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Gene expression profiling from Al treatment in rice root tips

ABSTRACT: The root tip of rice before or after Al stress have been used. And some gense were regulated in this stress. We used microarrays to detail the global programme of gene expression underlying Al stress and identified distinct classes of up-regulated genes during this process.

ORGANISM(S): Oryza sativa

PROVIDER: GSE107531 | GEO | 2018/05/10

REPOSITORIES: GEO

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Gene expression profiling from Al treatment in rice root tips

Project description:Gene expression profiling from Al treatment in rice root tips

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Agilent 44K Rice Oligo DNA Microarray RAP-DB (G2519F#15241); genome-wide transcriptional analysis of Aluminum-responsive genes in rice (Oryza sativa).

Project description:By comparing transcriptional profiling between a wild-type rice and an Al-sensitive rice mutant star1, we found that rice possesses novel mechanisms of Al-tolerance in addition to ART1-regulated mechanism in rice. The transcriptional profiling between the wild-type rice and an Al-sensitive mutant, star1. +Al vs. -Al in the roots of wild-type rice and star1 mutant. Biological replicates: +Al/-Al WT root tip 4 replicates, +Al/-Al WT basal tip 4 replicates, +Al/-Al star1 root tip 4 replicates, +Al/-Al star1 basal tip 4 replicates

2012-09-19 | E-GEOD-40964 | biostudies-arrayexpress

Expression data from root tips of Wildtype and Osaim1 mutant rice treated with or without salicylic acid (SA)

Project description:To determine the possible role of SA in root meristem activity, we compared the gene expression profiles of the root tip of Osaim1 and WT under control condition and SA treatment. We used microarrays to detail the global programme of gene expression underlying control condition and SA treatment between WT and Osaim1 mutant.

2017-03-22 | GSE80184 | GEO

Soil salinity and mechanical obstruction differentially affects embryonic root architecture in native rice varieties of West Bengal

Project description:Roots make the first contact with the soil environment and are the first responders of stress. These root behaviors are quantifiable and adaptive. The response of rice varieties in mechanical and salinity stress was measured in a novel experimental setup that mimics the soil environment. We analyzed the response of roots by means of SAC (Stress Adaptation Coefficient) in 28 rice varieties that include high-yield salt tolerant varieties as well as geographically isolated native rice varieties. cDNA microarray of IR64 root-tip shows about 6000 common transcripts to be differentially regulated among the two stresses and common pathways were identified. Overall, our study indicates that there is an important commonality in the molecular basis of salt and mechanical stress and presents an easy-to-perform early establishment stress screen for rice varieties.

2018-12-20 | GSE117170 | GEO

Small RNA analysis of ASR5 knockdown rice plants (ssp. Japonica cv. Nipponbare) under Al stress conditions

Project description:Aluminum (Al) toxicity in plants is one of the primary constraints in crop production. Al³⁺, the most toxic form of Al, is released into soil under acidic conditions and causes extensive damage to plants, especially in the roots. In rice, Al tolerance requires the ASR5 gene, but the molecular function of ASR5 has remained unknown. This data establish a comparative study of miRNAome profiles in ASR5 knockdown rice plants (ssp. Japonica cv. Nipponbare) under Al stress conditions.

2017-11-09 | GSE77046 | GEO

Single-cell transcriptomic analysis of rice root tips [scRNA-seq]

Project description:There are two main types of root systems in flowering plants, which are taproot systems in dicot and fibrous root systems in monocot. The cellular and molecular mechanism involved in root development are mainly from the study of dicot model Arabidopsis thaliana. However, mechanisms of root development and their conservation and divergence in monocot, which including the major crops, remain largely elusive. Here we profile the transcriptomes of more than 20,000 single cells in the root tips of two rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica). Single-cell analysis coupled with in situ hybridization identify the cell type-specific marker genes and annotate all the clusters. Comparison of single-cell transcriptome and analysis of mark gene expression suggest well-conserved molecular landscape between rice Nip and 93-11. Moreover, our analysis suggests specific functions gene expression patterns for each cell type cluster, including the hormone genes. Comparison to Arabidopsis single-cell RNA-sequencing dataset reveals extensive differences between Arabidopsis and rice cell types, and species-specific features emphasize the importance of directly studying rice root. Our study reveals transcriptome landscape of major cell types of rice root in singe-cell resolution and provides molecular insight of the cell type morphology of cell type evolution in plants.

