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Transcriptome analysis of Osbhlh148 mutant plants under controlled drought stress and well-watered conditions at vegetative stage

ABSTRACT: The members of bHLH transcription factor superfamily are known to play key role in plant development and abiotic stress response. Loss-of-function of OsbHLH148 gene resulted in increased sensitivity of rice plants to drought stress. To identify the targets of OsbHLH148 and dissect the drought stress response pathway regulated by it, we performed transcriptome profiling of Osbhlh148 mutant plants under drought stress as well as well-watered conditions by RNA-sequencing.

ORGANISM(S): Oryza sativa Japonica Group

PROVIDER: GSE65024 | GEO | 2015/01/16

SECONDARY ACCESSION(S): PRJNA272733

REPOSITORIES: GEO

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Transcriptome analysis of Osbhlh148 mutant plants under controlled drought stress and well-watered conditions at vegetative stage

Project description:The members of bHLH transcription factor superfamily are known to play key role in plant development and abiotic stress response. Loss-of-function of OsbHLH148 gene resulted in increased sensitivity of rice plants to drought stress. To identify the targets of OsbHLH148 and dissect the drought stress response pathway regulated by it, we performed transcriptome profiling of Osbhlh148 mutant plants under drought stress as well as well-watered conditions by RNA-sequencing. OsbHLH148 loss-of-function rice plants (Oryza sativa ssp. japonica cv. Nipponbare) were exposed to controlled drought stress and well-watered conditions at the vegetative stage. Controlled drought (DR) stress was applied on 45 day old plants following gravimetric approach. The soil water content was brought down to 40% field capacity over a period of 3-4 days and plants were maintained at that level for 10 days by weighing the pots daily at a fixed time of the day and replenishing the water lost through evapotranspiration. Another set of plants were maintained at 100% FC as well-watered (WW) condition. Total RNA isolated from leaf tissue was used for RNA-sequencing. Two biological replicates per sample were sequenced. cDNA library was constructed using TruSeq Stranded Total RNA with Ribo-Zero Plant kit (Illumina). Sequencing was carried out on each library to generate 50 bp SE reads using Illumina High-Seq 2000 platform. The transcriptome reads were mapped to the rice reference genome sequence (MSU 7.0) with tophat1.3.1 using the program’s default parameters (http://tophat.cbcb.umd.edu). Mapped RNA-Seq reads were assembled into transcripts by Cufflinks (http://cufflinks.cbcb.umd.edu/) and differentially expressed genes were identified by using Cuffdiff.

2015-01-16 | E-GEOD-65024 | biostudies-arrayexpress

Transcriptome analysis of Oshsfa2e mutant plants under controlled drought stress and well-watered conditions at vegetative stage

2015-01-16 | GSE65025 | GEO

Transcriptome analysis of Oshsfa2e mutant plants under controlled drought stress and well-watered conditions at vegetative stage

Project description:Heat shock factors (Hsfs) are known to regulate heat and drought stress response by controlling the expression of heat shock proteins and oxidative stress responsive genes. Loss-of-function of OsHSFA2e gene resulted in increased sensitivity of rice plants to drought and heat stress. To identify the targets of OsHSFA2e and dissect the stress response pathway regulated by it, we performed transcriptome profiling of Oshsfa2e mutant plants under drought stress as well as well-watered conditions by RNA-sequencing. OsHSFA2e loss-of-function rice plants (Oryza sativa ssp. japonica cv. Nipponbare) were exposed to controlled drought stress and well-watered conditions at the vegetative stage. Controlled drought (DR) stress was applied on 45 day old plants following gravimetric approach. The soil water content was brought down to 40% field capacity over a period of 3-4 days and plants were maintained at that level for 10 days by weighing the pots daily at a fixed time of the day and replenishing the water lost through evapotranspiration. Another set of plants were maintained at 100% FC as well-watered (WW) condition. Total RNA isolated from leaf tissue was used for RNA-sequencing. Two biological replicates per sample were sequenced. cDNA library was constructed using TruSeq Stranded Total RNA with Ribo-Zero Plant kit (Illumina). Sequencing was carried out on each library to generate 50 bp SE reads using Illumina High-Seq 2000 platform. The transcriptome reads were mapped to the rice reference genome sequence (MSU 7.0) with tophat1.3.1 using the program’s default parameters (http://tophat.cbcb.umd.edu). Mapped RNA-Seq reads were assembled into transcripts by Cufflinks (http://cufflinks.cbcb.umd.edu/) and differentially expressed genes were identified by using Cuffdiff.

