Transcriptome profiling of RHD6-regulated genes under Al stress
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA843998 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR19450954.fastq.gz | Fastqsanger.gz | |||
| SRR19450958.fastq.gz | Fastqsanger.gz | |||
| SRR19450961.fastq.gz | Fastqsanger.gz | |||
| SRR19450963.fastq.gz | Fastqsanger.gz |
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Project description:To further better understand the downstream responsive transcriptome networks of RHD6 in response to Al stress, the transcriptional profile of WT and rhd6-1 mutant in the absence or presence of Al stress was examined using RNAseq.
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Project description:Gene expression profiling in soybean under aluminum stress: genes differentially expressed between Al-tolerant and Al-sensitive genotypes. Aluminum toxicity is the most important constraint of crop production on acid soils. Understanding the molecular and genetic mechanisms of tolerance is crucial for developing efficient breeding programs to improve Al tolerance. This research was undertaken to identify candidate Al-tolerance genes in soybean. Two soybean genotypes PI 416937 (Al-tolerant) and Young (Al-sensitive) seedlings were exposed to zero or 10 µM Al in a growth chamber under hydroponic conditions for four time spans of 2, 12, 48 or 72 hrs. Microarray analysis was made on mRNA isolated from 1 cm long tap root tips using an Affymetrix soybean genome array. Both novel and previously reported aluminum-responsive genes were identified. The differentially expressed genes were enriched for metabolism, stress response and transporters. Multiple putative Al-tolerance genes uniquely induced in the tolerant genotype includes the up-regulation of previously identified transcription factors auxin down regulated-like protein (ADR6-like) and basic leucine zipper (bZIP 94), sulfur transmembrane transport protein and lipid transfer protein (Sec 14 ) and novel genes that include rare cold inducible protein (RCI2B ), GPI-transamidase, malonyl-COA: Isoflavone 7-O-glucoside-6˝-O-malontransferase, a cell proliferation protein (WPP2), Oleosin protein, pectinestrease inhibitor, and impaired sucrose induction1. The genes identified in this study will be utilized as important genetic resources for future improvement of Al tolerance in soybean. Key words: Soybean, Al tolerance, gene expression, microarray
2011-10-07 | GSE18517 | GEO
Project description:Gene expression profiling in soybean under aluminum stress: genes differentially expressed between Al-tolerant and Al-sensitive genotypes. Aluminum toxicity is the most important constraint of crop production on acid soils. Understanding the molecular and genetic mechanisms of tolerance is crucial for developing efficient breeding programs to improve Al tolerance. This research was undertaken to identify candidate Al-tolerance genes in soybean. Two soybean genotypes PI 416937 (Al-tolerant) and Young (Al-sensitive) seedlings were exposed to zero or 10 µM Al in a growth chamber under hydroponic conditions for four time spans of 2, 12, 48 or 72 hrs. Microarray analysis was made on mRNA isolated from 1 cm long tap root tips using an Affymetrix soybean genome array. Both novel and previously reported aluminum-responsive genes were identified. The differentially expressed genes were enriched for metabolism, stress response and transporters. Multiple putative Al-tolerance genes uniquely induced in the tolerant genotype includes the up-regulation of previously identified transcription factors auxin down regulated-like protein (ADR6-like) and basic leucine zipper (bZIP 94), sulfur transmembrane transport protein and lipid transfer protein (Sec 14 ) and novel genes that include rare cold inducible protein (RCI2B ), GPI-transamidase, malonyl-COA: Isoflavone 7-O-glucoside-6˝-O-malontransferase, a cell proliferation protein (WPP2), Oleosin protein, pectinestrease inhibitor, and impaired sucrose induction1. The genes identified in this study will be utilized as important genetic resources for future improvement of Al tolerance in soybean. Key words: Soybean, Al tolerance, gene expression, microarray Two genotypes: PI 416937 (p) and Young (y); two treatments: aluminum or untreated; four time points: 2, 12, 48, and 72 hrs; 2 or 3 replicates.
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Project description:To understand the molecular network underlying the regulation of ALMT1 under Al stress by CML24, the transcriptional profile of wild type and cml24-2 mutant roots in the absence or presence of Al stress was examined using RNAseq.In roots of wild type, 1173 and 1493 genes were up- or down-regulated, respectively, by Al, while 919 and 1057 genes were up- or down-regulated, respectively, in roots of cml24-2 plants. Totally 382 and 176 genes were up- or down-regulated, respectively, at least 2-fold in the roots of the cml24-2 mutant compared with wild type plants in absence of Al. In presence of Al, a total of 412 genes were up-regulated and 178 genes were down-regulated at least 2-fold comparing the cml24-2 mutant with wild type plants.
