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

Date Published: May 12, 2017

Publisher: Public Library of Science

Author(s): Chen Liu, Shufen Wang, Wenling Xu, Xianxian Liu, Yong Pyo Lim.

http://doi.org/10.1371/journal.pone.0177594

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.

Partial Text

Radish (Raphanus sativus L.) is an economically important root vegetable crop grown worldwide, particularly in China, Japan, Korea, and Southeast Asia [1]. For the nutrient-rich tuberous root, many breeding efforts on radish have been devoted to developing varieties with different size [2–4], color [5–9], cultivation season [5, 10, 11] and other characteristics [12–14]. Although all-season radish is available in many areas now, there are still a lot of practical problems in production, among which premature bolting is one of the most prominent. Before bolting, the plant needs a period of low temperature to accomplish vernalization. A better understanding of the molecular mechanism of vernalization will be helpful to solve these practical problems such as premature bolting.

The molecular mechanism of vernalization is still largely unknown in radish. One high throughput sequencing analysis aiming at radish vernalization has been reported, which was de novo assembled and mainly focused on the FLC genes [31]. In this study, we analyzed the radish transcriptome before and after vernalization with a reference genome and identified a series of vernalization-related genes. Our experiment includes three treatments in which, the plants were exposed to low temperature for 0, 3 and 20 days, respectively. A total of 39,118 transcripts were detected. Among the three treatments, the experiment for the pair RT vs.VE discovered more DEGs than the other two experiments, with the least number of DEGs in the experiment for VE vs. VL. The large amount of DEGs in RT vs.VE may be partly because of the cold stress responsive genes which had expression changes immediately after exposure to low temperature.

We presented a comprehensive analysis of the gene expression profiles in radish during vernalization, using the latest published genome sequence as the reference. A series of vernalization related genes were identified according to the annotations and the expression patterns. Cold stress responsive genes were also analyzed to further confirm the sequencing result. This study offers important insights into the molecular mechanism of vernalization in radish.

 

Source:

http://doi.org/10.1371/journal.pone.0177594