Transcriptional profiling by cDNA-AFLP analysis showed differential transcript abundance in response to water stress in Populus hopeiensis.
Identifieur interne : 002866 ( Main/Exploration ); précédent : 002865; suivant : 002867Transcriptional profiling by cDNA-AFLP analysis showed differential transcript abundance in response to water stress in Populus hopeiensis.
Auteurs : Yuepeng Song [République populaire de Chine] ; Zeliang Wang ; Wenhao Bo ; Yuanyuan Ren ; Zhiyi Zhang ; Deqiang ZhangSource :
- BMC genomics [ 1471-2164 ] ; 2012.
Descripteurs français
- KwdFr :
- ADN complémentaire (métabolisme), Analyse de polymorphisme de longueur de fragments amplifiés (MeSH), Analyse de profil d'expression de gènes (MeSH), Analyse de regroupements (MeSH), Apoptose (génétique), Bases de données génétiques (MeSH), Déshydratation (génétique), Gènes de plante (MeSH), Populus (génétique), Régulation de l'expression des gènes végétaux (MeSH), Sécheresses (MeSH).
- MESH :
- génétique : Apoptose, Déshydratation, Populus.
- métabolisme : ADN complémentaire.
- Analyse de polymorphisme de longueur de fragments amplifiés, Analyse de profil d'expression de gènes, Analyse de regroupements, Bases de données génétiques, Gènes de plante, Régulation de l'expression des gènes végétaux, Sécheresses.
English descriptors
- KwdEn :
- Amplified Fragment Length Polymorphism Analysis (MeSH), Apoptosis (genetics), Cluster Analysis (MeSH), DNA, Complementary (metabolism), Databases, Genetic (MeSH), Dehydration (genetics), Droughts (MeSH), Gene Expression Profiling (MeSH), Gene Expression Regulation, Plant (MeSH), Genes, Plant (MeSH), Populus (genetics).
- MESH :
- chemical , metabolism : DNA, Complementary.
- genetics : Apoptosis, Dehydration, Populus.
- Amplified Fragment Length Polymorphism Analysis, Cluster Analysis, Databases, Genetic, Droughts, Gene Expression Profiling, Gene Expression Regulation, Plant, Genes, Plant.
Abstract
BACKGROUND
Drought is one of the main environmental factors limiting tree growth and productivity of plantation forests worldwide. Populus hopeiensis Hu et Chow is one of the most important commercial plantation tree species in China. However, the genes controlling drought tolerance in this species have not been identified or characterized. Here, we conducted differential expression analyses and identified a number of genes that were up- or downregulated in P. hopeiensis during water stress. To the best of our knowledge, this is the first comprehensive study of differentially expressed genes in water-stressed P. hopeiensis.
RESULTS
Using the cDNA-AFLP detection technique, we used 256 primer combinations to identify differentially expressed genes in P. hopeiensis during water stress. In total, 415 transcript derived-fragments (TDFs) were obtained from 10× deep sequencing of 473 selected TDFs. Of the 415 TDFs, 412 were annotated by BLAST searches against various databases. The majority of these genes encoded products involved in ion transport and compartmentalization, cell division, metabolism, and protein synthesis. The TDFs were clustered into 12 groups on the basis of their expression patterns. Of the 415 reliable TDFs, the sequences of 35 were homologous to genes that play roles in short or long-term resistance to drought stress. Some genes were further selected for validation of cDNA-AFLP expression patterns using real-time PCR analyses. The results confirmed the expression patterns that were detected using the cDNA-AFLP technique.
CONCLUSION
The cDNA-AFLP technique is an effective and powerful tool for identifying candidate genes that are differentially expressed under water stress. We demonstrated that 415 TDFs were differentially expressed in water-stressed poplar. The products of these genes are involved in various biological processes in the drought response of poplar. The results of this study will aid in the identification of candidate genes of future experiments aimed at understanding this response of poplar.
