Eucalyptus spp. transcriptome response to field water deficit
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PROVIDER: PRJNA48983 | ENA |
REPOSITORIES: ENA
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Project description:Eucalyptus leaf and stem proteomes-water deficit experiment-two genotypes
2012-03-23 | PRD000259 | Pride
Project description:Cocoa is a crop of cultural, nutritional and social importance in Latin America. Cocoa production is mainly supported by smallholders and is central for the food security of these farmer families. Despite being part of their everyday diet and an important source of antioxidants and other healthy bioactive compounds, cocoa cropping is also a solid source of stable incomes supporting the livelihood of farmer families. Water deficit stress is one of the main limiting factors affecting crop yields. The ability of plants to tolerate or recover from the effects associated with this abiotic stress is of immense importance in terms of improvement in the context of climate change. Despite the emergence of functional genomics and phenotyping tools to approach these responses, many of these mechanisms are still little understood for many tropical food crops such as cocoa. For a transcriptomic analysis were selected 2 cocoa genotypes, from a hydric stress assay established in a greenhouse. 5-month-old plants of T. cacao of the genotypes EET 8 and TSH565 were tested for water deficit trial. A divided plot experimental design was applied: the hydric state of the 2 genotypes was evaluated with two levels: field capacity and water deficit by irrigation suspension during a period that generates severe stress (Leaf Water Potential of -3.0 Mpa). The irrigation suspension lasted 52 days.
2023-01-31 | E-MTAB-8525 | biostudies-arrayexpress
Project description:By sequencing 36 cDNA libraries with Illumina technology, we identified genes differentially expressed in soybean plants in response to water deficit and genes that were either up- or down-regulated in different periods of the day. Of 54,175 predicted soybean genes (Glyma v1.1), 35.52% exhibited expression oscillations in a 24 h period. This number increased to 39.23% when plants were submitted to water deficit. Major differences in gene expression were observed in the control plants from late day (ZT16) until predawn (ZT20) periods, indicating that gene expression oscillates during the course of 24 h in normal development. Under water deficit, dissimilarity increased in all time-periods, indicating that the applied stress influenced gene expression. Results suggest that time of day, as well as light and temperature oscillations that occur considerably affect the regulation of water deficit stress response in soybean plants.
2015-07-07 | GSE69469 | GEO
Project description:Soybean plants were subjected to water deficit, heat stress, and combination of water deficit and heat stress. Flower parts, sepal, anther, ovary and stigma were collected from 8-10 different plants at R1 stage growing under three above mentioned stress conditions, and under control conditions 10 days after initiation of the stresses. Differential gene expression compared to control was studied using RNAseq method.
2022-12-04 | GSE218146 | GEO
Project description:Purpose: to screen the candidate genes involved in the peanut drought stress response, we conducted global transcriptome analysis of peanut plants challenged with water deficit and ABA, using the Illumina HiSeq2000 sequencing platform. Methods: a sequences library of Yueyou7 were constructed at first. Then the profile of diffentialy expressed genes (DEGs) under three different treatments (control, water deficit without ABA, and water deficit with ABA) were conducted based on above sequence library. For sequencing library construction, plants were grown under normal conditions, as described previously , Seeds were planted in soil and kep in the greenhouse at temperature of 25-30℃ and water well. Three tissues (leaves, roots, and stems) were collected at three development stages (four-leaf, flowering and podding stages), respectively. Then all of these tissues were mixed to extract the total RNA for sequence library construction. For DEGs study, two-week-old plants were divided into three groups with three independent replication: (1). Water deficit without ABA groups. Plants directly steeped in water containing 30% PEG600 for 30 min in this groups. (2) Water deficit with ABA groups. Plant was subjected to 100 µmol/L ABA for 30 min and then steeped in water containing 30% PEG6000 for 30 min in this groups, (3) Control. Plants steeped in H2O. All treatments were conducted in parallel. After treatments, Total RNA was extracted from 100 mg of plant material, and RNA integrity was checked by gel electrophoresis. Also RNA quality was checked and RNA was quantified using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA) and Nanodrop ND-1000 (Thermo Scientific, Waltham, USA). Results: we generated 4.96×107 raw sequence reads and assembled the high quality reads into 92,390 unique genes. Compared with the control, we found that 621 genes (≥1.5 fold change) responded rapidly to water deficit and 2665 genes (≥1.5 fold change) responded rapidly to ABA. We found 279 genes that overlapped between water deficit and ABA responses, 264 genes that showed the same trend in expression while 15 genes expression that showed opposite trend. Among the identified genes, 257 showed high induction by ABA (>5 fold), and 19 showed high induction by drought (>5 fold). In addition, we identified 100 transcription factor genes among the ABA-inducible genes but only 22 transcription factor genes among the water deficit-inducible genes. Conclusions: we identified genes differentially expressed in the early response to water deficit or ABA. These genes were annotated with GO functional categories for water deficit (33 categories) or ABA (31 categories). We found that only 19 genes were highly induced by water deficit, but 257 genes were highly induced by ABA. Our previous work has examined many of these genes and our future work will reveal their functions and relationships. These data will facilitate functional genomic studies and have established a biotechnological platform for examination of the early drought- and ABA-responsive transcriptome regulatory network in peanut.
