Whole genome transcriptional responses to aluminum stress in rice roots
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE89494 | GEO | 2017/09/01
SECONDARY ACCESSION(S): PRJNA352557
REPOSITORIES: GEO
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2022-11-23 | GSE218416 | GEO
Project description:Investigation of whole genome gene expression level changes in a Azospirillum lipoferum 4B associated to artificial roots, Oryza sativa japonica cv. Cigalon roots and Oryza sativa japonica cv. Nipponbare roots, compared to the strain grown in liquid culture.
2014-01-01 | GSE42450 | GEO
Project description:Background Ionic aluminum (mainly Al3+) is rhizotoxic and can be present in acid soils at concentrations high enough to inhibit root growth. Many forest tree species grow naturally in acid soils and often tolerate high concentrations of Al. Previously, we have shown that aspen (Populus tremula) releases citrate and oxalate from roots in response to Al exposure. To obtain further insights into the root responses of aspen to Al, we investigated root gene expression at Al conditions that inhibit root growth. Results Treatment of the aspen roots with 500 µM Al induced a strong inhibition of root growth within 6 h of exposure time. The root growth subsequently recovered, reaching growth rates comparable to that of control plants. Changes in gene expression were determined after 6 h, 2 d, and 10 d of Al exposure. Replicated transcriptome analyses using the Affymetrix poplar genome array revealed a total of 175 significantly up-regulated and 69 down-regulated genes, of which 70% could be annotated based on Arabidopsis genome resources. Between 6 h and 2 d, the number of responsive genes strongly decreased from 202 to 26, and then the number of changes remained low. The responses after 6 h were characterized by genes involved in cell wall modification, ion transport, and oxidative stress. Two genes with prolonged induction were closely related to the Arabidopsis Al tolerance genes ALS3 (for Al sensitive 3) and MATE (for multidrug and toxin efflux protein, mediating citrate efflux). Patterns of expression in different plant organs and in response to Al indicated that the two aspen genes are homologs of the Arabidopsis ALS3 and MATE. Conclusion Exposure of aspen roots to Al results in a rapid inhibition of root growth and a large change in root gene expression. The subsequent root growth recovery and the concomitant reduction in the number of responsive genes presumably reflect the success of the roots in activating Al tolerance mechanisms. The aspen genes ALS3 and MATE may be important components of these mechanisms.
2010-08-24 | GSE19297 | GEO
Project description:Rice is highly sensitive to drought, and the effect of drought may vary with the different genotypes and development stages. Genome-wide gene expression profiling was used as the initial point to dissect molecular genetic mechanism of this complex trait and provide valuable information for the improvement of drought tolerance in rice. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice exposed to drought stress. The transcriptome from leaf, root, and young panicle at three developmental stages was comparatively analyzed combined with bioinformatics exploring drought stress related cis-elements. In this study, the gene expression patterns across six tissues including leaves and roots at tillering stage and panicle elongation stage, leaves and young panicle at booting stage ( TL: leaves at tillering stage; TR: roots at tillering stage; PL: leaves at panicle elongation stage; PR: roots at panicle elongation stage; BP: young panicle at booting stage; BL: leaves at booting stage) were characterized by using the Affymetrix rice microarray platform based on a drought tolerant rice line derived from IR64.
2010-12-23 | E-GEOD-26280 | biostudies-arrayexpress
Project description:Rice seedlings at 3-leaf stage were used for expression analysis in control and cold stressed (incloudling cold treatment for 3, 24hrs and recovery from cold stress for 24hrs) samples. Samples of shoots and roots from biological replicates of both genotypes were generated and the expression profiles were determined using Phalanx Rice OneArrayM-oM-<M- v1. Control and treated biological replicates of cold-tolerant cultivar TNG67 (japonica) and cold-sensitive cultivar TCN1 (indica) were analyzed
2014-10-15 | E-GEOD-57895 | biostudies-arrayexpress
Project description:Rice seedlings at 3-leaf stage were used for expression analysis in control and salt stressed (incloudling salt treatment for 3, 24hrs and recovery from cold stress for 24hrs) samples. Samples of shoots and roots from biological replicates of both genotypes were generated and the expression profiles were determined using Phalanx Rice OneArrayï¼ v1. Control and treated biological replicates of salt-tolerant cultivar TNG67 (japonica) and salt-sensitive cultivar TCN1 (indica) were analyzed
2016-06-30 | E-GEOD-76613 | biostudies-arrayexpress
Project description:Abiotic stresses such as salinity are very important factors limiting rice growth and productivity around the world. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice responsive to salinity stress, try to elucidate the difference of genome-wide gene expression profiling of two contrasting rice genotypes in response to salt stress and to discover the salinity related genes and gene interaction and networks. Under salinity condition, the number of differentially expressed genes (DEGs) in 177-103 was more than that in IR64, and most of up-regulated DEGs in 177-103 are response to stress. But in IR64, most of up-regulated DEGs are transcription related genes. The DEGs under salinity showed very strong tissue specificity, the number of DEGs in leaf was more than that in root. A lot of genes differentially expressed by exogenous ABA treatment under salinity condition, such as Leaf senescence protein, 1-deoxy-D-xylulose 5-phosphate synthase 2 precursor and Protein of unknown function DUF26 were induced by ABA and contributed to salinity tolerance. In this study, the gene expression patterns across two organs including leaves and roots at seedling stage were characterized under control, salinity, salinity+ABA treatments by using the Affymetrix rice microarray platform based on a salinity tolerant rice line derived from IR64.
