Radish transcriptome
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB51201 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To further verify the differences in IncRNA and miRNA during radish flowering, we conducted transcriptome analysis on samples taken before and after radish flowering. Obtain IncRNA and miRNA from the differential table and perform qRT-PCR validation on them.
2024-03-14 | GSE261303 | GEO
Project description:Two radish cultivars: Sading (SD) radish cultivar and Yangzhouyuanbai (YB) radish cultivar. Transcriptome
| PRJNA511407 | ENA
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
Project description:We report here NGS RNA-seqencing datasets for htree different vernalization time course of radish cultivar, "Taebaek".
2021-08-31 | GSE182885 | GEO
Project description:Resequencing data for radish germplasm
| PRJEB44749 | ENA
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
Project description:Pectobacterium atrosepticum (Pba) is a gram-negative bacterium which causes blackleg and tuber soft rot on potato. To investigate the molecular processes and responses involved in Pba-host (potato) and Pba-non-host (radish) interactions, under laboratory conditions, we used total RNA-sequencing to measure the gene expression patterns from all three species. Samples from infected and non-infected plant roots were collected after fourteen days of inoculation with Pba SCRI_1039 and subjected to total RNA-sequencing on an Illumina sequencing platform.
2024-01-17 | E-MTAB-13434 | biostudies-arrayexpress
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
Project description:Although Plasmodiophora brassicae is one of the most common pathogens worldwide, the causal agent of clubroot disease in Brassica crops, resistance mechanisms to it are still only poorly understood. To study the early defense response induced by P. brassicae infection, a global transcriptome profiling of the roots of two near-isogenic lines (NILs) of clubroot-resistant (CR BJN3-2) and clubroot-susceptible (BJN3-2) Chinese cabbage (Brassica rapa) was performed by RNA-seq. Among the 42,730 unique genes mapped to the reference genome of B. rapa, 1,875 and 2,103 genes were found to be up- and down-regulated between CR BJN3-2 and BJN3-2, respectively, at 0, 12, 72, and 96 hours after inoculation (hai). Functional annotation showed that most of the differently expressed genes are involved in metabolism, transport, signal transduction, and defense. Of the genes assigned to plant-pathogen interactions, 151 showed different expression patterns between two NILs, including genes associated with pathogen-associated molecular patterns (PAMPs) and effectors recognition, calcium ion influx, hormone signaling, pathogenesis-related (PR) genes, transcription factors, and cell wall modification. In particular, the expression level of effector receptors (resistance proteins), PR genes involved in salicylic acid (SA) signaling pathway, were higher in clubroot-resistant NIL, while half of the PAMP receptors were suppressed in CR BJN3-2. This suggests that there was a more robust effector-triggered immunity (ETI) response in CR BJN3-2 and that SA signaling was important to clubroot resistance. The dataset generated by our transcriptome profiling may prove invaluable for further exploration of the different responses to P. brassicae between clubroot-resistant and clubroot-susceptible genotypes, and it will strongly contribute to a better understanding of the molecular mechanisms of resistance genes of B. rapa against P. brassicae infection.
2016-02-01 | GSE74044 | GEO