Transcription profiling by array of Arabidopsis overexpressing ERD15 after treatment with abscisic acid
ABSTRACT: The aim of this experiment is to understand the impact of overexpression of ERD15 on the transcriptome of Arabidopsis thaliana. ERD15 was isolated from a screen for genes rapidly induced after pathogen treatment from Arabidopsis. This gene was originally found as early responsive to drought (Kiyosue et al., 1994, Plant Physiol 106, 1707). ABA is central phytohormone in drought response, but increasing information is pointing to its significant role in pathogen responses as well. We are interested to see the effect of this hormone on plants overexpressing ERD15 compared to control plants. The samples (rosette leaves)will be harvested from 3-week old soil grown plants 90 min after spraying with 100 micromolar ABA. Comparison will be made with non-treated plant samples. Experimenter name = Elina Helenius; Experimenter phone = +358 9 191 59085; Experimenter fax = +358 9 191 59079; Experimenter institute = University of Helsinki; Experimenter address = Viikinkaari 5 D; Experimenter address = P.O.Box 56; Experimenter address = Helsinki; Experimenter zip/postal_code = 00014; Experimenter country = Finland Experiment Overall Design: 4 samples were used in this experiment
Project description:The aim of this experiment is to understand the impact of overexpression of ERD15 on the transcriptome of Arabidopsis thaliana. ERD15 was isolated from a screen for genes rapidly induced after pathogen treatment from Arabidopsis. This gene was originally found as early responsive to drought (Kiyosue et al., 1994, Plant Physiol 106, 1707). ABA is central phytohormone in drought response, but increasing information is pointing to its significant role in pathogen responses as well. We are interested to see the effect of this hormone on plants overexpressing ERD15 compared to control plants. The samples (rosette leaves)will be harvested from 3-week old soil grown plants 90 min after spraying with 100 micromolar ABA. Comparison will be made with non-treated plant samples. Experimenter name = Elina Helenius Experimenter phone = +358 9 191 59085 Experimenter fax = +358 9 191 59079 Experimenter institute = University of Helsinki Experimenter address = Viikinkaari 5 D Experimenter address = P.O.Box 56 Experimenter address = Helsinki Experimenter zip/postal_code = 00014 Experimenter country = Finland Keywords: compound_treatment_design Overall design: 4 samples were used in this experiment
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. 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.
Project description:Abiotic stress and more specifically drought is the major limiting factor for sunflower production. ABA is a key hormone for drought stress response in plants and sunflower. This experiment aims at identifying ABA responsive pathways in order to better understand sunflower responses to drought. We studied in parallel microRNA profiles on the same samples and we will try to identify sunflower microRNA regulated genes in response to ABA. The ultimate goal will be improve sunflower breeding through selection of key drought response genes.-The experiment consisted of 3 repeats of four 12-day-old-plantlets of sunflower genotype SF193 (INRA code: XRQ) grown in growth chamber conditions and submitted to a 6-hour-treatment of 10 µM absissic acid or not. Growth conditions were 14h light at 23°C and 10h night at 20°C under fluorescent bulbs. Plants were grown in 6 hydroponic boxes containing 20 litres of aerated liquid culture medium (as described in Massonneau et al., 2001 Planta). Leaves (not cotyledons) 1 to 4 were harvested 4 hours after light onset and frozen immediately in liquid nitrogen. 6 arrays - SUNFLOWER; treated vs untreated comparison
Project description:4 weeks old rooted plantlets of P. × canescens (Clone INRA717 1-B4) were cultivated in hydroponics in 2 l pots in Long Ashton nutrient solution in a culture room for 8 weeks before treatments started. Three treatments were applied to the plants: control treatment (-ABA), continuous 100 µM ABA treatment (+ABA) and discontinuous 100 µM ABA treatment (±ABA). ABA was fed to +ABA plants during the whole treatment period of 30 days. ABA was fed to ±ABA plants for three days in two weeks. Developing xylem and mature xylem were collected separately during the harvest and shortly frozen in liquid nitrogen. RNA was extracted from these samples and followed by RNA-sequencing.
Project description:We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome under drought, cold, high-salinity and ABA treatment conditions and idenfied many stress- or ABA- responsive putative functional RNAs and fully-overlapping sense-antisense transcripts in Arabidopsis genome. Keywords: stress response Two-week-old Arabidopsis plants grown on the agar plates were subjected to the stress- or ABA- treatments. The total RNA was prepared from the treated- and untreated- plants, and used for the microarray hybridization. Three replicative hybridization experiments for each strand array were carried out using the independent biological RNA samples.
Project description:4 weeks old rooted plantlets (P. tremula × tremuloides) of wildtype (T89) and 35S::abi1-1 lines (line 76-1 and line 76-3) were potted in soil in 1.5 l pots and were kept in a chamber with 1000 ppm CO2 supplement. The plants were grown for six weeks and well irrigated before the treatment started. Three treatments of well-watered (control), ABA feeding and drought stress were applied. Woody samples were collected after 4 weeks of treatment for RNA extraction and RNA sequencing.
