Silicon supplemented cucumber cultures
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR662024.fastq.gz | Fastqsanger.gz | |||
| ERR662025.fastq.gz | Fastqsanger.gz | |||
| ERR662026.fastq.gz | Fastqsanger.gz | |||
| ERR662027.fastq.gz | Fastqsanger.gz | |||
| ERR662028.fastq.gz | Fastqsanger.gz |
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Project description:Cucumber (Cucumis sativus L.) is an economically important vegetable cultivated all over the world. Grafting can produce bloomless or sparse-bloom cucumber, which is welcomed by increasing consumers. Bloom granule is tine glandular hair, which is hard and rare studied on its formation and related genes. Mutifunctional RNA-seq is a recently developed analytical approach for transcriptome profiling via high-throughput sequencing and has been recently applied to a wide variety of organisms, which provide us reliable technical means detect bloom formation and related genes. In this study, we chose a cucumber inbred line (Shannong No.5) and two pumpkin rootstock lines as materials, and constructed four tested cucumbers, grew plants in “Yamazaki cucumber nutrient solution formula” prepared by deionized water, treated plants with or without 1.7mM potassium silicate 2 hours before collecting pericarp. Each treatment were duplicated twice.16 cDNA libraries were constructed from pericarp of a cucumber inbred line (own-rooted cucumber), C/C (self-grafted cucumber), M/C (More bloom, cucumber grafted onto “3225” rootstock) and L/C(Less bloom, cucumber grafted onto “3212” rootstock). We obtained 17,215,769~17,529,047 high quality reads, and 18,804~19,358 genes from each sample. All reads can be mapped to the cucumber genome (Version 2). By RPKM comparing, we got 38 comparing combinations with differentially expressed genes (DEGs), obtained 38 significantly expressed combinations by FDR≤0.001 and the absolute value of log2Ratio≥1 as the thresholds. These results suggest that there are many differences and genes expression mode among effects of grafting or added silicon. This study addresses a preliminary analysis and offers a foundation for future genomic research in the bloom formation of cucumber.
2020-04-02 | GSE79829 | GEO
Project description:Salinity seriously reduces the yield and quality of crops. Silicon (Si) has been widely reported to have beneficial effects on plant growth and development under salt stress. However, the mechanism is still poorly understood. In an attempt to identify genes or gene networks that may be orchestrated to improve salt tolerance of cucumber plants, we profiled the RNA-seq transcriptomes of both control and salt-stressed cucumber leaves in the presence or absence of added Si. The comparative transcriptome analysis revealed that Si plays an important role in shaping the transcriptome of cucumber: the expression levels of >1,000 genes (differtially expressed genes, DEGs) were changed in response to Si treatment as compared with the control, and these genes were mainly involved in ion transport, hormone and signal transduction, biosynthesis and metabolic processes, stress and defense responses, and antioxidant activity. Under salt stress, many genes functionally associated with metabolic processes and responses to environmental stimuli were strongly up- or down-regulated in their expressions. Si treatment showed a tendency that induced the transcriptomic profile of salt-stressed cucumber back to that of the control with large majority of Na down-regulated DEGs and about half of Na up-regulated DEGs being adjusted back to CT levels. This study provides a novel insight into the mechanism for Si-mediated alleviation of salt stress in plants at the transcriptome level, and it suggests that Si may act as an elicitor to precondition cucumber plants and induce salt tolerance.
2018-06-27 | GSE116265 | GEO
Project description:Silicon (Si) has long been known to play a major physiological role in certain organisms, including some sponges and many diatoms and higher plants, leading to the recent identification of multiple proteins responsible for silicon transport in a range of algal and plant species. In mammals, despite several convincing studies suggesting that silicon is an important factor in bone development and connective tissue health, there is a critical lack of understanding in biochemical pathways that enable silicon homeostasis. Here we report the identification of a mammalian efflux silicon transporter, namely Slc34a2 (also known as NaPiIIb), which was upregulated in the kidneys of rats following chronic dietary silicon deprivation. When heterologously expressed in Xenopus laevis oocytes, the protein displayed marked silicon transport activity, specifically efflux, comparable to plant OsLsi2 transfected in the same fashion and independent of sodium and/or phosphate influx. This is the first evidence for a specific active transporter protein for silicon in mammals and suggests an important role for silicon in vertebrates.
2017-04-05 | GSE58404 | GEO
Project description:Transcriptomic dynamics provides an insight into the mechanism for silicon-mediated alleviation of salt stress in cucumber plants
| PRJNA477930 | ENA
Project description:Although Cochliobolus miyabeanus is an important fungal leaf pathogen on rice plants worldwide, it is largely neglected by molecular plant phytopathologists. To shed new light on the molecular and genetic basis of the rice – C. miyabeanus interaction, we compared the transcriptome of rice leaves 12h post inoculation to uninfected leaves. Even though usable sources of resistance against brown spot disease caused by C. miyabeanus are scarce, silicon application emerges as a sustainable protection strategy. Many articles report the beneficial effect of silicon on brown spot resistance. however the underlying mechanisms remain largely unclear. The influence of silicon application on the transcriptome of healthy and infected rice leaves 12hpi was compared as well in an attempt to disentangle the modulation of silicon-induced brown spot resistance.
