</name></author><author><name sortKey="Carletti, Giorgia" sort="Carletti, Giorgia" uniqKey="Carletti G" first="Giorgia" last="Carletti">Giorgia Carletti</name></author><author><name sortKey="Recupero, Giuseppe Reforgiato" sort="Recupero, Giuseppe Reforgiato" uniqKey="Recupero G" first="Giuseppe Reforgiato" last="Recupero">Giuseppe Reforgiato Recupero</name></author><author><name sortKey="Marocco, Adriano" sort="Marocco, Adriano" uniqKey="Marocco A" first="Adriano" last="Marocco">Adriano Marocco</name></author></analytic><series><title level="j">Journal of plant physiology</title><idno type="eISSN">1618-1328</idno><imprint><date when="2010" type="published">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Citrus sinensis (genetics)</term><term>Citrus sinensis (growth & development)</term><term>Cluster Analysis</term><term>Expressed Sequence Tags</term><term>Fruit (genetics)</term><term>Fruit (growth & development)</term><term>Gene Expression Profiling (methods)</term><term>Gene Expression Regulation, Plant</term><term>Oligonucleotide Array Sequence Analysis (methods)</term><term>Pigmentation (genetics)</term><term>Reverse Transcriptase Polymerase Chain Reaction</term><term>Solubility</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Citrus sinensis</term><term>Fruit</term><term>Pigmentation</term></keywords><keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Citrus sinensis</term><term>Fruit</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Gene Expression Profiling</term><term>Oligonucleotide Array Sequence Analysis</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Cluster Analysis</term><term>Expressed Sequence Tags</term><term>Gene Expression Regulation, Plant</term><term>Reverse Transcriptase Polymerase Chain Reaction</term><term>Solubility</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">A flesh-specific oligonucleotide custom array was designed to study gene expression during blood orange ripening. The array included 301 probes derived from a subtracted SSH library, a cDNA-AFLP collection, and a set of regulatory genes from the Harvest citrus database. The custom array was hybridized using samples of Moro, a pigmented cultivar, and Cadenera, a common cultivar, at three different ripening stages: the immature phase, the halfway point of maturation (corresponding to the start of Moro pigmentation) and the full ripening. Of the 301 probes, 27 in total, corresponding to 20 different transcripts, indicated differential expression in stage-to-stage and/or cultivar-to-cultivar comparisons. Transcripts encoding for anthocyanin biosynthesis represented most of the total over-expressed probes. The remaining differentially expressed transcripts were functionally associated with primary metabolism as flavor biosynthesis, defense and signal transduction. The expressed products associated with probes indicating differential expression were confirmed by qRT-PCR. The microarray was designed considering a small collection of sequences useful for monitoring specific pathways and regulatory genes related to fruit ripening and anthocyanin pigmentation. The main novelty of this customization is the use of expressed sequences specifically derived from blood orange flesh to study different cultivars and ripening stages, and the provision of further information about processes related to anthocyanin pigmentation in citrus fruit flesh.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">19864041</PMID><DateCreated><Year>2010</Year><Month>2</Month><Day>9</Day></DateCreated><DateCompleted><Year>2010</Year><Month>05</Month><Day>04</Day></DateCompleted><DateRevised><Year>2010</Year><Month>2</Month><Day>9</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1618-1328</ISSN><JournalIssue CitedMedium="Internet"><Volume>167</Volume><Issue>4</Issue><PubDate><Year>2010</Year><Month>Mar</Month><Day>1</Day></PubDate></JournalIssue><Title>Journal of plant physiology</Title><ISOAbbreviation>J. Plant Physiol.</ISOAbbreviation></Journal><ArticleTitle>Use of a custom array to study differentially expressed genes during blood orange (Citrus sinensis L. Osbeck) ripening.</ArticleTitle><Pagination><MedlinePgn>301-10</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.jplph.2009.09.009</ELocationID><Abstract><AbstractText>A flesh-specific oligonucleotide custom array was designed to study gene expression during blood orange ripening. The array included 301 probes derived from a subtracted SSH library, a cDNA-AFLP collection, and a set of regulatory genes from the Harvest citrus database. The custom array was hybridized using samples of Moro, a pigmented cultivar, and Cadenera, a common cultivar, at three different ripening stages: the immature phase, the halfway point of maturation (corresponding to the start of Moro pigmentation) and the full ripening. Of the 301 probes, 27 in total, corresponding to 20 different transcripts, indicated differential expression in stage-to-stage and/or cultivar-to-cultivar comparisons. Transcripts encoding for anthocyanin biosynthesis represented most of the total over-expressed probes. The remaining differentially expressed transcripts were functionally associated with primary metabolism as flavor biosynthesis, defense and signal transduction. The expressed products associated with probes indicating differential expression were confirmed by qRT-PCR. The microarray was designed considering a small collection of sequences useful for monitoring specific pathways and regulatory genes related to fruit ripening and anthocyanin pigmentation. The main novelty of this customization is the use of expressed sequences specifically derived from blood orange flesh to study different cultivars and ripening stages, and the provision of further information about processes related to anthocyanin pigmentation in citrus fruit flesh.</AbstractText><CopyrightInformation>Copyright 2009 Elsevier GmbH. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Bernardi</LastName><ForeName>Jamila</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Istituto di Agronomia, Genetica e Coltivazioni erbacee, Università Cattolica del Sacro Cuore, via Emilia Parmense 84, 29100 Piacenza, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Licciardello</LastName><ForeName>Concetta</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Russo</LastName><ForeName>Maria Patrizia</ForeName><Initials>MP</Initials></Author><Author ValidYN="Y"><LastName>Luisa Chiusano</LastName><ForeName>Maria</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Carletti</LastName><ForeName>Giorgia</ForeName><Initials>G</Initials></Author><Author ValidYN="Y"><LastName>Recupero</LastName><ForeName>Giuseppe Reforgiato</ForeName><Initials>GR</Initials></Author><Author ValidYN="Y"><LastName>Marocco</LastName><ForeName>Adriano</ForeName><Initials>A</Initials></Author></AuthorList><Language>ENG</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2009</Year><Month>Oct</Month><Day>27</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>J Plant Physiol</MedlineTA><NlmUniqueID>9882059</NlmUniqueID><ISSNLinking>0176-1617</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D032084" MajorTopicYN="N">Citrus sinensis</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="Y">growth & development</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016000" MajorTopicYN="N">Cluster Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020224" MajorTopicYN="N">Expressed Sequence Tags</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005638" MajorTopicYN="N">Fruit</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="Y">growth & development</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="Y">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020411" MajorTopicYN="N">Oligonucleotide Array Sequence Analysis</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010858" MajorTopicYN="N">Pigmentation</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020133" MajorTopicYN="N">Reverse Transcriptase Polymerase Chain Reaction</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012995" MajorTopicYN="N">Solubility</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2009</Year><Month>4</Month><Day>30</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2009</Year><Month>9</Month><Day>3</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2009</Year><Month>9</Month><Day>4</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2009</Year><Month>10</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2009</Year><Month>10</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2010</Year><Month>5</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">19864041</ArticleId><ArticleId IdType="pii">S0176-1617(09)00384-8</ArticleId><ArticleId IdType="doi">10.1016/j.jplph.2009.09.009</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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