Transcriptomic analysis of Sorghum bicolor responding to combined heat and drought stress
Ontology highlight
ABSTRACT:
ORGANISM(S): Sorghum bicolor
SUBMITTER: Fei Ling Lim
PROVIDER: E-GEOD-48205 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Considering global climate changes, incidences of combined drought and heat stress are likely to increase in the future and will considerably influence plant-pathogen interactions. Until now, little is known about plants exposed to simultaneously occurring abiotic and biotic stresses. To shed some light on molecular plant responses to multiple stress factors, a versatile multi-factorial test system, allowing simultaneous application of heat, drought and virus stress, was developed. Comparative analysis of single, double and triple stress responses by transcriptome and metabolome analysis revealed that gene expression under multi-factorial stress is not predictable from single stress treatments. Hierarchical cluster and principal component analysis identified heat as the major stress factor clearly separating heat-stressed from non-heat stressed plants. We identified 11 genes differentially regulated in all stress combinations as well as 23 genes specifically-regulated under triple stress. Furthermore, we showed that virus treated plants displayed enhanced expression of defense genes, which was abolished in plants additionally subjected to heat and drought stress. Triple stress also reduced expression of genes involved in the R-mediated disease response and increased the cytoplasmic protein response which was not seen under single stress conditions. These observations suggested that abiotic stress factors significantly altered TuMV-specific signaling networks which lead to a deactivation of defense responses and a higher susceptibility of plants. Collectively, our transcriptome and metabolome data provide a powerful resource to study plant responses during multi-factorial stress and allows identifying metabolic processes and functional networks involved in tripartite interactions of plants with their environment. Stress induced gene expression in Arabidopsis leaves was measured after exposure to single and combined abiotic and biotic stress. Plants were grown on soil for 21 days till virus infection. Eight days later controlled drought stress was applied. At the end of the treatments heat was applied for three days. Four biological replicates have been hybridized for each treatment. Furthermore, Arabidopsis plants were exposed to a single severe heat stress (37°C day/33°C night) to mimic the severity of the triple stress experiment.
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Project description:This experiment contains microarray measurements for 135 Arabidopsis thaliana rosette leaf samples covering three genotypes under six different environmental conditions. The three genotypes comprise the Col-0 wildtype and two loss-of-function mutants of aquaporins, a pip2;1 pip2;2 double mutant and a pip2;1 pip2;2 pip2;4 triple mutant (respective AGI locus identifiers: AT3G53420, AT2G37170, AT5G60660). The six conditions include control condition (well-watered, 22°C, 70% relative air humidity), drought stress (one week without watering), heat stress without changing the absolute humidity of the ambient air (6 hours at 33°C, 37% relative air humidity), heat stress with supplemented air humidity to maintain a constant vapor pressure deficit before and during the heat episode (6 hours at 33°C, 84% relative air humidity), and the combinations of drought pretreatment with each of the two heat stress variants (one week of drought followed by 6 hours of heat stress). Samples from all conditions were harvested at the same time (within 15 min starting at 5 p.m.).
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Project description:Considering global climate changes, incidences of combined drought and heat stress are likely to increase in the future and will considerably influence plant-pathogen interactions. Until now, little is known about plants exposed to simultaneously occurring abiotic and biotic stresses. To shed some light on molecular plant responses to multiple stress factors, a versatile multi-factorial test system, allowing simultaneous application of heat, drought and virus stress, was developed. Comparative analysis of single, double and triple stress responses by transcriptome and metabolome analysis revealed that gene expression under multi-factorial stress is not predictable from single stress treatments. Hierarchical cluster and principal component analysis identified heat as the major stress factor clearly separating heat-stressed from non-heat stressed plants. We identified 11 genes differentially regulated in all stress combinations as well as 23 genes specifically-regulated under triple stress. Furthermore, we showed that virus treated plants displayed enhanced expression of defense genes, which was abolished in plants additionally subjected to heat and drought stress. Triple stress also reduced expression of genes involved in the R-mediated disease response and increased the cytoplasmic protein response which was not seen under single stress conditions. These observations suggested that abiotic stress factors significantly altered TuMV-specific signaling networks which lead to a deactivation of defense responses and a higher susceptibility of plants. Collectively, our transcriptome and metabolome data provide a powerful resource to study plant responses during multi-factorial stress and allows identifying metabolic processes and functional networks involved in tripartite interactions of plants with their environment. Stress induced gene expression in Arabidopsis leaves was measured after exposure to single and combined abiotic and biotic stress. Plants were grown on soil for 21 days till virus infection. Eight days later controlled drought stress was applied. At the end of the treatments heat was applied for three days. In parallel, a homozougus T-DNA insertion line SALK_021115C (N672283), located in the Arabidopsis gene At5g45000 has been exposed to the same stress conditions. Four biological replicates have been hybridized for each treatment.
