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Brassica campestris ssp. chinensis var. rosularis Tsen et Lee

ABSTRACT: Brassica rapa subsp. chinensis Transcriptome or Gene expression

PROVIDER: PRJNA1077639 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28000539_1.fastq.gz	Fastqsanger.gz
	SRR28000539_2.fastq.gz	Fastqsanger.gz
	SRR28000540_1.fastq.gz	Fastqsanger.gz
	SRR28000540_2.fastq.gz	Fastqsanger.gz
	SRR28000541_1.fastq.gz	Fastqsanger.gz

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Differential expression of salt tolerance related genes in Brassica campestris L. ssp. chinensis (L.) Makino var. communis Tsen et Lee.

Project description:We examined salt tolerance responsive genes in Pak-choi under salt stress and analyze their potential function. The mRNA differential display was used to screen the transcript derived fragments (TDFs) related to salinity tolerance in tolerant and moderately tolerant Pak-choi germplasm. Seventy-eight primer combinations generated 101 differential cDNA fragments, which were divided into 10 expression types. Seven cDNA sequences (GenBank accession Nos. DQ006915~DQ006921) obtained and sequenced were highly homologous to some known expression genes or the genes related to the signaling pathways in plants under different abiotic stress.

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Development of EST-SSR markers in flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee) based on de novo transcriptomic assemblies.

Project description:Flowering Chinese cabbage is one of the most important vegetable crops in southern China. Genetic improvement of various agronomic traits in this crop is underway to meet high market demand in the region, but the progress is hampered by limited number of molecular markers available in this crop. This study aimed to develop EST-SSR markers from transcriptome sequences generated by next-generation sequencing. RNA-seq of eight cabbage samples identified 48,975 unigenes. Of these unigenes, 23,267 were annotated in 56 gene ontology (GO) categories, 6,033 were mapped to 131 KEGG pathways, and 7,825 were assigned to clusters of orthologous groups (COGs). From the unigenes, 8,165 EST-SSR loci were identified and 98.57% of them were 1-3 nucleotide repeats with 14.32%, 41.08% and 43.17% of mono-, di- and tri-nucleotide repeats, respectively. Fifty-eight types of motifs were identified with A/T, AG/CT, AT/AT, AC/GT, AAG/CTT and AGG/CCT the most abundant. The lengths of repeated nucleotide sequences in all SSR loci ranged from 12 to 60 bp, with most (88.51%) under 20 bp. Among 170 primer pairs were randomly selected from a total of 4,912 SSR primers we designed, 48 yielded unambiguously polymorphic bands with high reproducibility. Cluster analysis using 48 SSRs classified 34 flowering Chinese cabbage cultivars into three groups. A large number of EST-SSR markers identified in this study will facilitate marker-assisted selection in the breeding programs of flowering Chinese cabbage.

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Brassica rapa subsp. chinensis cultivar:Makino var. Utilis Tsen et Lee

Project description:Brassica rapa subsp. chinensis cultivar:Makino var. Utilis Tsen et Lee Transcriptome or Gene expression

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Brassica rapa subsp. chinensis Transcriptome

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Integrated Analysis of Transcriptomic and Metabolomic Data Reveals the Mechanism by Which LED Light Irradiation Extends the Postharvest Quality of Pak-choi (Brassica campestris L. ssp. chinensis (L.) Makino var. communis Tsen et Lee).

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