Brassica rapa subsp. chinensis
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA298459 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2626161_1.fastq.gz | Fastqsanger.gz | |||
| SRR2626161_2.fastq.gz | Fastqsanger.gz | |||
| SRR2626153_1.fastq.gz | Fastqsanger.gz | |||
| SRR2626153_2.fastq.gz | Fastqsanger.gz | |||
| SRR2626154_1.fastq.gz | Fastqsanger.gz |
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Project description:Next Generation Sequencing of non-heading Chinese cabbage (Brassica rapa ssp. chinensis)
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Project description:Next-generation sequencing has been applied on seedling of two genotypes of noheading Chinese cabbage, Huaq and Wut. The goals of this study are to compare the different expression of small RNAs which is possible effect the phynotype of close genetic relation cultivars.
2014-06-14 | GSE38722 | GEO
Project description:Leafy head is the main product of Chinese cabbage, and also is the primary character to determine its yield and quality. Cloning and characterizing key genes involved in leafy head formation is imperative for varietal improvement in Chinese cabbage. From an EMS mutagenesis population of a heading wild-type ‘FT’ of Chinese cabbage, we identified two allelic non-heading mutants, nhm3-1 and nhm3-2. Genetic analysis showed that the mutant character was controlled by a single recessive gene. MutMap and Kompetitive Allele Specific PCR genotyping results revealed that BraA05g012440.3C encoding an ent-kaurenoic acid oxidase 2 which functions in the GA biosynthetic pathway, was the causal gene for leafy-head formation, and we named it as BrKAO2. Two kinds of non-synonymous mutations in the second exon of BrKAO2 were responsible for the nhm3-1 and nhm3-2 mutant phenotype, respectively. BrKAO2 was expressed at all stages of leaf development, and there was no significant difference between the wild-type ‘FT’ and the mutants nhm3-1 and nhm3-2. The mutant phenotype was restored to the wild-type through the application of exogenous GA3. RNA-Seq was performed on the rosette leaves of wild-type ‘FT’, nhm3-1 and nhm3-1+GA3 plants, and a number of key genes involving in GA biosynthesis, signal transduction and leafy head development were identified. These findings indicated that BrKAO2 is responsible for leafy head formation of nhm3, and a new mechanism of the leafy head formation in Chinese cabbage was proposed.
2021-09-12 | GSE183651 | GEO
Project description:Next-generation sequencing has been applied on seedling of two genotypes of noheading Chinese cabbage, Huaq and Wut. The goals of this study are to compare the different expression of small RNAs which is possible effect the phynotype of close genetic relation cultivars. Two genotypes small mRNA profiles of 21-day old Huaq and Wut seedling were generated by deep sequencing, using Illumina GAIIx.
2014-06-14 | E-GEOD-38722 | biostudies-arrayexpress
Project description:Deep sequencing provided evidence that a novel subset of small RNAs were derived from the chloroplast genome of Chinese cabbage (Brassica rapa) and Arabidopsis (Ler). The chloroplast small RNAs (csRNAs) include those derived from mRNA, rRNA, tRNA and intergenic RNA. The rRNA-derived csRNA were preferentially located at the 3M-CM-"M-BM-^@M-BM-^Y-ends of the rRNAs, while the tRNA-derived csRNAs were mainly located at 5M-CM-"M-BM-^@M-BM-^Y-termini of the tRNAs. After heat treatment, the abundance of csRNAs decreased in chinese cabbage seedlings, except those of 24 nt in length. The novel heat-responsive csRNAs and their locations in the chloroplast were verified by Northern blotting. The regulation of some csRNAs to the putative target genes were identified by real-time PCR. Our results indicated that high temperature regulated the production of some csRNAs, which may have potential roles in transcriptional or post-transcriptional regulation, and affected putative target genes expression in chloroplast. Examination of two replicates of heat treated (HT) and control (MT) Chinese cabbage sample respectively, and one Arabidopsis (Ler) RNA sample.
