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
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.
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.
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.
Project description:Low-intensity (10 ?mol m-2 s-1) white LED (light-emitting diode) light effectively delayed senescence and maintained the quality of postharvest pakchoi during storage at 20 °C. To investigate the mechanism of LED treatment in maintaining the quality of pakchoi, metabolite profiles reported previously were complemented by transcriptomic profiling to provide greater information. A total of 7761 differentially expressed genes (DEGs) were identified in response to the LED irradiation of pak-choi during postharvest storage. Several pathways were markedly induced by LED irradiation, with photosynthesis being the most notable. More specifically, porphyrin and chlorophyll metabolism and glucosinolate biosynthesis were significantly induced by LED irradiation, which is consistent with metabolomics reported previously. Additionally, chlorophyllide a, chlorophyll, as well as total glucosinolate content was positively induced by LED irradiation. Overall, LED irradiation delayed the senescence of postharvest pak-choi mainly by activating photosynthesis, inducting glucosinolate biosynthesis, and inhibiting the down-regulation of porphyrin and chlorophyll metabolism pathways. The present study provides new insights into the effect and the underlying mechanism of LED irradiation on delaying the senescence of pak-choi. LED irradiation represents a useful approach for extending the shelf life of pak-choi.