2015-01-16 | E-GEOD-65025 | biostudies-arrayexpress

Expression analysis in roots and leaves of asparagus bean accesions B47 and B128 under well-watered and soil drought conditions

Project description:Investigation of whole genome gene expression level changes in two asparagus bean accesions B47 and B128 under drought stress, compared to well-watered conditions. Two organs, leaf and root, were sampled for each accesion under both well-watered and drought conditions.

2014-11-26 | GSE63636 | GEO

Genome-wide transcriptome analysis of rice in response to controlled drought stress at vegetative

2015-01-16 | GSE65022 | GEO

Comparative expression analysis of roots of two soybean cultivars with contrasting drought-tolerant phenotype under well-watered and dehydration conditions.

2015-07-02 | GSE65553 | GEO

Comparative expression analysis of roots of two soybean cultivars with contrasting drought-tolerant phenotype under well-watered and dehydration conditions.

Project description:To understand the responses of plants to environmental stresses will help mitigate the problems via creating stress-tolerant crop cultivars. We have carried out comparative expression analysis of roots of two soybean varieties Williams 82 and DT2008 that have constrasting drought-responsive phenotype under dehydration and well-watered (control) conditions. Affymetrix’s whole Soybean Gene Expression Microarray (66K) was used. The Williams 82 and DT2008 soybean plants were grown for 14 days in the vermiculite soil under greenhouse conditions. The whole plants of 14-d-old plants were detached and exposed to dehydration on KimTowel papers for 0 (well-watered, control), 2 and 10 h. All roots of independent 14-d-old plants were collected. Total RNA was prepared and used for the microarray hybridization. Three independent biological replicates were used for each plant sample.

2015-07-02 | E-GEOD-65553 | biostudies-arrayexpress

Genome-wide transcriptome analysis of rice in response to controlled drought stress at vegetative

Project description:In this study, genome-wide transcriptome profiling was used to understand molecular genetic mechanism of drought tolerance in rice. Illumina High-Seq 2000 platform was used for sequencing RNA from leaf tissue of rice plants exposed to controlled drought stress and well-watered conditions. The differentially expressed genes were used to identify biological process and cis-regulatory elements enriched under drought stress compared to well-watered conditions. Oryza sativa ssp. japonica cv. Nipponbare plants were exposed to controlled drought stress and well-watered conditions at the vegetative stage. Controlled drought (DR) stress was applied on 45 day old plants following gravimetric approach. The soil water content was brought down to 40% field capacity over a period of 3-4 days and plants were maintained at that level for 10 days by weighing the pots daily at a fixed time of the day and replenishing the water lost through evapotranspiration. Another set of plants were maintained at 100% FC as well-watered (WW) condition. Total RNA isolated from leaf tissue was used for RNA-sequencing. Two biological replicates per sample were sequenced. cDNA library was constructed using TruSeq Stranded Total RNA with Ribo-Zero Plant kit (Illumina). Sequencing was carried out on each library to generate 50 bp SE reads using Illumina High-Seq 2000 platform. The transcriptome reads were mapped to the rice reference genome sequence (MSU 7.0) with tophat1.3.1 using the program’s default parameters (http://tophat.cbcb.umd.edu). Mapped RNA-Seq reads were assembled into transcripts by Cufflinks (http://cufflinks.cbcb.umd.edu/) and differentially expressed genes were identified by using Cuffdiff.

2015-01-16 | E-GEOD-65022 | biostudies-arrayexpress

Drought stress: Analysis of FDH (Formate dehydrogenase) insertion mutants in response to drought stress

Project description:adt04-03_fdh_drought - drought stress - What is the role of the mitochondrial formate dehydrogenase in the response to drought? - Wild type and mutant arabidopsis plants were grown in soil for 6 weeks under short days. Each lot of plants is shared into 2 groups, one of which was watered normally (arr) whislt the other half was not watered for a week (sech). Keywords: gene knock out,treated vs untreated comparison

2008-02-13 | GSE10427 | GEO

Affymetrix Cotton Genome array expression data of root tissue of Gossypium herbaceum under drought stress and watered condition

Project description:Genome-wide Transcriptional Analysis of Genes Associated with Drought Stress in Gossypium herbaceum root This experiment was designed to investigate the molecular mechanism associated with drought tolerance in root tissue of Gossypium herbaceum. The gene expression profiles of the root tissue using Affymetrix Cotton Genome Array were compared with drought tolerant and drought sensitive genotype of G.herbaceum under drought stress and watered condition. Many genes in various molecular function or biological processes were over- or under-represented between drought tolerant and sensitive genotype, suggesting various molecular mechanism and biochemical pathways are interlinked and tolerant genotype have developed multiple mechanisms as an adaptory behavior against drought stress.

2012-03-29 | GSE36249 | GEO

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