2012-03-30 | E-GEOD-28281 | biostudies-arrayexpress
Project description:Deep sequencing provided evidence that a novel subset of small RNAs were derived from the chloroplast genome of Chinese cabbage (Brassica rapa) and Arabidopsis (Ler). The chloroplast small RNAs (csRNAs) include those derived from mRNA, rRNA, tRNA and intergenic RNA. The rRNA-derived csRNA were preferentially located at the 3â-ends of the rRNAs, while the tRNA-derived csRNAs were mainly located at 5â-termini of the tRNAs. After heat treatment, the abundance of csRNAs decreased in chinese cabbage seedlings, except those of 24 nt in length. The novel heat-responsive csRNAs and their locations in the chloroplast were verified by Northern blotting. The regulation of some csRNAs to the putative target genes were identified by real-time PCR. Our results indicated that high temperature regulated the production of some csRNAs, which may have potential roles in transcriptional or post-transcriptional regulation, and affected putative target genes expression in chloroplast.
2012-03-31 | GSE28281 | GEO
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.
2013-05-01 | E-MTAB-4192 | biostudies-arrayexpress
Project description:Three Chinese Cabbage parents and their F2 generation Raw sequence reads
| PRJNA817372 | ENA
Project description:To identify genes associated with genic male sterility (GMS) that could be useful for hybrid breeding in Chinese cabbage (Brassica rapa ssp. pekinensis), floral bud transcriptome analysis was carried out using a B. rapa microarray with 300,000 probes (Br300K). Among 47,548 clones deposited on a Br300K microarray with seven probes of 60 nt length within the 3' 150 bp region, a total of 10,622 genes were differentially expressed between fertile and sterile floral buds; 4,774 and 5,848 genes were up-regulated over 2-fold in fertile and sterile buds, respectively. However, the expression of 1,413 and 199 genes showed fertile and sterile bud-specific features, respectively. Genes expressed specifically in fertile buds, possibly GMS-related genes, included homologs of several Arabidopsis male sterility-related genes, genes associated with the cell wall and synthesis of its surface proteins, pollen wall and coat components, signaling components, and nutrient supplies. However, most early genes for pollen development, genes for primexine and callose formation, and genes for pollen maturation and anther dehiscence showed no difference in expression between fertile and sterile buds. Some of the known genes associated with Arabidopsis pollen development showed similar expression patterns to those seen in this study, while others did not. BrbHLH89 and BrMYP99 are putative GMS genes. Additionally, 17 novel genes identified only in B. rapa were specifically and highly expressed only in fertile buds, implying the possible involvement in male fertility. All data suggest that Chinese cabbage GMS might be controlled by genes acting in post-meiotic tapetal development that are different from those known to be associated with Arabidopsis male sterility. A total of 14 chips were used for the microarray experiment. Experiments were performed with two biological replicates.
2013-10-22 | E-GEOD-47665 | biostudies-arrayexpress
Project description:To identify genes associated with genic male sterility (GMS) that could be useful for hybrid breeding in Chinese cabbage (Brassica rapa ssp. pekinensis), floral bud transcriptome analysis was carried out using a B. rapa microarray with 300,000 probes (Br300K). Among 47,548 clones deposited on a Br300K microarray with seven probes of 60 nt length within the 3' 150 bp region, a total of 10,622 genes were differentially expressed between fertile and sterile floral buds; 4,774 and 5,848 genes were up-regulated over 2-fold in fertile and sterile buds, respectively. However, the expression of 1,413 and 199 genes showed fertile and sterile bud-specific features, respectively. Genes expressed specifically in fertile buds, possibly GMS-related genes, included homologs of several Arabidopsis male sterility-related genes, genes associated with the cell wall and synthesis of its surface proteins, pollen wall and coat components, signaling components, and nutrient supplies. However, most early genes for pollen development, genes for primexine and callose formation, and genes for pollen maturation and anther dehiscence showed no difference in expression between fertile and sterile buds. Some of the known genes associated with Arabidopsis pollen development showed similar expression patterns to those seen in this study, while others did not. BrbHLH89 and BrMYP99 are putative GMS genes. Additionally, 17 novel genes identified only in B. rapa were specifically and highly expressed only in fertile buds, implying the possible involvement in male fertility. All data suggest that Chinese cabbage GMS might be controlled by genes acting in post-meiotic tapetal development that are different from those known to be associated with Arabidopsis male sterility.
2013-10-22 | GSE47665 | GEO