Brassica rapa var. perviridis
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB10521 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR243801_1.fastq.gz | Fastqsanger.gz | |||
| DRR243801_2.fastq.gz | Fastqsanger.gz | |||
| DRR243802_1.fastq.gz | Fastqsanger.gz | |||
| DRR243802_2.fastq.gz | Fastqsanger.gz | |||
| DRR243803_1.fastq.gz | Fastqsanger.gz |
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Project description:Among Brassica rapa, rapid cycling Brassica rapa and Brassica rapa inbred line Kenshin showed contrasting leaf morphology. To identify genes associated with leaf morphology, four distinct F2 progeny of RcBr X Kenshin cross and their parents were selected. Leaf samples were collected from 6 materials, isolated total RNA, and subjected to newly developved 135K microarray. Experiments were performed with three or two biologic
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Project description:Transcription profiling by array of 10 days old Brassica rapa ssp. chinensis seedlings treated with 2mM methyl jasmonate by spraying and harvesting 48 hours past treatment
2015-01-24 | E-MTAB-2386 | biostudies-arrayexpress
Project description:Root and leaf samples from Brassica rapa line R-O-18 were compared. The results will be compared to the same samples hybridised to the Affymetrix Brassica Exon 1.0 ST array.
2010-09-10 | GSE23409 | GEO
Project description:Comparison of transcriptome profiles by Fusarium oxysporum inoculation between Fusarium yellows resistant and susceptible lines in Brassica rapa
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Project description:A mapping population of Brassica rapa (BraIRRI, IMB211xR500) was grown under four external calcium and magnesium concentrations in controlled conditions. RNA was extracted and hybridised to the Affymetrix Brassica Exon 1.0 ST array. The aim of the experiment was to identify cis- and trans- expression quantitative trait loci.
2014-05-21 | GSE44185 | GEO
Project description:The mapping and functional analysis of quantitative traits in Brassica rapa can be greatly improved with the availability of physically positioned, gene-based genetic markers and accurate genome annotation. In this study, deep transcriptome RNA sequencing (RNA-Seq) of Brassica rapa was undertaken with two objectives: SNP detection and improved transcriptome annotation. We performed SNP detection on two varieties that are parents of a mapping population to aid in development of a marker system for this population and subsequent development of high-resolution genetic map. An improved Brassica rapa transcriptome was constructed to detect novel transcripts and to improve the current genome annotation. Deep RNA-Seq of two Brassica rapa genotypesâR500 (var. trilocularis, Yellow Sarson) and IMB211 (a rapid cycling variety)âusing eight different tissues (root, internode, leaf, petiole, apical meristem, floral meristem, silique, and seedling) grown across three different environments (growth chamber, greenhouse and field) and under two different treatments (simulated sun and simulated shade) generated 2.3 billion high-quality Illumina reads. In this experiment, two pools were made, with one pool consisting of 66 samples collected from growth chamber and another pool consisting of 60 samples collected from greenhouse and field. Each pool was sequenced on eight lanes (total 16 lanes) of an Illumina Genome Analyzer (GAIIx) as 100-bp paired end reads.
2014-04-22 | E-MTAB-4276 | biostudies-arrayexpress
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.
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Project description:Root and leaf samples from Brassica rapa line R-O-18 were compared. The results will be compared to the same samples hybridised to the Affymetrix Brassica Exon 1.0 ST array. 6 samples were hybridised. Triplcate samples of 11 day old roots and 2 semi-expanded leaves from 23 day old Brassica rapoa R-O-18 plants.
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Project description:Deep RNA-Seq of two Brassica rapa genotypes—R500 (var. trilocularis, Yellow Sarson) and IMB211 (a rapid cycling variety)—using eight different tissues (root, internode, leaf, petiole, apical meristem, floral meristem, silique, and seedling) grown across three different environments (growth chamber, greenhouse and field) and under two different treatments (simulated sun and simulated shade) generated 2.3 billion high-quality Illumina reads.
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Project description:Cytosine DNA methylation (mC) can silence transposable elements (TEs) and regulate gene expression. However, the mechanism and function of DNA methylation reprogramming during plant development are still largely unknown. To explore the DNA methylation dynamics during the male sexual-lineage development in the Brassicaceae family, we assessed the mC level in meiocyte, microspore and pollen of a Brassica rapa doubled haploid (DH) line by whole genome bisulfite sequencing (WGBS). Analysis of global mC profiles showed that significant reprogramming of CHH methylation occurred in the Brassica rapa male sex cells, similar to that observed in Arabidopsis. Analysis of differential methylation sites identified specific methylation loci in sex cells that can target and possibly regulate gene expression, suggesting a mechanism consistent with that of Arabidopsis. Quite a few long terminal repeat (LTR) transposable elements were activated in meiocyte and microspore, which correlated with reduced DNA methylation. Expression analysis of key genes that affect DNA methylation showed that active methylation and demethylation occurred during male sexual lineage development. These results suggest a conserved DNA methylation reprogramming mechanism during Brassica rapa male sex lineage development. The transcriptome and DNA methylome data obtained will also be useful for other mechanism studies in Brassica rapa.
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