2020-12-25 | GSE146034 | GEO

Abscission layer (AL) at the base of flower in rice using laser micro-dissection: NIL(qSH1) AL vs. Nipponbare AL, NIL(qSH1) AL vs. NIL(qSH1) upper region of AL, and NIL(qSH1) AL vs. NIL(qSH1) lower region of AL

Project description:Tissue-specific transcriptional profiling of the abscission layer (AL) at the base of young flower in rice using laser micro-dissection: NIL(qSH1) vs. Nipponbare.

2012-04-01 | GSE33409 | GEO

Transcriptome analysis of rice roots and tips in early development by massive parallel sequencing

Project description:Despite the major physiological dissimilarities between roots and their tips, differences in their gene expression profiles remain largely unexplored. In this research, the transcriptome of rice (Oryza sativa L. subsp. Japonica) mature root tissue and root tips was monitored using mRNA-Seq at 2 time points. Almost 50 million 76 bp reads were mapped onto the rice genome sequence, differential expression patterns between tissues and time points were investigated and at least 1,006 novel transcriptionally active regions (nTARs) were detected to be expressed in rice root tissue. More than 30,000 genes were found to be expressed in rice roots, among which 1,761 root-specific and 306 tip-specific transcripts. Mature root tissue appears to respond more strongly to external stimuli than tips, showing a higher expression of for instance auxin responsive and ABA-responsive genes, as well as the phenylpropanoid pathway and photosynthesis upon light. The root tip-specific transcripts are mainly involved in mitochondrial electron transport, organelle development, secondary metabolism, DNA replication and metabolism, translation, and cellular component organization. As roots developed, genes involved in electron transport, response to oxidative stress, protein phosphorylation and metabolic processes were activated. For some nTARs a potential role in root development can be put forward based on homology to genes involved in CLAVATA signaling, cell cycle regulators and hormone signaling. A subset of differentially expressed genes and novel transcripts was confirmed using (q)RT-PCR. These results uncover previously unrecognized tissue-specific expression profiles and provide an interesting starting point to study the different regulation of transcribed regions of these tissues.

2012-01-12 | GSE30367 | GEO

An iTRAQ-based proteomics screen analysis of potential regulators of wheat (Triticum aestivum L.) root growth inhibition due to Al stress

Project description:Aluminum (Al)-induced root tip cell elongation inhibition is a major cause of plant root elongation suppression. Root tip cell elongation inhibition is caused by disruption to cell wall component metabolism, growth signaling, or cellular damage. The aim of this study was to identify the proteins involved in root elongation under Al stress in the tolerant wheat (Triticum aestivum L.) ET8. We investigated wheat root protein profiles using isobaric tags for relative and absolute quantification (iTRAQ). In total, 97 differentially expressed proteins from Al-tolerant wheat roots were screened and 11 of the 97 proteins were root elongation related. The 14-3-3 protein, plasma membrane ATPase, phospholipase D, and peroxidase are involved in cell wall component metabolism. The cellulase activity and callase activity were down-regulated by Al stress, whereas, the PAL, CAD, and POD activities were up-regulated. In addition, the callose, cellulose, lignin, and H2O2 contents varied significantly. Furthermore, Al stress inhibited root elongation in a metabolic enzyme and carbohydrate-dependent manner. The results indicated that the protein involved with growth signaling is elongation factor 1-α. The cellular damage related proteins are glycosyltransferase and sucrose 1-fructosyltransferase. The iTRAQ analysis highlighted candidate proteins associated with root cell elongation and revealed several new aspects of the metabolic processes underlying Al toxicity and tolerance. We propose that Al stress leads to marked variations in metabolic enzyme activity, carbohydrate content, and cellular damage, followed by inhibition of root elongation in wheat roots. This study has provided the most integrated view of the adaptive root responses to Al-toxicity.

2018-01-15 | PXD008684 | iProX

Proteomics studies of outer and inner cellular layers of tomato root-tips for Al stress

Project description:Excess levels of Al3+ become highly harmful to plant roots. The epidermal and outer cortical layers of root-tips experience more severe damages than the inner tissues from Al toxicity. This project used laser capture microdissection (LCM) technology to isolate the outer and inner cell layers of cells in root-tips. Tomato "MicroTom" plants were grown in hydroponic solution supplemented with Al. Seeds derived from plants previously exposed to four generations of Al-treated solutions were considered stress-acclimated, these seeds were named G4Al+. Seeds harvested from soil-grown plants were also used, these seeds were named G0 seeds. Tandem mass tag (TMT) proteomics was used to identify differential proteomics responses among cells localized at different spaces in root-tips and those between the stress-acclimated and non-acclimated plants.

2022-02-14 | PXD021994 | Pride

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