Multi-omics profiling of 5 Arabidopsis accessions in response to combined water and nitrogen deficiencies
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE206890 | GEO | 2024/05/23
REPOSITORIES: GEO
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Project description:In this study, we build an in-depth multi-omics profile of 5 Arabidopsis accessions, in order to find the inner relations of N deficit, mild drought, and combined stress response at different scales. We used our own phenotyping platform (Phenoscope) to handle hundreds of Arabidopsis plants across 20 modalities (5 Genotypes x 2 Treatments of Water availability x 2 Treatments of Nitrogen availablity), phenotype those plants for growth-related traits and ultimately harvest the samples used in transcriptomics, metabolomics and physiological profiling. Then we have analysed those data to reveal in particular the specificities of the response to stress in each accession, as well as the W x N interactions leading to patterns that are specific to the combined stress response. The metabolomics data is particularly useful to highlight for instance the very specific profile of the Cvi-0 accession overall, or the larger extent of the metabolite responsiveness to N-deficiency with respect to mild drought. The share of the stress response that is specific to the combined stress condition is also quite variable between the 5 accessions.
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Project description:Pierce’s disease, caused by the bacterium Xylella fastidiosa, is one of the most devastating diseases of cultivated grapes. To test the long-standing hypothesis that Pierce’s disease results from pathogen-induced drought stress, we used the Affymetrix Vitis GeneChip to compare the transcriptional response of Vitis vinifera to Xylella infection, water deficit, or a combination of the two stresses. The results reveal a massive redirection of gene transcription involving 822 genes with a minimum 2-fold change (p<0.05), including the upregulation of transcripts for phenylpropanoid and flavonoid biosynthesis, pathogenesis related (PR) proteins, absisic acid (ABA)/jasmonic acid (JA)-responsive transcripts, and down-regulation of transcripts related to photosynthesis, growth and nutrition. Although the transcriptional response of plants to Xylella infection was largely distinct from the response of healthy plants to water stress, we find that 138 of the pathogen-induced genes exhibited a significantly stronger transcriptional response when plants were simultaneously exposed to infection and drought stress, suggesting a strong interaction between disease and water deficit. This interaction between drought stress and disease was mirrored in planta at the physiological level for aspects of water relations and photosynthesis, and in terms of the severity of disease symptoms and the extent of pathogen colonization, providing a molecular correlation of the classical concept of the disease triangle where environment impacts disease severity.
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Project description:Pierce's disease, caused by the bacterium Xylella fastidiosa, is one of the most devastating diseases of cultivated grapes. To test the long-standing hypothesis that Pierce's disease results from pathogen-induced drought stress, we used the Affymetrix Vitis GeneChip to compare the transcriptional response of Vitis vinifera to Xylella infection, water deficit, or a combination of the two stresses. The results reveal a massive redirection of gene transcription involving 822 genes with a minimum 2-fold change (p<0.05), including the upregulation of transcripts for phenylpropanoid and flavonoid biosynthesis, pathogenesis related (PR) proteins, absisic acid (ABA)/jasmonic acid (JA)-responsive transcripts, and down-regulation of transcripts related to photosynthesis, growth and nutrition. Although the transcriptional response of plants to Xylella infection was largely distinct from the response of healthy plants to water stress, we find that 138 of the pathogen-induced genes exhibited a significantly stronger transcriptional response when plants were simultaneously exposed to infection and drought stress, suggesting a strong interaction between disease and water deficit. This interaction between drought stress and disease was mirrored in planta at the physiological level for aspects of water relations and photosynthesis, and in terms of the severity of disease symptoms and the extent of pathogen colonization, providing a molecular correlation of the classical concept of the disease triangle where environment impacts disease severity. Mature leaves were sampled from 2-year old V. vinifera cv. Cabernet sauvignon clone 8 vines 4 and 8 weeks post-mock or inoculation with Xylella fastidiosa (Pierce's disease). Vines were grown in growth chambers under non-water limiting and water limiting conditions (moderate and severe water stress)
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Project description:These data provide a basis for the detection of sequence based polymorphisms between 10 Spring annual accessions of Arabidopsis thaliana. The experimental data provides an initial characterization of differences among the accessions, as well as a means for improving gene expression studies with the filtering of SFP from arrays studies. Recent studies have documented remarkable genetic variation among Arabidopsis thaliana accessions collected from diverse habitats and across its geographical range. Of particular interest are accessions with putatively locally adapted phenotypes – i.e., accessions with attributes that are likely adaptive under the climatic or habitat conditions of their sites of origin. These genotypes are especially valuable as they may provide insight into the genetic basis of adaptive evolution as well as allow the discovery of genes of ecological importance. The gene expression studies were conducted under two levels of soil moisture and accompanied by physiological measurements to characterize early responses to soil moisture deficit.