Project description:The aim of this proposal is to understand the impact of the pho3 mutation on the transcriptome.The mutant pho3 was isolated on the basis of a failure to induce acid phosphatase activity in roots in response to low Pi. The pho3 mutant had a P deficient phenotype in vitro and in the leaves of soil grown pho3 plants the total P content was again reduced. pho3 exhibited a number of characteristics normally associated with low-P stress, including severely reduced growth, increased anthocyanin content and starch accumulation. pho3 was shown to have an absolute requirement for exogenous sucrose as pho3 seedlings were arrested in early seedling development on sucrose-free medium and was unaffected by Pi-availability. pho3 was found to be insensitive to high concentrations of exogenous sucrose (10%) but was sensitive to glucose. pho3 also exhibited reduced sensitivity of seed germination to exogenous ABA (abi-phenotype), a response which has been linked to sucrose insensitivity in both sugar-sensing and ABA mutants. Two developmental stages have been selected on the basis of the physiological characterisation of pho3. Seedlings (1.02; 2 rosette leaves) grown in agar and compost-grown plants (3.90; rosette growth complete). Agar will be supplemented with 1% sucrose and 1/2 strength MS; plants will be grown under a 16 h light/8 h dark cycle. Comparisons will be made between pho3 and Wassilewskija (the genetic background of the mutant) at each stage. Experimenter name: Julie Lloyd Experimenter phone: 01206 873307 Experimenter institute: Department of Biological Sciences, University of Essex Experimenter address: Colchester!Series_summary = Experimenter zip/postal_code: CO4 3SQ Experimenter country: UK Keywords: genetic_modification_design Overall design: 6 samples were used in this experiment
Project description:Microarray experiments were performed using Arabidopsis wild type plants (Col-0) and srk2dei triple knockout mutant to investigate the functions of ABA-activated protein kinases, SRK2D/SnRK2.2, SRK2E/OST1 and SRK2I/SnRK2.3. Transcription profiles of wild type and mutants were compared under ABA treatment or dehydration stress for 0 and 90 min. The srk2dei mutant was established by crossing T-DNA insertion mutants provided from Arabidopsis Biological Resource Center.
Project description:Arabidopsis seed germination is coordinated with the strong induction of metabolic pathways required for the mobilisation and utilization of seed storage reserves. These are essential to support the seedling before the establishment of photoauxotrophic growth. The activity of genes encoding enzymes required for lipid mobilisation is regulated largely at the level of transcription, but our knowledge of how this regulation occurs is extremely limited. After germination the rate of lipid reserve mobilisation is determined by the carbohydrate status of the seedling and by the osmotic potential of the growth substrate. The plant response to both of these requires the action of the hormone abscisic acid (ABA). We have shown that this regulation is tissue specific (Penfield et al., 2004 Plant Cell 16, 2705-2718), and that although lipid breakdown in the embryo is inhibited by ABA, lipid breakdown in the endosperm tissues is not. Furthermore, in many species the action of the endosperm is central to the processes controlling seed germination, yet very little is known about gene expression in this tissue, or of the function of the endosperm in mature Arabidopsis seeds. Mature Arabidopsis seeds can be dissected into embryo and endosperm/seed coat fractions, with the latter fraction containing RNA only from the endosperm as the seed coat cells undergo programmed cell death during the latter stages of seed development. In this experiment we divide seeds into embryo and endosperm tissues and transcript profile both shortly after germination, or when germination and lipid reserve mobilisation are inhibited by ABA or by the gibberellin biosynthesis inhibitor paclobutrazol. In this way we can discover the endosperm transcriptome and uncover candidate regulators of lipid mobilisation by searching for genes showing differential expression between embryo and endosperm before and after ABA treatment. Experimenter name = Steven Penfield Experimenter phone = 01904 328759 Experimenter fax = 01904 328762 Experimenter department = Department of Biology Experimenter institute = Centre for Novel Agricultural Products Experimenter address = University of York Experimenter address = PO BOX 373 Experimenter address = York Experimenter zip/postal_code = YO10 5YW Experimenter country = UK Keywords: organism_part_comparison_design Overall design: 18 samples were used in this experiment
Project description:Jasmonates (JA) and abscisic acid (ABA) are phytohormones known to play important roles in plant response and adaptation to various abiotic stresses including salinity, drought, wounding, and cold. JAZ (JASMONATE ZIM-domain) proteins have been reported to play negative roles in JA signaling. However, direct evidence is still lacking that JAZ proteins regulate drought resistance. In this study, OsJAZ1 was investigated for its role in drought resistance in rice. Expression of OsJAZ1 was strongly responsive to JA treatment, and it was slightly responsive to ABA, salicylic acid, and abiotic stresses including drought, salinity, and cold. The OsJAZ1-overexpression rice plants were more sensitive to drought stress treatment than the wild-type rice Zhonghua 11 (ZH11) at both the seedling and reproductive stages, while the jaz1 T-DNA insertion mutant plants showed increased drought tolerance compared to the wild-type plants. The OsJAZ1-overexpression plants were hyposensitive to MeJA and ABA, whereas the jaz1 mutant plants were hypersensitive to MeJA and ABA. In addition, there were significant differences in shoot and root length between the OsJAZ1 transgenic and wild-type plants under the MeJA and ABA treatments. A subcellular localization assay indicated that OsJAZ1 was localized in both the nucleus and cytoplasm. Transcriptome profiling analysis by RNA-seq revealed that the expression levels of many genes in the ABA and JA signaling pathways exhibited significant differences between the OsJAZ1-overexpression plants and wild-type ZH11 under drought stress treatment. Quantitative real-time PCR confirmed the expression profiles of some of the differentially expressed genes, including OsNCED4, OsLEA3, RAB21, OsbHLH006, OsbHLH148, OsDREB1A, OsDREB1B, SNAC1, and OsCCD1. These results together suggest that OsJAZ1 plays a role in regulating the drought resistance of rice partially via the ABA and JA pathways. Overall design: Transcriptome analysis of ZH11, OsJAZ1-OE plants under both severe drought stress and normal growth conditions.