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Insertional mutations on RsFLC2 compromises vernalization response of radish (Raphanus sativus L.)

ABSTRACT: Insertional mutations on RsFLC2 compromises vernalization response of radish (Raphanus sativus L.)

PROVIDER: PRJNA1000708 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25469914_1.fastq.gz	Fastqsanger.gz
	SRR25469914_2.fastq.gz	Fastqsanger.gz
	SRR25469915_1.fastq.gz	Fastqsanger.gz
	SRR25469915_2.fastq.gz	Fastqsanger.gz
	SRR25469916_1.fastq.gz	Fastqsanger.gz

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Insertional mutations on RsFLC2 compromises vernalization response of radish (Raphanus sativus L.)

Project description:In this study, scientific efforts to grasp molecular details underlying vernalization-triggered floral transition were undertaken in radish (Raphanus sativus L.). We performed a comparative transcriptomic analysis between normal flowering ‘Jinjudaepyung’ and very late flowering inbred line, ‘Simu’.

2023-11-01 | GSE239735 | GEO

RNA-seqencing datasets for three different vernalization time course of radish

Project description:We report here NGS RNA-seqencing datasets for htree different vernalization time course of radish cultivar, "Taebaek".

2021-08-31 | GSE182885 | GEO

Radish (Raphanus sativus L.)

Project description:Two radish cultivars: Sading (SD) radish cultivar and Yangzhouyuanbai (YB) radish cultivar. Transcriptome

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RNA-seqencing datasets for three different vernalization time course of radish

Project description:RNA-seqencing datasets for three different vernalization time course of radish

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Identification of differentially expressed genes related to cytoplasmic male sterility in radish (Raphanus sativus L.) by comparative transcriptome analysis

Project description:Cytoplasmic male sterility (CMS), a typically maternally inherited trait, causes a failure in producing functional pollen. Although the radish CMS has be widely used to produce hybrid varieties in breeding program, the molecular mechanism of CMS in radish is poorly understood. In this study, two radish CMS lines (HYBP-A and YH-A) and their corresponding maintainer lines (HYBP-B and YH-B) were used to identify genes potentially involving in CMS using Illumina pair-end sequencing. A total of 167.86 million clean sequence reads were generated from the eight libraries (two replicates for each line). These reads were eventually assembled into 130,240 unigenes. Of them, 67,173 (51.6%) unigenes were annotated for their function. Comparison of gene expression levels between CMS line and maintainer line revealed 5,893 differentially expressed genes (DEGs) in HYBP, and 3,739 DEGs inYH. There were 990 DEGs commonly identified in both HYBP and YH, with same direction of expression change in two CMS lines relative to their corresponding maintainer lines, which suggested these 990 DEGs is likely related to CMS of radish. The expression levels of 20 DEGs were further confirmed by real-time quantitative PCR (qRT-PCR). Two pathways and eight functional categories exhibited a significant enrichment with DEGs in HYBP, and one pathway and six functional categories were markedly enriched by DEGs in YH. Among these pathways/functional categories, four of them were enriched in both varieties. A series of candidate genes and pathways that may contribute to the CMS will be helpful for increasing our understanding for this trait in radish.

2016-01-21 | GSE65142 | GEO

Identification of flowering time genes associated with vernalization in Chinese cabbage and their differential expression in radish

Project description:We conducted genome-wide transcriptome analysis using the inbred Chinese cabbage line, ‘4004’, which displayed early flowering in response to vernalization. A total of 1,677 differentially-expressed genes (DEGs) were identified with and without vernalization. Transcriptome analysis identified 223 homologs of Arabidopsis Ft genes in Chinese cabbage, and 50 of these genes responded to vernalization. RT-qPCR analysis of major Ft genes showed that the majority of flowering enhancers were up-regulated in response to vernalization, whereas most flowering repressors were down-regulated in response to vernalization. Among the major Ft genes, the expression of BrCOL1-2, BrFT1/2, BrSOC1/2/3, BrFLC1/2/3/5, and BrMAF was strongly affected by vernalization.

2018-11-02 | GSE106444 | GEO

The flowering-related genes responsible for differences in bolting time between two radish lines

Project description:To elucidate the molecular mechanisms that determine the differences in flowering times between two radish lines, NH-JS1 (late bolting) and NH-JS2 (early bolting) by high-throughput RNA sequencing analysis. In total, 71,188 unigenes were identified by reference-guided assembly, of which 309, 788, and 980 genes were differentially expressed between the two inbred lines after 0, 15, and 35 days of vernalization, respectively.

2017-02-10 | GSE89312 | GEO

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

Project 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.

| S-EPMC5428929 | biostudies-literature

The Molecular Mechanisms of m6A Methylation Modification in Regulating Bolting and Flowering in Radish

Project description:N6-methyladenosine (m6A) is a crucial epigenetic modification in mRNA and the most abundant methylation in eukaryotes. However, research on m6A modification in radish (Raphanus sativus) is not as extensive as in model plants. In this study, we analyzed m6A modification during the vegetative and reproductive growth stages of radish using m6A-seq and RNA-seq to explore its potential role in bolting and flowering. The results showed that m6A peaks significantly increased during the reproductive growth stage compared to the vegetative stage, with more m6A modification sites in the stop codon, 3' UTR, and promoter regions. Overexpression of the RsALKBH10B gene led to a global reduction in m6A modification and resulted in an early bolting and flowering phenotype, with transcription levels of key flowering factors RsSOC1 and RsFT increasing by 10-40 fold. Correlation analysis between differential m6A modification and differentially expressed genes indicated that genes such as RsSUF4, RsAGL13, and RsCDF5 might regulate bolting and flowering. Overexpression of RsSUF4 delayed bolting and flowering and decreased overall m6A modification levels; in positive transgenic plants, higher m6A levels of RsSUF4 were associated with lower transcription levels. These findings suggest that m6A methylation may regulate gene expression related to bolting and flowering in radish by affecting mRNA stability, ultimately leading to bolting and flowering.

2024-06-22 | GSE270351 | GEO

Transcriptomic and metabolic analyses revealed the modulatory effect of vernalization on glucosinolate metabolism in radish (Raphanus sativus L.).

Project description:Vernalization is the process by which long-term cold like winter triggers transition to flowering in plants. Many biennial and perennial plants including Brassicaceae family plants require vernalization for floral transition. Not only floral transition, but dynamic physiological and metabolic changes might also take place during vernalization. However, vernalization-mediated metabolic change is merely investigated so far. One of secondary metabolites found in Brassiceceae family plants is glucosinolates (GSLs). GSLs provides defense against pathogens and herbivores attack in plants and also exhibits inhibitory activity against human cancer cell. Profiles of GSLs are highly modulated by different environmental stresses in Brassciaceae family plants. To grasp the effect of vernalization on GSLs metabolic dynamics in radish (Raphanus sativus L.), we performed transcriptomic and metabolic analysis during vernalization in radish. Through transcriptome analysis, we found many GSLs metabolic genes were significantly down-regulated by vernalization in radish plants. Ultra-High Performance Liquid Chromatography analysis also revealed that GSLs compounds were substantially reduced in vernalized radish samples compared to non-vernalized radish samples. Furthermore, we found that repressive histone modification (i.e. H3K27me3) is involved in the modulation of GSLs metabolism via epigenetic suppression of Glucoraphasatin Synthase 1 (GRS1) during vernalization in radish. This study revealed that GSLs metabolism is modulated by vernalization, suggestive of a newly identified target of vernalization in radish.

| S-EPMC8674254 | biostudies-literature

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