Radish (Raphanus sativus L.)
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ABSTRACT:
PROVIDER: PRJNA511407 | ENA |
REPOSITORIES: ENA
Similar Datasets
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: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:Radish (Raphanus sativus L., n = 9) is one of the major vegetables in Asia. Since the genomes of Brassica and related species including radish underwent genome rearrangement, it is quite difficult to perform functional analysis based on the reported genomic sequence of Brassica rapa. Therefore, we performed genome sequencing of radish. Short reads of genomic sequences of 191.1 Gb were obtained by next-generation sequencing (NGS) for a radish inbred line, and 76,592 scaffolds of ? 300 bp were constructed along with the bacterial artificial chromosome-end sequences. Finally, the whole draft genomic sequence of 402 Mb spanning 75.9% of the estimated genomic size and containing 61,572 predicted genes was obtained. Subsequently, 221 single nucleotide polymorphism markers and 768 PCR-RFLP markers were used together with the 746 markers produced in our previous study for the construction of a linkage map. The map was combined further with another radish linkage map constructed mainly with expressed sequence tag-simple sequence repeat markers into a high-density integrated map of 1,166 cM with 2,553 DNA markers. A total of 1,345 scaffolds were assigned to the linkage map, spanning 116.0 Mb. Bulked PCR products amplified by 2,880 primer pairs were sequenced by NGS, and SNPs in eight inbred lines were identified.
| S-EPMC4195494 | biostudies-literature
Project description:Spontaneous tumors can develop in different organs of various plant species without any pathogen infection and, as a rule, appear in plants with a certain genotype: Mutants, interspecific hybrids, etc. In particular, among the inbred lines of radish (Raphanus sativus L.), lines that form spontaneous tumors on the taproot during the flowering period were obtained many years ago. In this work, we analyzed the differential gene expression in the spontaneous tumors of radish versus the lateral roots using the RNA-seq method. Data were obtained indicating the increased expression of genes associated with cell division and growth (especially genes that regulate G2-M transition and cytokinesis) in the spontaneous tumor. Among genes downregulated in the tumor tissue, genes participating in the response to stress and wounding, mainly involved in the biosynthesis of jasmonic acid and glucosinolates, were enriched. Our data will help elucidate the mechanisms of spontaneous tumor development in higher plants.
| S-EPMC8147785 | biostudies-literature