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Project description:These data provide a basis for exploration of gene expression differences between physiologically diverse accessions of Arabidopsis thaliana. Recent studies have documented remarkable genetic variation among Arabidopsis thaliana accessions collected from diverse habitats and across its geographical range. Of particular interest are accessions with putatively locally adapted phenotypes – i.e., accessions with attributes that are likely adaptive under the climatic or habitat conditions of their sites of origin. These genotypes are especially valuable as they may provide insight into the genetic basis of adaptive evolution as well as allow the discovery of genes of ecological importance. Therefore we studied the physiology, genome content and gene expression of 18 physiologically diverse accessions. The gene expression studies were conducted under two levels of soil moisture and accompanied by physiological measurements to characterize early responses to soil moisture deficit.
2012-03-12 | GSE27550 | GEO
Project description:These data provide a basis for exploration of gene expression differences between physiologically diverse Spring annual accessions of Arabidopsis thaliana. Recent studies have documented remarkable genetic variation among Arabidopsis thaliana accessions collected from diverse habitats and across its geographical range. Of particular interest are accessions with putatively locally adapted phenotypes – i.e., accessions with attributes that are likely adaptive under the climatic or habitat conditions of their sites of origin. These genotypes are especially valuable as they may provide insight into the genetic basis of adaptive evolution as well as allow the discovery of genes of ecological importance. Therefore we studied the physiology, genome content and gene expression of 18 physiologically diverse accessions. The gene expression studies were conducted under two levels of soil moisture and accompanied by physiological measurements to characterize early responses to soil moisture deficit.
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Project description:These data provide a basis for the detection of sequence based polymorphisms between the Col-1, Tsu-1, and Kas-1 accessions of Arabidopsis thaliana. The experimental data provides an initial characterization of differences among the accessions, as well as a means for improving gene expression studies with the filtering of SFP from arrays studies. Recent studies have documented remarkable genetic variation among Arabidopsis thaliana accessions collected from diverse habitats and across its geographical range. Of particular interest are accessions with putatively locally adapted phenotypes – i.e., accessions with attributes that are likely adaptive under the climatic or habitat conditions of their sites of origin. These genotypes are especially valuable as they may provide insight into the genetic basis of adaptive evolution as well as allow the discovery of genes of ecological importance. Therefore we studied the physiology, genome content and gene expression of two physiologically extreme accessions (Tsu-1 from a wet environment in Tsushima, Japan and Kas-1 from a dry environment in Kashmir, India). The gene expression studies were conducted under two levels of soil moisture and accompanied by physiological measurements to characterize early responses to soil moisture deficit. Genomic hybridization experiments identified 42,503 single feature polymorphisms (SFP) between accessions, providing an initial screen for putative SNPs, indels, or changes in gene content.
2010-02-17 | GSE20340 | GEO
Project description:Water deficit stress between the booting and grain filling stages significantly affect grain yield and quality of hard red winter wheat. Several stress tolerant cultivars with different adaptation mechanisms have been released and are widely cultivated on the Southern Great Plains of the US. However, the physiological, molecular, and genetic basis of adaptation to drought stress for these cultivars remains unknown. Use of transcriptome profiling to identify drought responsive genes in hexaploid wheat is a challenging process given the quantitative nature of drought stress, genome complexity, and the intricacy of interaction effects. If the information generated from functional genomics studies is to be used in molecular breeding programs for cultivar development, it is highly desirable to use cultivars better adapted for the region. In the current study we used two well-adapted, drought-tolerant, high-yielding, cultivated varieties, TAM 111 and TAM 112, which appear to have different adaptation mechanisms, to identify drought stress induced transcripts during heading and early dough stages. A set of 24 Affymetrix GeneChip wheat genome arrays (2 cultivars; 2 water treatments; 2 sampling stages; 3 biological replicates) from plants subjected to water deficit stress under controlled glasshouse conditions. Differentially expressed genes were identified using a ANOVA (p<0.01) controlling false discovery rate (FDR, q<0.01) using Benjamini Hochberg approach.
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