Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Differentially expressed genes under different stress conditions in rice

ABSTRACT: Rice is one of important crop and, the genome has been already completely sequenced. Moreover we collected more than 30K rice FL-cDNA clones as transcriptome resources. However, the cDNA collection did not reveal the transcription activity and specificity of expression. So, we designed 60-mer oligo array based on the array system of Agilent Technologies (GPL477) as custom array. For validation of the array, we tested the reproducibility of labeling and hybridization. After this validation, 22K rice oligo array was supplied from Agilent Technologies (GPL892). 2: reproducibility of hybridization-2: We made a dye-swap experiment to validate dye-effect and data reproducibility between arrays. We hybridized shoot (as control) and stress-treated shoot. This data also indicated the diversity of gene expression profile among stress response. In addition, array data of samples treated for 24 hours have been already published on NCBI-GEO (GSE2415) Keywords: variety among tissues organisms: Oryza sativa ssp. japonica (Nipponbare) tissue: shoot derived from more than 100 plants treatement1: cold stress (10 degreeC) time course1: 48, 72 hours tissue1: shoot treatment2: drought stress (25% polyethylene glycol 6000) time course2: 1, 9 hours tissue: shoot treatment3: flood and lay-down stress time course3: 1, 6, 24, 48 hours tissue3: shoot treatment4: flood stress time course4: 1, 24, 48, 72 hours tissue4: shoot treatment5: lay-down stress for 24 hours tissue5: shoot hybridization : two dye method hybridization: Dye-swap experiment replication: samples were not replicated. array: 2 array per 1 experiment (total 26 arrays)

ORGANISM(S): Oryza sativa Japonica Group

SUBMITTER: Kouji Satoh

PROVIDER: E-GEOD-7532 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Adventitious root formation at the base of plant cuttings is an innate de novo organogenesis process that allows massive vegetative propagation of many economically and ecologically important species. The early molecular events following shoot excision are not well understood. Using whole-genome microarrays, we detected significant transcriptome remodeling during 48 hours following shoot removal in Populus softwood cuttings in the absence of exogenous auxin, with 27% and 36% of the gene models showing differential abundance between 0 and 6 hours, and 6 and 24 hours, respectively. During these two time intervals, gene networks involved in protein turnover, protein phosphorylation, molecular transport and translation were among the most significantly regulated. Transgenic lines expressing a constitutively active form of the Populus type-B response regulator PtRR13 (ÎDDKPtRR13) have a delayed rooting phenotype and cause misregulation of COV1, a negative regulator of vascularization; PDR9, an auxin efflux transporter; two AP2/ERF genes with sequence similarity to TINY1. Cytokinin action appeared to disrupt root development 24 hours after shoot excision, when root founder cells are hypothesized to be sensitive to the negative effects of cytokinin. Our results suggest that PtRR13 acts downstream of cytokinin to repress adventitious root formation in intact plants, and that reduced cytokinin signaling after shoot excision enables coordinated expression of ethylene, auxin and vascularization pathways leading to adventitious root development. Populus tremula x Populus alba INRA-clone No. 717-1-B4 plants expressing a constitutively active form of the Populus type-B response regulator PtRR13 (ÎDDKPtRR13) were generated via an Agrobacterium-mediated protocol developed by Han et al. (2000). Non-transgenic and ÎDDKPtRR13 line were grown to a height of 60 cm. A 14 cm tall apical cuttings were collected from the mother plants. Cuttings were placed in 25 cm2 pots Fafard mix #4 and placed on a mist bench with intermittent mist to prevent shoot desiccation. Samples were collected at the indicated time points and consisted of a 5 mm section measured up from the base of the cutting (one sample per cutting). Total RNA was extracted with the RNeasy mini kit (Qiagen USA) and DNase treated in-column with the RNase-Free DNase set (Qiagen USA). Double-stranded cDNA was synthesized using SuperScript Double Strand cDNA Synthesis Kit (Invitrogen USA, Carlsbad, CA) with oligo-dT primers following the manufacturerâs protocol except that the synthesis step was extended to 16 hours. Cy-3 labeling and hybridization steps were performed by NimbleGen using their standard procedures. A custom-designed microarray platform was used comprising single 60-mer probes designed against 55,793 annotated gene models from the sequenced genome of P. trichocarpa. Each 60-mer probe was chosen form a group of 6-7 non-overlapping probes designed against different parts of the gene model. The probe whose value was the most similar to the average of 6-7 experimental probes was assumed to be the most reliable for transcript level estimation. A total of 39 microarray chips were used in these experiments: 39 chips = 2 genotypes (NT and ÎDDK) x 4 time points (0, 6, 24 and 48 hours) x 5 biological replications, except for the 0 hour ÎDDK where 4 biological replications were used. Signal intensities were log2 transformed and quantile normalized (Sugiharto et al., 1992). Normalized signals were analyzed in SAS 9.1 (SAS Institute, Cary, NC) using a mixed model analysis of variance (ANOVA) with genotype and genotype by time interactions as fixed effects, and biological replication as a random effect.

Project description:Purpose: To identify abiotic stress responsive and tissue specific miRNAs at genome wide level in wheat (Triticum aestivum) Results: Small RNA libraries were constructed from four tissues (root, shoot, mature leaf and spikelets) and three stress treatments of wheat seedlings (control, high temperature, salinity and water-deficit). A total of 59.5 million reads were obtained by high throughput sequencing of eight wheat libraries, of which 32.5 million reads were found to be unique. Using UEA sRNA workbench we identified 47 conserved miRNAs belonging to 20 families, 1030 candidate novel and 51 true novel miRNAs. Several of these miRNAs displayed tissue specific expression whereas few were found to be responsive to abiotic stress treatments. Target genes were predicted for miRNAs identified in this study and their grouping into functional categories revealed that the putative targets were involved in diverse biological processes. RLM-RACE of predicted targets of three conserved miRNAs (miR156, miR160 and miR164) confirmed their mRNA cleavage, thus indicating their regulation at post-transcriptional level by corresponding miRNAs. Expression profiling of confirmed target genes of these miRNAs was also performed. Conclusions: This is the first comprehensive study on profiling of miRNAs in a variety of tissues and in response to several abiotic stresses in wheat. Our findings provide valuable resource for better understanding on the role of miRNAs in stress tolerance as well as plant development. Additionally, this information could be utilized for designing wheat plants for enhanced abiotic stress tolerance and higher productivity. Total eight (three stress, one control and four tissue specific small RNA libraries were pepared and sequenced independently [wheat control (WC), wheat high temperature stressed (WHTS), wheat salinity stressed (WSS) and wheat drought stressed (WDS), wheat shoot(WSH), wheat leaf (WLF), wheat flower(WFL), wheat root(WRT)] on Illumina GAIIx

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Differentially expressed genes under different stress conditions in rice

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