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Project description:Considering global climate changes, incidences of combined drought and heat stress are likely to increase in the future and will considerably influence plant-pathogen interactions. Until now, little is known about plants exposed to simultaneously occurring abiotic and biotic stresses. To shed some light on molecular plant responses to multiple stress factors, a versatile multi-factorial test system, allowing simultaneous application of heat, drought and virus stress, was developed. Comparative analysis of single, double and triple stress responses by transcriptome and metabolome analysis revealed that gene expression under multi-factorial stress is not predictable from single stress treatments. Hierarchical cluster and principal component analysis identified heat as the major stress factor clearly separating heat-stressed from non-heat stressed plants. We identified 11 genes differentially regulated in all stress combinations as well as 23 genes specifically-regulated under triple stress. Furthermore, we showed that virus treated plants displayed enhanced expression of defense genes, which was abolished in plants additionally subjected to heat and drought stress. Triple stress also reduced expression of genes involved in the R-mediated disease response and increased the cytoplasmic protein response which was not seen under single stress conditions. These observations suggested that abiotic stress factors significantly altered TuMV-specific signaling networks which lead to a deactivation of defense responses and a higher susceptibility of plants. Collectively, our transcriptome and metabolome data provide a powerful resource to study plant responses during multi-factorial stress and allows identifying metabolic processes and functional networks involved in tripartite interactions of plants with their environment. Stress induced gene expression in Arabidopsis leaves was measured after exposure to single and combined abiotic and biotic stress. Plants were grown on soil for 21 days till virus infection. Eight days later controlled drought stress was applied. At the end of the treatments heat was applied for three days. Four biological replicates have been hybridized for each treatment.
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Project description:Rice is the major staple food for more than half of world's population. As global climate changes, we are observing more floods, droughts and severe heat waves. Two rice cultivars with contrasting genetic backgrounds and levels of tolerance to drought, Nipponbare and IAC1131, were used in this study. Four-week-old seedlings of both cultivars were grown in large soil volumes and then exposed to moderate and extreme drought for 7 days, followed by 3 days of re-watering. Mature leaves were harvested from plants from each treatment for protein extraction and subsequent shotgun proteomic analysis, with validation of selected proteins by western blotting. Gene Ontology (GO) annotations of differentially expressed proteins provide insights into the metabolic pathways that are involved in drought stress resistance. Our data indicate that IAC1131 appears to be better able to cope with stressful conditions by up regulating a suite of stress and defence response related proteins. Nipponbare, in contrast, lacks the range of stress responses shown by the more stress tolerant variety, and responds to drought stress by initiating a partial shutdown of chlorophyll biosynthesis in an apparent attempt to preserve resources.
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Project description:The present study is expected to reveal differentially expressed genes under drought stress of Sorghum bicolor. The seeds of Sorghum genotype drought tolerant (DT) were grown at 28-32°C day/night temperature with 12/12 h light/dark period in the phytotron glass house. The fully opened uppermost leaves from control and drought stressed seedlings were sampled and stored at -80°C. For RNA-Seq libraries, one microgram of total RNA was extracted with Trizol reagent (Invitrogen, USA) and mRNA libraries were produced using the TruSeq mRNA-Seq library kit (Illumina) according to manufacturer’s instructions. The libraries generated were quantitated using an Agilent Bioanalyzer DNA 1000 chip. (Agilent Technologies, Santa Clara, CA) and a 2x101 cycle paired end sequencing (sequenced by Sandor Pvt. Ltd., Hyderabad, India) was performed using an Illumina HiScanSQ sequencer (Illumina Inc.). Initially, raw reads were processed by NGSQC toolkit (http://59.163.192.90:8080/ngsqctoolkit/) and high quality reads were subjected to de-novo assembly using Trinity assembler (Patel and Jain, 2012). Assembled transcripts were quantified by standard pipeline (Trinity→RSEM→R→DESeq) and those transcripts were removed which has zero FPKM in all four samples (Anders, 2010; Grabherr, et al., 2011; Li and Dewey, 2011). These transcripts were further processed by transdecoder tool to retrieve full length coding sequence and subsequent annotated by FastAnnotator (http://fastannotator.cgu.edu.tw/index.php) (Chen, et al., 2012). Pathway enrichment analysis was performed for the predicted transcripts by KEGG Automatic Annotation Server (KAAS; www.genome.jp/tools/kaas/) for the classification of spatial and temporally governed pathways.
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Project description:The present study is expected to reveal regulatory network of small RNAs under drought in Sorghum (Sorghum bicolor (L.) Moench). Sorghum genotype drought tolerant (DT) and drought susceptible (DS) were grown at 28-32 degrees C day/night temperature with 12/12 h light/dark period in the phytotron glass house. The fully opened uppermost leaves from control and drought stressed seedlings were sampled and stored at -80 degrees C, and used for generation of a small RNA library. Total RNA was isolated from the leaves using the TRIzol reagent (Invitrogen, USA). Small RNA sequencing libraries were prepared using Illumina Truseq small RNA Library preparation kit following manufacturer's protocol and these libraries were sequenced on GAIIx platform (Illumina Inc., USA). Small RNA reads contaminated with poor-quality and adaptor sequences were trimmed by using the UEA sRNA workbench 2.4- Plant version sequence file pre-processing (http://srna-tools.cmp.uea.ac.uk/). Then, all unique reads were submitted to the UEA sRNA toolkit-Plant version miRCat pipeline (http://srna-tools.cmp.uea.ac.uk/) to predict novel miRNAs from high-throughput small RNA sequencing data.
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