Genome scale transcriptome analysis of shoot organogenesis in Populus.
Identifieur interne : 003614 ( Main/Exploration ); précédent : 003613; suivant : 003615Genome scale transcriptome analysis of shoot organogenesis in Populus.
Auteurs : Yanghuan Bao [États-Unis] ; Palitha Dharmawardhana ; Todd C. Mockler ; Steven H. StraussSource :
- BMC plant biology [ 1471-2229 ] ; 2009.
Descripteurs français
- KwdFr :
- ARN des plantes (génétique), Analyse de profil d'expression de gènes (MeSH), Analyse de regroupements (MeSH), Gènes de plante (MeSH), Génome végétal (MeSH), Populus (croissance et développement), Populus (génétique), Pousses de plante (croissance et développement), Pousses de plante (génétique), Régulation de l'expression des gènes au cours du développement (MeSH), Régulation de l'expression des gènes végétaux (MeSH), Séquençage par oligonucléotides en batterie (MeSH).
- MESH :
- croissance et développement : Populus, Pousses de plante.
- génétique : ARN des plantes, Populus, Pousses de plante.
- Analyse de profil d'expression de gènes, Analyse de regroupements, Gènes de plante, Génome végétal, Régulation de l'expression des gènes au cours du développement, Régulation de l'expression des gènes végétaux, Séquençage par oligonucléotides en batterie.
English descriptors
- KwdEn :
- Cluster Analysis (MeSH), Gene Expression Profiling (MeSH), Gene Expression Regulation, Developmental (MeSH), Gene Expression Regulation, Plant (MeSH), Genes, Plant (MeSH), Genome, Plant (MeSH), Oligonucleotide Array Sequence Analysis (MeSH), Plant Shoots (genetics), Plant Shoots (growth & development), Populus (genetics), Populus (growth & development), RNA, Plant (genetics).
- MESH :
- chemical , genetics : RNA, Plant.
- genetics : Plant Shoots, Populus.
- growth & development : Plant Shoots, Populus.
- Cluster Analysis, Gene Expression Profiling, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Genes, Plant, Genome, Plant, Oligonucleotide Array Sequence Analysis.
Abstract
BACKGROUND
Our aim is to improve knowledge of gene regulatory circuits important to dedifferentiation, redifferentiation, and adventitious meristem organization during in vitro regeneration of plants. Regeneration of transgenic cells remains a major obstacle to research and commercial deployment of most taxa of transgenic plants, and woody species are particularly recalcitrant. The model woody species Populus, due to its genome sequence and amenability to in vitro manipulation, is an excellent species for study in this area. The genes recognized may help to guide the development of new tools for improving the efficiency of plant regeneration and transformation.
RESULTS
We analyzed gene expression during poplar in vitro dedifferentiation and shoot regeneration using an Affymetrix array representing over 56,000 poplar transcripts. We focused on callus induction and shoot formation, thus we sampled RNAs from tissues: prior to callus induction, 3 days and 15 days after callus induction, and 3 days and 8 days after the start of shoot induction. We used a female hybrid white poplar clone (INRA 717-1 B4, Populus tremula x P. alba) that is used widely as a model transgenic genotype. Approximately 15% of the monitored genes were significantly up-or down-regulated when controlling the false discovery rate (FDR) at 0.01; over 3,000 genes had a 5-fold or greater change in expression. We found a large initial change in expression after the beginning of hormone treatment (at the earliest stage of callus induction), and then a much smaller number of additional differentially expressed genes at subsequent regeneration stages. A total of 588 transcription factors that were distributed in 45 gene families were differentially regulated. Genes that showed strong differential expression included components of auxin and cytokinin signaling, selected cell division genes, and genes related to plastid development and photosynthesis. When compared with data on in vitro callogenesis in Arabidopsis, 25% (1,260) of up-regulated and 22% (748) of down-regulated genes were in common with the genes regulated in poplar during callus induction.
CONCLUSION
The major regulatory events during plant cell organogenesis occur at early stages of dedifferentiation. The regulatory circuits reflect the combinational effects of transcriptional control and hormone signaling, and associated changes in light environment imposed during dedifferentiation.