DOI: 10.1186/1471-2164-13-286
PubMed: 22747754
PubMed Central: PMC3443059
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Wang</name></author><author><name sortKey="Bo, Wenhao" sort="Bo, Wenhao" uniqKey="Bo W" first="Wenhao" last="Bo">Wenhao Bo</name></author><author><name sortKey="Ren, Yuanyuan" sort="Ren, Yuanyuan" uniqKey="Ren Y" first="Yuanyuan" last="Ren">Yuanyuan Ren</name></author><author><name sortKey="Zhang, Zhiyi" sort="Zhang, Zhiyi" uniqKey="Zhang Z" first="Zhiyi" last="Zhang">Zhiyi Zhang</name></author><author><name sortKey="Zhang, Deqiang" sort="Zhang, Deqiang" uniqKey="Zhang D" first="Deqiang" last="Zhang">Deqiang Zhang</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2012">2012</date><idno type="RBID">pubmed:22747754</idno><idno type="pmid">22747754</idno><idno type="doi">10.1186/1471-2164-13-286</idno><idno type="pmc">PMC3443059</idno><idno type="wicri:Area/Main/Corpus">002979</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">002979</idno><idno type="wicri:Area/Main/Curation">002979</idno><idno 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type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Wang, Zeliang" sort="Wang, Zeliang" uniqKey="Wang Z" first="Zeliang" last="Wang">Zeliang Wang</name></author><author><name sortKey="Bo, Wenhao" sort="Bo, Wenhao" uniqKey="Bo W" first="Wenhao" last="Bo">Wenhao Bo</name></author><author><name sortKey="Ren, Yuanyuan" sort="Ren, Yuanyuan" uniqKey="Ren Y" first="Yuanyuan" last="Ren">Yuanyuan Ren</name></author><author><name sortKey="Zhang, Zhiyi" sort="Zhang, Zhiyi" uniqKey="Zhang Z" first="Zhiyi" last="Zhang">Zhiyi Zhang</name></author><author><name sortKey="Zhang, Deqiang" sort="Zhang, Deqiang" uniqKey="Zhang D" first="Deqiang" last="Zhang">Deqiang Zhang</name></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2012" type="published">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amplified Fragment Length Polymorphism Analysis (MeSH)</term><term>Apoptosis (genetics)</term><term>Cluster Analysis (MeSH)</term><term>DNA, Complementary (metabolism)</term><term>Databases, Genetic (MeSH)</term><term>Dehydration (genetics)</term><term>Droughts (MeSH)</term><term>Gene Expression Profiling (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Populus (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN complémentaire (métabolisme)</term><term>Analyse de polymorphisme de longueur de fragments amplifiés (MeSH)</term><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Analyse de regroupements (MeSH)</term><term>Apoptose (génétique)</term><term>Bases de données génétiques (MeSH)</term><term>Déshydratation (génétique)</term><term>Gènes de plante (MeSH)</term><term>Populus (génétique)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Sécheresses (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>DNA, Complementary</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Apoptosis</term><term>Dehydration</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Apoptose</term><term>Déshydratation</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ADN complémentaire</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amplified Fragment Length Polymorphism Analysis</term><term>Cluster Analysis</term><term>Databases, Genetic</term><term>Droughts</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Plant</term><term>Genes, Plant</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de polymorphisme de longueur de fragments amplifiés</term><term>Analyse de profil d'expression de gènes</term><term>Analyse de regroupements</term><term>Bases de données génétiques</term><term>Gènes de plante</term><term>Régulation de l'expression des gènes végétaux</term><term>Sécheresses</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Drought is one of the main environmental factors limiting tree growth and productivity of plantation forests worldwide. Populus hopeiensis Hu et Chow is one of the most important commercial plantation tree species in China. However, the genes controlling drought tolerance in this species have not been identified or characterized. Here, we conducted differential expression analyses and identified a number of genes that were up- or downregulated in P. hopeiensis during water stress. To the best of our knowledge, this is the first comprehensive study of differentially expressed genes in water-stressed P. hopeiensis.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>Using the cDNA-AFLP detection technique, we used 256 primer combinations to identify differentially expressed genes in P. hopeiensis during water stress. In total, 415 transcript derived-fragments (TDFs) were obtained from 10× deep sequencing of 473 selected TDFs. Of the 415 TDFs, 412 were annotated by BLAST searches against various databases. The majority of these genes encoded products involved in ion transport and compartmentalization, cell division, metabolism, and protein synthesis. The TDFs were clustered into 12 groups on the basis of their expression patterns. Of the 415 reliable TDFs, the sequences of 35 were homologous to genes that play roles in short or long-term resistance to drought stress. Some genes were further selected for validation of cDNA-AFLP expression patterns using real-time PCR analyses. The results confirmed the expression patterns that were detected using the cDNA-AFLP technique.