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Transcriptome profiling of laser-captured crown root primordia reveals new pathways activated during early stages of crown root formation in rice
Crown roots constitute the main part of the rice root system. Several key genes involved in crown root initiation and development have been identified by functional genomics approaches. Nevertheless, these approaches are impaired by functional redundancy and mutant lethality. To overcome these limit...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7676735/ https://www.ncbi.nlm.nih.gov/pubmed/33211715 http://dx.doi.org/10.1371/journal.pone.0238736 |
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author | Lavarenne, Jérémy Gonin, Mathieu Champion, Antony Javelle, Marie Adam, Hélène Rouster, Jacques Conejéro, Geneviève Lartaud, Marc Verdeil, Jean-Luc Laplaze, Laurent Sallaud, Christophe Lucas, Mikael Gantet, Pascal |
author_facet | Lavarenne, Jérémy Gonin, Mathieu Champion, Antony Javelle, Marie Adam, Hélène Rouster, Jacques Conejéro, Geneviève Lartaud, Marc Verdeil, Jean-Luc Laplaze, Laurent Sallaud, Christophe Lucas, Mikael Gantet, Pascal |
author_sort | Lavarenne, Jérémy |
collection | PubMed |
description | Crown roots constitute the main part of the rice root system. Several key genes involved in crown root initiation and development have been identified by functional genomics approaches. Nevertheless, these approaches are impaired by functional redundancy and mutant lethality. To overcome these limitations, organ targeted transcriptome analysis can help to identify genes involved in crown root formation and early development. In this study, we generated an atlas of genes expressed in developing crown root primordia in comparison with adjacent stem cortical tissue at three different developmental stages before emergence, using laser capture microdissection. We identified 3975 genes differentially expressed in crown root primordia. About 30% of them were expressed at the three developmental stages, whereas 10.5%, 19.5% and 12.8% were specifically expressed at the early, intermediate and late stages, respectively. Sorting them by functional ontology highlighted an active transcriptional switch during the process of crown root primordia formation. Cross-analysis with other rice root development-related datasets revealed genes encoding transcription factors, chromatin remodeling factors, peptide growth factors, and cell wall remodeling enzymes that are likely to play a key role during crown root primordia formation. This atlas constitutes an open primary data resource for further studies on the regulation of crown root initiation and development. |
format | Online Article Text |
id | pubmed-7676735 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-76767352020-12-02 Transcriptome profiling of laser-captured crown root primordia reveals new pathways activated during early stages of crown root formation in rice Lavarenne, Jérémy Gonin, Mathieu Champion, Antony Javelle, Marie Adam, Hélène Rouster, Jacques Conejéro, Geneviève Lartaud, Marc Verdeil, Jean-Luc Laplaze, Laurent Sallaud, Christophe Lucas, Mikael Gantet, Pascal PLoS One Research Article Crown roots constitute the main part of the rice root system. Several key genes involved in crown root initiation and development have been identified by functional genomics approaches. Nevertheless, these approaches are impaired by functional redundancy and mutant lethality. To overcome these limitations, organ targeted transcriptome analysis can help to identify genes involved in crown root formation and early development. In this study, we generated an atlas of genes expressed in developing crown root primordia in comparison with adjacent stem cortical tissue at three different developmental stages before emergence, using laser capture microdissection. We identified 3975 genes differentially expressed in crown root primordia. About 30% of them were expressed at the three developmental stages, whereas 10.5%, 19.5% and 12.8% were specifically expressed at the early, intermediate and late stages, respectively. Sorting them by functional ontology highlighted an active transcriptional switch during the process of crown root primordia formation. Cross-analysis with other rice root development-related datasets revealed genes encoding transcription factors, chromatin remodeling factors, peptide growth factors, and cell wall remodeling enzymes that are likely to play a key role during crown root primordia formation. This atlas constitutes an open primary data resource for further studies on the regulation of crown root initiation and development. Public Library of Science 2020-11-19 /pmc/articles/PMC7676735/ /pubmed/33211715 http://dx.doi.org/10.1371/journal.pone.0238736 Text en © 2020 Lavarenne et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Lavarenne, Jérémy Gonin, Mathieu Champion, Antony Javelle, Marie Adam, Hélène Rouster, Jacques Conejéro, Geneviève Lartaud, Marc Verdeil, Jean-Luc Laplaze, Laurent Sallaud, Christophe Lucas, Mikael Gantet, Pascal Transcriptome profiling of laser-captured crown root primordia reveals new pathways activated during early stages of crown root formation in rice |
title | Transcriptome profiling of laser-captured crown root primordia reveals new pathways activated during early stages of crown root formation in rice |
title_full | Transcriptome profiling of laser-captured crown root primordia reveals new pathways activated during early stages of crown root formation in rice |
title_fullStr | Transcriptome profiling of laser-captured crown root primordia reveals new pathways activated during early stages of crown root formation in rice |
title_full_unstemmed | Transcriptome profiling of laser-captured crown root primordia reveals new pathways activated during early stages of crown root formation in rice |
title_short | Transcriptome profiling of laser-captured crown root primordia reveals new pathways activated during early stages of crown root formation in rice |
title_sort | transcriptome profiling of laser-captured crown root primordia reveals new pathways activated during early stages of crown root formation in rice |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7676735/ https://www.ncbi.nlm.nih.gov/pubmed/33211715 http://dx.doi.org/10.1371/journal.pone.0238736 |
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