2014-05-13 | GSE56439 | GEO
Project description:Periods of soil water deficit could occur at any time during the crop season, but maize is particularly sensitive to water stress around flowering time. At this time the stress usually causes remarkable yield loss. Heading time, which is just before tassel flowering, is one of the most important stages that maize productivity would be affected severely if plants encounter water stress. The whole-genomic gene expression changes of maize plants in response to water deficit stress at this stage have not been studied. The present work utilized an Arizona Maize Oligonucleotide Array Version 1.9，which was consisted of A and B slides carrying with a total of 57,452 maize 70-mer oligonucleotides, was used to monitor gene expression profile changes in maize leaves subjected to 1 day and 7 days water-deficit stress respectively at the heading stage. Keywords: stress response
2008-02-25 | GSE10596 | GEO
Project description:A transcriptome analysis of P. alba cambial zone was performed with the aim to unravel the gene network underlying the response to water deficit within the cambium and the differentiating derivatives cambial cells. Water stress was induced on one-year-old plant of Populus alba by withholding water for 9 days. At that time, leaf Ψpd fell down to -0,8 MPa resulting in a significant reduction of the stomatal conductance, CO2 assimilation, consistent increment of stem shrinkage and cessation of the radial growth. These effects were almost fully reversed by re-hydration. The water deficit resulted in changes in gene expression that affected a few functional categories as protein metabolism, cell wall metabolism, stress response, transporters and transcriptional regulation. The function of up- and down-regulated genes is discussed considering the physiological response of the plants to water deficit.
2009-12-22 | GSE18675 | GEO
Project description:By sequencing 36 cDNA libraries with Illumina technology, we identified genes differentially expressed in soybean plants in response to water deficit and genes that were either up- or down-regulated in different periods of the day. Of 54,175 predicted soybean genes (Glyma v1.1), 35.52% exhibited expression oscillations in a 24 h period. This number increased to 39.23% when plants were submitted to water deficit. Major differences in gene expression were observed in the control plants from late day (ZT16) until predawn (ZT20) periods, indicating that gene expression oscillates during the course of 24 h in normal development. Under water deficit, dissimilarity increased in all time-periods, indicating that the applied stress influenced gene expression. Results suggest that time of day, as well as light and temperature oscillations that occur considerably affect the regulation of water deficit stress response in soybean plants. Gene expression analysis of soybean leaves under water deficit in 6 periods of day by sequencing 36 libraries, in triplicate, in Illumina platform.
2015-07-07 | E-GEOD-69469 | biostudies-arrayexpress
Project description:The study was conducted to identify differentially expressed polyethylene glycol (PEG) induced water stress responsive genes in E. grandis. Forty day old rooted cutting of E. grandis was subjected to -0.225 MPa PEG treatment and total RNA was isolated from leaves of water treated control and PEG treated samples after three hours of treatment. The differential expression of water stress responsive genes was analyzed using microarray technique. Agilent two-color experiment, Organism: Eucalyptus,Custom Agilent Eucalyptus 8x60k Microarray Gene expression (AMADID: 59849 ) designed by Genotypic Technology Pvt.Ltd.
2016-07-03 | E-GEOD-73106 | biostudies-arrayexpress
Project description:affy_popsec_nancy_leaves_poplar - affy_popsec_nancy_leaves2007_poplar - This project aims to identify genes of interest for water deficit acclimation and/or adaptation in a tree species: poplar. We look for genes and gene expression networks related to drought stress. We intend to analyse the transcriptome in mature leaves, in two genotypes, Carpaccio and Soligo, at various stages and intensities of stress. During water deficit, leaves underwent many processes aiming to maintain cells integrity such as water status adjustment through osmoregulation or cell detoxication. These analyses intend to identify genes of interest involved in homeostasis maintenance. The comparison between medium and severe stress intensities and between early and long term stresses will power the selection of genes of interest. The co-analysis of two genotypes of contrasted tolerance to water deficit should help to discriminate genes presenting a potential adaptative character from genes responding passively to the constraint-In a first experiment, two poplar clones, Soligo (S) and Carpacio (C) were submitted to 4 treatments: control, mild water deficit, moderate water deficit (12-day long for both) and early-drought stress (about 36-h long). Growth and physiology was characterised on a batch of plants and samples collected on another batch of plants. In a second experiment, two poplar clones, Soligo (S) and Carpacio (C) were submitted to 2 treatments: control and moderate water deficit. Mature leaves were collected and total RNAs were extracted from each tree individually. Two pools of 3 (or 2) individuals were made using equimolar ratio. A pool is considered as one biological replicate and corresponds to one Affimetrix slide. Keywords: treated vs untreated comparison
2011-01-15 | GSE17230 | GEO