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Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa

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...

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Autores principales: Dharmawardhana, Palitha, Brunner, Amy M, Strauss, Steven H
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2846914/
https://www.ncbi.nlm.nih.gov/pubmed/20199690
http://dx.doi.org/10.1186/1471-2164-11-150
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author Dharmawardhana, Palitha
Brunner, Amy M
Strauss, Steven H
author_facet Dharmawardhana, Palitha
Brunner, Amy M
Strauss, Steven H
author_sort Dharmawardhana, Palitha
collection PubMed
description 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 ≤ 0.05; >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.
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spelling pubmed-28469142010-03-30 Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa Dharmawardhana, Palitha Brunner, Amy M Strauss, Steven H BMC Genomics Research Article 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 ≤ 0.05; >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. BioMed Central 2010-03-04 /pmc/articles/PMC2846914/ /pubmed/20199690 http://dx.doi.org/10.1186/1471-2164-11-150 Text en Copyright ©2010 Dharmawardhana et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Dharmawardhana, Palitha
Brunner, Amy M
Strauss, Steven H
Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa
title Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa
title_full Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa
title_fullStr Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa
title_full_unstemmed Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa
title_short Genome-wide transcriptome analysis of the transition from primary to secondary stem development in Populus trichocarpa
title_sort genome-wide transcriptome analysis of the transition from primary to secondary stem development in populus trichocarpa
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2846914/
https://www.ncbi.nlm.nih.gov/pubmed/20199690
http://dx.doi.org/10.1186/1471-2164-11-150
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