2014-02-25 | GSE55330 | GEO
Project description:Corynespora leaf spot (CSL), caused by Corynespora cassiicola, has become one of the most important foliar diseases of cultivated cucumber. However, the defense mechanisms of cucumber plants in response to C. cassiicola are still poorly understood. Here, proteins from resistant plants were analyzed using isobaric tags for relative and absolute quantification (iTRAQ). A total of 286 differentially expressed proteins were identified (P<0.05, ratio>1.2 or <0.83) at 6 and 24 h after pathogen inoculation in the resistant cucumber cultivar Jinyou 38. Some of the early responses to C. cassiicola infection were revealed, and four vital clues regarding the resistance of Cucumis sativus to cucumber CLS were discovered. First, the proteomic approach revealed the modulation of signaling pathways in resistant cucumber plants in response to C. cassiicola infection. Second, the plant immune system recognizes the pathogen and initiates the expression of basal immune response proteins, including those related to defense and stress responses, signal transduction, cell metabolism and redox regulation. Third, the common stress pathways were activated by C. cassiicola; in particular, mildew resistance locus O (MLO) proteins played a crucial role in the prevention of CLS. Fourth, the rapid activation of the carbohydrate and secondary metabolic pathways, the modification and reinforcement of cell walls, and the adjustment of the apoplectic environment to high-stress conditions were crucial in cucumber resistance to CLS disease. Overall, our data increase the knowledge of incompatible interactions between plants and pathogens and provide new insight into the contribution of molecular processes in cucumber to disease resistance.
2019-09-26 | PXD012903 | Pride
Project description:Previous study we have reported the cucumber TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) family gene BRANCHED1 (CsBRC1) as a main transcription factor functions to regulate shoot branching. Here, we found CsBRC1 (CsTCP18b in this study) had a paralogous gene CsTCP18a. To investigate whether the function of CsTCP18a was same as CsTCP18b, we carried out biochemical experiments and genetic transformation. The Real-Time PCR and in situ hybridization showed that CsTCP18a displayed different expression patterns in cucumber compared with CsTCP18b. Ectopic expression of CsTCP18a in Arabidopsis tcp18 (brc1) mutants resulted in a decreased number of rosette branches and rosette leaves, whereas silencing CsTCP18a in cucumber only led to a deformed true leaf of seedling without influencing the shoot branching. RNA-seq analysis of wild-type plants and CsTCP18a-RNAi lines implicated that CsTCP18a regulated early leaf development of cucumber through affecting the transcripts of auxin and cytokinin related genes. Further studies indicated that CsTCP18a could directly interact with CsTCP10 and CsTCP18b in vitro and in vivo. Therefore, our data suggested that CsTCP18a had functional redundancy with CsTCP18b in inhibiting axillary buds outgrowth, and it could also regulate leaf development during cucumber seedling.
2022-11-20 | GSE140737 | GEO
Project description:The supply of soluble silicon (Si) to plants has been associated with many benefits that remain poorly explained and often contested. In this work, the effect of Si was studied on wheat plants under both control and pathogen stress (Blumeria graminis f.sp. tritici (Bgt)) conditions by conducting an exhaustive transcriptomic analysis (55,000 genes) aimed at comparing the differential response of plants under four treatments. The response to the supply of Si on control (uninfected) plants was limited to 47 genes providing little evidence of regulation of a specific metabolic process. Plants reacted to inoculation with Bgt by an up-regulation of many genes linked to stress and metabolic processes and a down-regulation of genes linked to photosynthesis. Supplying Si to inoculated plants largely prevented disease development, a phenotypic response that translated into a nearly perfect reversal of genes regulated by the effect of Bgt alone. These results suggest that Si plays a limited role on a plant’s metabolism in absence of stress, even in the case of a high-Si accumulating monocot such as wheat. On the other hand, the benefits of Si, in the form of biotic stress alleviation, were remarkably aligned with a counter-response to transcriptomic changes induced by the pathogen Bgt. Keywords: stress type and molecule effect
2009-06-30 | GSE12936 | GEO
Project description:We compared organ specific chloroplast gene expression in cucumber between fully developed leaves (12th counting from the bottom of plant) and growing tips, female flowers, young leaves, young fruits (3-5 cm long). We have also characterized chloroplast gene transcription in cucumber etiolated seedlings in comparison to mature cucumber leaves.
2011-06-30 | E-MEXP-3227 | biostudies-arrayexpress
Project description:The experiment was made do to assess the influence of increased salt concentration on cucumber chloroplast transcription. We used 0,4M NaCl water solution and we checked its influence on plants after 0, 4, 8, 24, 48 hours. We have also measured changes in chloroplast gene expression after recovery of plants in water (48 hours of 0,4M NaCl solution treatment followed by 48 hours in clean water). Other growth conditions weren't changed comparing to those of standard plants growth in our experiments (check: versatile chamber growth protocol)
2011-09-10 | E-MEXP-3234 | biostudies-arrayexpress