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Genome-wide transcriptome profiling of radish (Raphanus sativus L.) in response to vernalization
Vernalization is a key process for premature bolting. Although many studies on vernalization have been reported, the molecular mechanism of vernalization is still largely unknown in radish. In this study, we sequenced the transcriptomes of radish seedlings at three different time points during verna...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5428929/ https://www.ncbi.nlm.nih.gov/pubmed/28498850 http://dx.doi.org/10.1371/journal.pone.0177594 |
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author | Liu, Chen Wang, Shufen Xu, Wenling Liu, Xianxian |
author_facet | Liu, Chen Wang, Shufen Xu, Wenling Liu, Xianxian |
author_sort | Liu, Chen |
collection | PubMed |
description | Vernalization is a key process for premature bolting. Although many studies on vernalization have been reported, the molecular mechanism of vernalization is still largely unknown in radish. In this study, we sequenced the transcriptomes of radish seedlings at three different time points during vernalization. More than 36 million clean reads were generated for each sample and the portions mapped to the reference genome were all above 67.0%. Our results show that the differentially expressed genes (DEGs) between room temperature and the early stage of vernalization (4,845) are the most in all treatments pairs. A series of vernalization related genes, including two FLOWERING LOCUS C (FLC) genes, were screened according to the annotations. A total of 775 genes were also filtered as the vernalization related candidates based on their expression profiles. Cold stress responsive genes were also analyzed to further confirm the sequencing result. Several key genes in vernalization or cold stress response were validated by quantitative RT-PCR (RT-qPCR). This study identified a number of genes that may be involved in vernalization, which are useful for other functional genomics research in radish. |
format | Online Article Text |
id | pubmed-5428929 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-54289292017-05-26 Genome-wide transcriptome profiling of radish (Raphanus sativus L.) in response to vernalization Liu, Chen Wang, Shufen Xu, Wenling Liu, Xianxian PLoS One Research Article Vernalization is a key process for premature bolting. Although many studies on vernalization have been reported, the molecular mechanism of vernalization is still largely unknown in radish. In this study, we sequenced the transcriptomes of radish seedlings at three different time points during vernalization. More than 36 million clean reads were generated for each sample and the portions mapped to the reference genome were all above 67.0%. Our results show that the differentially expressed genes (DEGs) between room temperature and the early stage of vernalization (4,845) are the most in all treatments pairs. A series of vernalization related genes, including two FLOWERING LOCUS C (FLC) genes, were screened according to the annotations. A total of 775 genes were also filtered as the vernalization related candidates based on their expression profiles. Cold stress responsive genes were also analyzed to further confirm the sequencing result. Several key genes in vernalization or cold stress response were validated by quantitative RT-PCR (RT-qPCR). This study identified a number of genes that may be involved in vernalization, which are useful for other functional genomics research in radish. Public Library of Science 2017-05-12 /pmc/articles/PMC5428929/ /pubmed/28498850 http://dx.doi.org/10.1371/journal.pone.0177594 Text en © 2017 Liu 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 Liu, Chen Wang, Shufen Xu, Wenling Liu, Xianxian Genome-wide transcriptome profiling of radish (Raphanus sativus L.) in response to vernalization |
title | Genome-wide transcriptome profiling of radish (Raphanus sativus L.) in response to vernalization |
title_full | Genome-wide transcriptome profiling of radish (Raphanus sativus L.) in response to vernalization |
title_fullStr | Genome-wide transcriptome profiling of radish (Raphanus sativus L.) in response to vernalization |
title_full_unstemmed | Genome-wide transcriptome profiling of radish (Raphanus sativus L.) in response to vernalization |
title_short | Genome-wide transcriptome profiling of radish (Raphanus sativus L.) in response to vernalization |
title_sort | genome-wide transcriptome profiling of radish (raphanus sativus l.) in response to vernalization |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5428929/ https://www.ncbi.nlm.nih.gov/pubmed/28498850 http://dx.doi.org/10.1371/journal.pone.0177594 |
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