Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa.
Identifieur interne : 003280 ( Main/Corpus ); précédent : 003279; suivant : 003281Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa.
Auteurs : Palitha Dharmawardhana ; Amy M. Brunner ; Steven H. StraussSource :
- BMC genomics [ 1471-2164 ] ; 2010.
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), Multigene Family (MeSH), Oligonucleotide Array Sequence Analysis (MeSH), Plant Stems (genetics), Plant Stems (growth & development), Populus (genetics), Populus (growth & development), RNA, Plant (genetics), Reverse Transcriptase Polymerase Chain Reaction (MeSH), Wood (genetics), Wood (growth & development).
- MESH :
- chemical , genetics : RNA, Plant.
- genetics : Plant Stems, Populus, Wood.
- growth & development : Plant Stems, Populus, Wood.
- Cluster Analysis, Gene Expression Profiling, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Genes, Plant, Genome, Plant, Multigene Family, Oligonucleotide Array Sequence Analysis, Reverse Transcriptase Polymerase Chain Reaction.
Abstract
BACKGROUND
With its genome sequence and other experimental attributes, Populus trichocarpa has become the model species for genomic studies of wood development. Wood is derived from secondary growth of tree stems, and begins with the development of a ring of vascular cambium in the young developing stem. The terminal region of the developing shoot provides a steep developmental gradient from primary to secondary growth that facilitates identification of genes that play specialized functions during each of these phases of growth.
RESULTS
Using a genomic microarray representing the majority of the transcriptome, we profiled gene expression in stem segments that spanned primary to secondary growth. We found 3,016 genes that were differentially expressed during stem development (Q-value 2-fold expression variation), and 15% of these genes encode proteins with no significant identities to known genes. We identified all gene family members putatively involved in secondary growth for carbohydrate active enzymes, tubulins, actins, actin depolymerizing factors, fasciclin-like AGPs, and vascular development-associated transcription factors. Almost 70% of expressed transcription factors were upregulated during the transition to secondary growth. The primary shoot elongation region of the stem contained specific carbohydrate active enzyme and expansin family members that are likely to function in primary cell wall synthesis and modification. Genes involved in plant defense and protective functions were also dominant in the primary growth region.
CONCLUSION
Our results describe the global patterns of gene expression that occur during the transition from primary to secondary stem growth. We were able to identify three major patterns of gene expression and over-represented gene ontology categories during stem development. The new regulatory factors and cell wall biogenesis genes that we identified provide candidate genes for further functional characterization, as well as new tools for molecular breeding and biotechnology aimed at improvement of tree growth rate, crown form, and wood quality.
DOI: 10.1186/1471-2164-11-150
PubMed: 20199690
PubMed Central: PMC2846914
Links to Exploration step
pubmed:20199690Le document en format XML
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Brunner</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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Wood is derived from secondary growth of tree stems, and begins with the development of a ring of vascular cambium in the young developing stem. The terminal region of the developing shoot provides a steep developmental gradient from primary to secondary growth that facilitates identification of genes that play specialized functions during each of these phases of growth.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>Using a genomic microarray representing the majority of the transcriptome, we profiled gene expression in stem segments that spanned primary to secondary growth. We found 3,016 genes that were differentially expressed during stem development (Q-value 2-fold expression variation), and 15% of these genes encode proteins with no significant identities to known genes. We identified all gene family members putatively involved in secondary growth for carbohydrate active enzymes, tubulins, actins, actin depolymerizing factors, fasciclin-like AGPs, and vascular development-associated transcription factors. Almost 70% of expressed transcription factors were upregulated during the transition to secondary growth. The primary shoot elongation region of the stem contained specific carbohydrate active enzyme and expansin family members that are likely to function in primary cell wall synthesis and modification. Genes involved in plant defense and protective functions were also dominant in the primary growth region.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSION</b></p><p>Our results describe the global patterns of gene expression that occur during the transition from primary to secondary stem growth. We were able to identify three major patterns of gene expression and over-represented gene ontology categories during stem development. The new regulatory factors and cell wall biogenesis genes that we identified provide candidate genes for further functional characterization, as well as new tools for molecular breeding and biotechnology aimed at improvement of tree growth rate, crown form, and wood quality.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">20199690</PMID><DateCompleted><Year>2010</Year><Month>05</Month><Day>03</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>11</Volume><PubDate><Year>2010</Year><Month>Mar</Month><Day>04</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa.</ArticleTitle><Pagination><MedlinePgn>150</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2164-11-150</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">With its genome sequence and other experimental attributes, Populus trichocarpa has become the model species for genomic studies of wood development. Wood is derived from secondary growth of tree stems, and begins with the development of a ring of vascular cambium in the young developing stem. The terminal region of the developing shoot provides a steep developmental gradient from primary to secondary growth that facilitates identification of genes that play specialized functions during each of these phases of growth.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">Using a genomic microarray representing the majority of the transcriptome, we profiled gene expression in stem segments that spanned primary to secondary growth. We found 3,016 genes that were differentially expressed during stem development (Q-value 2-fold expression variation), and 15% of these genes encode proteins with no significant identities to known genes. We identified all gene family members putatively involved in secondary growth for carbohydrate active enzymes, tubulins, actins, actin depolymerizing factors, fasciclin-like AGPs, and vascular development-associated transcription factors. Almost 70% of expressed transcription factors were upregulated during the transition to secondary growth. The primary shoot elongation region of the stem contained specific carbohydrate active enzyme and expansin family members that are likely to function in primary cell wall synthesis and modification. Genes involved in plant defense and protective functions were also dominant in the primary growth region.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">Our results describe the global patterns of gene expression that occur during the transition from primary to secondary stem growth. We were able to identify three major patterns of gene expression and over-represented gene ontology categories during stem development. 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