Cucumis sativus
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ABSTRACT:
PROVIDER: PRJNA427603 | ENA |
REPOSITORIES: ENA
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Project description:Genotyping arrays are tools for high throughput genotyping, which is required in genome-wide association studies (GWAS). Since the first cucumber genome draft was reported, genetic maps were constructed mainly based on simple-sequence repeats (SSRs) or on combinations of SSRs and other sequence-related amplified polymorphism (SRAP). In this study we developed the first cucumber genotyping array which consisted of 32,864 single nucleotide polymorphisms (SNPs). These markers cover the cucumber genome every 2.1Kb and have parents/F1 hybridizations as a training set. The training set was validated with Fludigm technology and had 98% concordance. The application of the genotyping array was illustrated by constructed a genetic map of 600 cM in length based on recombinant inbred lines (RIL) population of a 9930XGy14 cross of which compromise of 11564 SNPs. The markers collinearity between the genetic map and genome references of the two parents estimated as R2=0.97. Moreover, this comparison supports a translocation in the beginning of chromosome 5 that occurred in the lineage of 9930 and Gy14 as well as local variation in the recombination rate. We also used the array to investigate the local allele frequencies along the cucumber genome and found specific region with segregation distortions. We believe that the genotyping array together with the training set would be a powerful tool in applications such as quantitative-trait loci (QTL) analysis and GWAS.
2015-05-01 | GSE57294 | GEO
Project description:Transcriptome analysis of cucumber fruit development Raw sequence reads
| PRJNA999046 | ENA
Project description:Cucumis sativus cultivar:cucumber Raw sequence reads
| PRJNA767264 | ENA
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of gene expression profiles of cucumber under short-term chilling stress. The goals of this study are to transcriptome analysis of cucumber leaves under chilling stress. Methods: mRNA profiles of seedlings exposed to an air temperature of 6°C in the absence of light at 0, 2, 6, and 12 h were generated by deep sequencing, in triplicate, using Illumina Hiseq platform. The reference genome and gene model annotation files were downloaded from the genome website （http://cucurbitgenomics.org/）. An index of the reference genome was built using Bowtie v.2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v.2.0.12. qRT–PCR validation was performed using SYBR Green assays. Results: A total of 55.7 million clean reads was generated. Based on the threshold values of absolute value of log2 ratio ≥ 1 and FDR ≤ 0.05, a total of 2113 DEGs was identified at three time points (2, 6, and 12 h). A total of 30 genes was detected at all time points. The number of DEGs increased with time. In total, 100 TFs from 22 families in three subsets were detected. And 19 kinase families were identified in three subsets. The DEGs identified by RNA sequencing were confirmed by qRT-PCR analysis, indicating that the data were reliable. These findings provide information that can be useful for investigating the molecular mechanisms underlying the response to chilling stress in cucumber and other plants. Conclusions: The results presented here reveal changes in the transcriptome profile of cucumber in response to chilling stress. Exposure to a low temperature induced genes involved in hormone regulation, lipid metabolism, and photosynthesis, including NAC, WRKY, AP2/ERF, ERD, MYB as well as zinc finger TFs and protein kinases such as receptor-like protein kinase, MAPK, and CDK. Most TFs were upregulated whereas CDKs were downregulated. These findings provide information that can be useful for investigating the molecular mechanisms underlying the response to chilling stress in cucumber and other plants.
2018-08-20 | GSE111998 | GEO
Project description:Genotyping by Sequencing (GBS) of Cucumber (Cucumis sativus L.) Raw sequence reads
| PRJNA910816 | ENA
Project description:To identify the differentially expressed genes(DEGs) in the ventral and dorsal of cucumber bending fruits，cucumber bending fruit mRNA profiles of 2-day-old ventral and dorsal were generated by deep sequencing. After removing the low quality reads, the total number of clean reads in two library were 27.07 million and16.52 million, accounted for 85.21% and 80.71% of total reads .We identified a total of 4313 sequences differentially expressed in ventral and dorsal of bending fruit with a 2-fold or greater change and P < 0.01 , the Dorsal (D2) served as a control, in which 2351 up-regulated genes and 1962 down-regulated genes.For up-regulated genes, protein kinase activity, ethylene mediated signaling pathway, regulation of cell shape, auxin polar transport were significantly enriched, whereas down-regulated genes, the functional classes photosynthesis, oxidation reduction, response to auxin stimulus were significantly enriched. Moreover, among DEGs related to ethylene, we identified an ERF/AP2 gene CsERF025 that was significant difference in the dorsal and ventral of cucumber. up-regulation of CsERF025 in cucumber promoted fruit bendng and Increased the fruit bending angle, suggesting that CsERF025 plays an important role in cucumber bending fruit.
2019-12-07 | GSE91085 | GEO