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Project description:Nano-aluminium oxide (nAl2O3) is one of the most widely used nanomaterials, but the molecular toxic mechanism of nAl2O3 on plants is still not clarified completely. In this study, we compared the toxic effects of nAl2O3 and Al3+ ion at the physiological and molecular levels. The shoot weight and root weight of Arabidopsis thaliana were decrease to 57.01% and 45.15% after the Al3+ ion exposure , while nAl2O3 increased the root weight by 48.07% and length by 38.53% at the selected concentration (98 mmol/L) for 10 d exposure. Physiological research showed that the photosystem (chlorophyll fluorescence parameters down-regulated) and antioxidant system (MDA and H2O2 content up-regulated) in A. thaliana were severely injured by the Al3+ ion. Data from transcriptome analysis clarified how nAl2O3 and Al3+ ion selectively affected root development and growth. nAl2O3 stimulated root growth directly (e.g., up-regulation of the root hair-specific gene family and root development genes, POLARIS protein), or indirectly (e.g., up-regulation of N and P absorption-related genes). Conversely, Al3+ ion disturbed ion homeostasis (up-regulated Al and Cu content) and caused severe oxidative stress, thus activating the salicylic acid (SA) signaling pathway and up-regulating nitric oxide (NO)-related genes, inducing the plant defense response. However, the overproduced SA and NO (up-regulated 2.60-fold) led to the inhibition of CAT activity (down-regulation of CAT1 and CAT2 genes) and increased the H2O2 level (up-regulated 2.84-fold). Subsequently, root development-related genes (e.g., auxin induced in root cultures 1) were down-regulated. This work gives us new insight into understanding the different molecular mechanisms of the plant response to nAl2O3 and Al3+ stresses.
2018-03-31 | GSE97308 | GEO
Project description:Tissue culture is used to establish desired phenotypes in plants. Callus culture and regeneration are critical steps in this process. Calli of Oryza sativa japonica (cv. TNG67) and Oryza sativa indica (cv. IR64) have varying regeneration efficiencies. Genetic diversity could partly account for such differences but the epigenetic response to different cell culture environment could also play a role. We aimed to study the role of DNA methylation during the tissue culture process in determining its outcome.
2017-06-01 | GSE82138 | GEO
Project description:Most blue color in flowers is due to anthocyanin, and considerable proportion of blue coloration can be attributed to metal-complexed anthocyanins. Recently, we reported vacuolar localized iron-transporter in blue petal cells of Tulipa gesneriana. However the mechanism of another metal ion transporters and subsequent flower color development has yet to be fully explored. In Hydrangea macrophylla, Al3+ is involved in blue coloration and the anthocyanin is formed Al3+-complex in vacuoles. To identify the molecular mechanism of blue coloration in hydrangea flowers, we tried to isolate the related genes transporting metal ion into vacuoles. From the sepal cDNA library we read the sequences of ca. 12000 genes, then a microarray analysis was carried out. From the sequences information, we chose several genes that might localize vacuolar membrane and transport Al3+. By using Al3+-sensitive yeast strain, we could identify the gene transporting Al3+ into vacuole. From the functional similarity and predicted localization, we could also identify the gene transporting Al3+ into cytosol. We will report the Al3+ mobilization from out of cell into vacuole in the sepal of Hydrangea macrophylla.
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