DOI: 10.1186/1471-2229-9-132
PubMed: 19919717
PubMed Central: PMC2784466
Affiliations:
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Mockler</name></author><author><name sortKey="Strauss, Steven H" sort="Strauss, Steven H" uniqKey="Strauss S" first="Steven H" last="Strauss">Steven H. 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Mockler</name></author><author><name sortKey="Strauss, Steven H" sort="Strauss, Steven H" uniqKey="Strauss S" first="Steven H" last="Strauss">Steven H. Strauss</name></author></analytic><series><title level="j">BMC plant biology</title><idno type="eISSN">1471-2229</idno><imprint><date when="2009" type="published">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Cluster Analysis (MeSH)</term><term>Gene Expression Profiling (MeSH)</term><term>Gene Expression Regulation, Developmental (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Oligonucleotide Array Sequence Analysis (MeSH)</term><term>Plant Shoots (genetics)</term><term>Plant Shoots (growth & development)</term><term>Populus (genetics)</term><term>Populus (growth & development)</term><term>RNA, Plant (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN des plantes (génétique)</term><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Analyse de regroupements (MeSH)</term><term>Gènes de plante (MeSH)</term><term>Génome végétal (MeSH)</term><term>Populus (croissance et développement)</term><term>Populus (génétique)</term><term>Pousses de plante (croissance et développement)</term><term>Pousses de plante (génétique)</term><term>Régulation de l'expression des gènes au cours du développement (MeSH)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Séquençage par oligonucléotides en batterie (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Plant</term></keywords><keywords scheme="MESH" qualifier="croissance et développement" xml:lang="fr"><term>Populus</term><term>Pousses de plante</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Plant Shoots</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Plant Shoots</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN des plantes</term><term>Populus</term><term>Pousses de plante</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Cluster Analysis</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Developmental</term><term>Gene Expression Regulation, Plant</term><term>Genes, Plant</term><term>Genome, Plant</term><term>Oligonucleotide Array Sequence Analysis</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Analyse de regroupements</term><term>Gènes de plante</term><term>Génome végétal</term><term>Régulation de l'expression des gènes au cours du développement</term><term>Régulation de l'expression des gènes végétaux</term><term>Séquençage par oligonucléotides en batterie</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Our aim is to improve knowledge of gene regulatory circuits important to dedifferentiation, redifferentiation, and adventitious meristem organization during in vitro regeneration of plants. Regeneration of transgenic cells remains a major obstacle to research and commercial deployment of most taxa of transgenic plants, and woody species are particularly recalcitrant. The model woody species Populus, due to its genome sequence and amenability to in vitro manipulation, is an excellent species for study in this area. The genes recognized may help to guide the development of new tools for improving the efficiency of plant regeneration and transformation.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>We analyzed gene expression during poplar in vitro dedifferentiation and shoot regeneration using an Affymetrix array representing over 56,000 poplar transcripts. We focused on callus induction and shoot formation, thus we sampled RNAs from tissues: prior to callus induction, 3 days and 15 days after callus induction, and 3 days and 8 days after the start of shoot induction. We used a female hybrid white poplar clone (INRA 717-1 B4, Populus tremula x P. alba) that is used widely as a model transgenic genotype. Approximately 15% of the monitored genes were significantly up-or down-regulated when controlling the false discovery rate (FDR) at 0.01; over 3,000 genes had a 5-fold or greater change in expression. We found a large initial change in expression after the beginning of hormone treatment (at the earliest stage of callus induction), and then a much smaller number of additional differentially expressed genes at subsequent regeneration stages. A total of 588 transcription factors that were distributed in 45 gene families were differentially regulated. Genes that showed strong differential expression included components of auxin and cytokinin signaling, selected cell division genes, and genes related to plastid development and photosynthesis. When compared with data on in vitro callogenesis in Arabidopsis, 25% (1,260) of up-regulated and 22% (748) of down-regulated genes were in common with the genes regulated in poplar during callus induction.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSION</b></p><p>The major regulatory events during plant cell organogenesis occur at early stages of dedifferentiation. The regulatory circuits reflect the combinational effects of transcriptional control and hormone signaling, and associated changes in light environment imposed during dedifferentiation.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">19919717</PMID><DateCompleted><Year>2010</Year><Month>01</Month><Day>27</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2229</ISSN><JournalIssue CitedMedium="Internet"><Volume>9</Volume><PubDate><Year>2009</Year><Month>Nov</Month><Day>17</Day></PubDate></JournalIssue><Title>BMC plant biology</Title><ISOAbbreviation>BMC Plant Biol</ISOAbbreviation></Journal><ArticleTitle>Genome scale transcriptome analysis of shoot organogenesis in Populus.</ArticleTitle><Pagination><MedlinePgn>132</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2229-9-132</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Our aim is to improve knowledge of gene regulatory circuits important to dedifferentiation, redifferentiation, and adventitious meristem organization during in vitro regeneration of plants. Regeneration of transgenic cells remains a major obstacle to research and commercial deployment of most taxa of transgenic plants, and woody species are particularly recalcitrant. The model woody species Populus, due to its genome sequence and amenability to in vitro manipulation, is an excellent species for study in this area. The genes recognized may help to guide the development of new tools for improving the efficiency of plant regeneration and transformation.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We analyzed gene expression during poplar in vitro dedifferentiation and shoot regeneration using an Affymetrix array representing over 56,000 poplar transcripts. We focused on callus induction and shoot formation, thus we sampled RNAs from tissues: prior to callus induction, 3 days and 15 days after callus induction, and 3 days and 8 days after the start of shoot induction. We used a female hybrid white poplar clone (INRA 717-1 B4, Populus tremula x P. alba) that is used widely as a model transgenic genotype. Approximately 15% of the monitored genes were significantly up-or down-regulated when controlling the false discovery rate (FDR) at 0.01; over 3,000 genes had a 5-fold or greater change in expression. We found a large initial change in expression after the beginning of hormone treatment (at the earliest stage of callus induction), and then a much smaller number of additional differentially expressed genes at subsequent regeneration stages. A total of 588 transcription factors that were distributed in 45 gene families were differentially regulated. Genes that showed strong differential expression included components of auxin and cytokinin signaling, selected cell division genes, and genes related to plastid development and photosynthesis. When compared with data on in vitro callogenesis in Arabidopsis, 25% (1,260) of up-regulated and 22% (748) of down-regulated genes were in common with the genes regulated in poplar during callus induction.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">The major regulatory events during plant cell organogenesis occur at early stages of dedifferentiation. 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sortKey="Mockler, Todd C" sort="Mockler, Todd C" uniqKey="Mockler T" first="Todd C" last="Mockler">Todd C. Mockler</name><name sortKey="Strauss, Steven H" sort="Strauss, Steven H" uniqKey="Strauss S" first="Steven H" last="Strauss">Steven H. Strauss</name></noCountry><country name="États-Unis"><noRegion><name sortKey="Bao, Yanghuan" sort="Bao, Yanghuan" uniqKey="Bao Y" first="Yanghuan" last="Bao">Yanghuan Bao</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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