Genome-wide transcriptome profiling of radish (Raphanus sativus L.) in response to vernalization

PloS One
Chen LiuXianxian Liu

Abstract

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.

References

Jan 12, 2005·Trends in Plant Science·Yuehui He, Richard M Amasino
Oct 4, 2005·Molecular Genetics and Genomics : MGG·Attila VágújfalviLuigi Cattivelli
Apr 21, 2006·The Plant Journal : for Cell and Molecular Biology·Chris A HelliwellElizabeth S Dennis
Apr 28, 2006·The Plant Journal : for Cell and Molecular Biology·Carina Barth, Georg Jander
Mar 5, 2008·Plant Molecular Biology·Andrea K KnoxJorge Dubcovsky
Jul 4, 2008·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Young-Pyo LeeSunggil Kim
May 7, 2009·Proceedings of the National Academy of Sciences of the United States of America·Sandra N OliverBen Trevaskis
Jul 7, 2009·Annual Review of Cell and Developmental Biology·Dong-Hwan KimRichard M Amasino
Oct 29, 2010·Genome Biology·Simon Anders, Wolfgang Huber
Jan 21, 2011·Nature·Raphaël Margueron, Danny Reinberg
Apr 11, 2012·International Journal of Molecular Sciences·Feng XuShuiyuan Cheng
May 23, 2012·Current Biology : CB·Pierre A PinAndreas E Müller
Oct 5, 2012·BMC Genomics·Stefan K SchulzeAndreas S Beutler
Jun 20, 2013·International Journal of Molecular Sciences·Leonid V KurepinNorman P A Hüner
Mar 22, 2014·The Arabidopsis Book·Dong-Hwan Kim, Sibum Sung
May 23, 2014·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Hiroyasu KitashibaTakeshi Nishio
Oct 31, 2015·PloS One·Mengxia SunMeilan Li

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Citations

Oct 18, 2018·International Journal of Molecular Sciences·Qiang ZhouZhipeng Liu

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Datasets Mentioned

BETA
SRP093947

Methods Mentioned

BETA
RNA-Seq
PCR
Illumina sequencing

Software Mentioned

DEGseq package
TopHat2
Cufflinks

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