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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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.
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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.
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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
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