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSION</b></p><p>The cDNA-AFLP technique is an effective and powerful tool for identifying candidate genes that are differentially expressed under water stress. We demonstrated that 415 TDFs were differentially expressed in water-stressed poplar. The products of these genes are involved in various biological processes in the drought response of poplar. The results of this study will aid in the identification of candidate genes of future experiments aimed at understanding this response of poplar.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">22747754</PMID><DateCompleted><Year>2013</Year><Month>01</Month><Day>25</Day></DateCompleted><DateRevised><Year>2019</Year><Month>01</Month><Day>08</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>13</Volume><PubDate><Year>2012</Year><Month>Jun</Month><Day>29</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Transcriptional profiling by cDNA-AFLP analysis showed differential transcript abundance in response to water stress in Populus hopeiensis.</ArticleTitle><Pagination><MedlinePgn>286</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2164-13-286</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Drought is one of the main environmental factors limiting tree growth and productivity of plantation forests worldwide. Populus hopeiensis Hu et Chow is one of the most important commercial plantation tree species in China. However, the genes controlling drought tolerance in this species have not been identified or characterized. Here, we conducted differential expression analyses and identified a number of genes that were up- or downregulated in P. hopeiensis during water stress. To the best of our knowledge, this is the first comprehensive study of differentially expressed genes in water-stressed P. hopeiensis.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">Using the cDNA-AFLP detection technique, we used 256 primer combinations to identify differentially expressed genes in P. hopeiensis during water stress. In total, 415 transcript derived-fragments (TDFs) were obtained from 10× deep sequencing of 473 selected TDFs. Of the 415 TDFs, 412 were annotated by BLAST searches against various databases. The majority of these genes encoded products involved in ion transport and compartmentalization, cell division, metabolism, and protein synthesis. The TDFs were clustered into 12 groups on the basis of their expression patterns. Of the 415 reliable TDFs, the sequences of 35 were homologous to genes that play roles in short or long-term resistance to drought stress. Some genes were further selected for validation of cDNA-AFLP expression patterns using real-time PCR analyses. The results confirmed the expression patterns that were detected using the cDNA-AFLP technique.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">The cDNA-AFLP technique is an effective and powerful tool for identifying candidate genes that are differentially expressed under water stress. We demonstrated that 415 TDFs were differentially expressed in water-stressed poplar. The products of these genes are involved in various biological processes in the drought response of poplar. The results of this study will aid in the identification of candidate genes of future experiments aimed at understanding this response of poplar.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Song</LastName><ForeName>Yuepeng</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P R China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Zeliang</ForeName><Initials>Z</Initials></Author><Author ValidYN="Y"><LastName>Bo</LastName><ForeName>Wenhao</ForeName><Initials>W</Initials></Author><Author ValidYN="Y"><LastName>Ren</LastName><ForeName>Yuanyuan</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Zhiyi</ForeName><Initials>Z</Initials></Author><Author 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sortKey="Ren, Yuanyuan" sort="Ren, Yuanyuan" uniqKey="Ren Y" first="Yuanyuan" last="Ren">Yuanyuan Ren</name><name sortKey="Wang, Zeliang" sort="Wang, Zeliang" uniqKey="Wang Z" first="Zeliang" last="Wang">Zeliang Wang</name><name sortKey="Zhang, Deqiang" sort="Zhang, Deqiang" uniqKey="Zhang D" first="Deqiang" last="Zhang">Deqiang Zhang</name><name sortKey="Zhang, Zhiyi" sort="Zhang, Zhiyi" uniqKey="Zhang Z" first="Zhiyi" last="Zhang">Zhiyi Zhang</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Song, Yuepeng" sort="Song, Yuepeng" uniqKey="Song Y" first="Yuepeng" last="Song">Yuepeng Song</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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