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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.
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Project description:Transcriptome analysis of barley root meristem under Al and low pH stress
| PRJNA704034 | ENA
Project description:Gene expression profiling in soybean under aluminum stress: Transcriptome response to Al stress in roots of Al-tolerant genotype (PI 416937). Aluminum (Al) toxicity is a major constraint of crop production on acid soils. Many commercial soybean cultivars and advanced breeding lines have been evaluated for Al tolerance. Aluminum tolerance is quantitatively inherited trait in soybean making it difficult for genetic improvement. Understanding the molecular and genetic mechanisms of tolerance is crucial for developing efficient and effective programs aimed at improving Al tolerance trait The molecular mechanisms of Al tolerance is poorly understood in soybean. The objective of the research was to identify candidate aluminum tolerance genes in soybean Al-tolerant soybean genotype PI 416937 seedlings were exposed to zero or 10 µM Al in growth chamber under hydroponic conditions for four time span of 2, 12, 48 and 72 hrs in a randomized complete block design with three replications. Microarray analysis was made on mRNA isolated from 1 cm log tap root tips using Affymetrix soybean array with over 68,000 probe sets Glycine max L and wild soybean combined. Both novel and known genes were discovered in response to Al treatment. They include Al tolerance relevant proteins, families of transcription factors, zinc finger, bZIP, WRKY, MYB, ADR6, and NAC domain proteins were induced likely regulating Al tolerance downstream genes. Stress related proteins, cytochrome P450, glutathione-s transferase, glutaredoxin family and ascorbic acid biosynthesis protein were induced as signatures of cellular detoxification mechanisms. An ABC type multidrug resistance protein that could act as citrate transporter or Al exporter was up-regulated, a key Al tolerance mechanisms in several species. A cell wall loosening enzyme endoxylglucan hydrolases were also up-regulated probably reversing the wall rigidification caused by Al and promoting root growth under Al stress. Phytosulfokines growth factor involved in cell division and proliferation was up-regulated likely as a direct counter action to Al toxicity which inhibits root growth by limiting cell division and elongation. In conclusion, the Al tolerance candidate genes identified herein are potential targets for future genetic engineering and molecular breeding work on Al tolerance trait in soybean which in turn would contribute to gain in soybean productivity on acid soils.
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Project description: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.
2018-05-10 | GSE107531 | GEO
Project description:Aluminum (Al) is the most common metal in the Earth’s crust and Al toxicity is considered to be the most harmful abiotic stress in acidic soils that today comprise more than 50% of the world’s arable lands. The first symptom of Al toxicity is the reduction of root growth, resulting in decreased water and nutrients uptake, plant growth retardation, and finally, yield reduction. Barley (Hordeum vulgare L.), which is the fourth cereal crop in regards to cultivation area and production tonnage, belongs to crops most sensitive to toxic aluminum ions in low pH soils. We present the RNA-seq transcriptome analysis of root meristems of barley seedlings grown in hydroponics at optimal pH (6.0), low pH (4.0), and low pH with Al (10 µM of bioavailable Al3+ ions). Two independent experiments were conducted: with short-term (24 h) and long-term (7 days) Al treatment. Interestingly, in the short-term experiment, more genes were differentially expressed between root meristems grown at pH=6.0 and pH=4.0, than between those grown at pH=4.0 with and without Al treatment. The upregulated genes that were overrepresented at conditions of low pH, compared to optimal pH, were associated with response to oxidative stress, cell wall organization, and iron ion binding. Among genes downregulated by low pH were mainly those related to chromatin organization. These results show that low pH itself is a severe stress for barley plants. Among genes upregulated by short Al treatment, overrepresented were those related to response to stress condition and calcium ion binding. After 7 days of hydroponics, the number of DEGs between hydroponics at pH=4.0 and 6.0 were still high but lower than in the short-term experiment, which suggests that plants partially adapted to the low pH. Interestingly, 7 day Al treatment caused massive changes in the transcriptome profile compared to the condition of low pH alone. Over 4 000 genes were upregulated and almost 2 000 genes were downregulated by long-term Al stress. These DEGs were related to e.g. stress response, cell wall development and metal ion transport. Based on our results we can assume that both, Al3+ ions and low pH are harmful to barley plants.Additionally, we phenotyped in detail the root system of barley seedlings grown in the same hydroponic conditions for 7 days at pH=6.0, pH=4.0, and pH=4.0 with Al. The results correspond to transcriptomic data and show that low pH itself is a stress facor that causes a significant reduction of root growth and the addition of aluminum further increases this reduction. It should be underlined that in the acidic arable lands, plants are exposed simultaneously to both of these stresses (low pH and Al), as Al becomes soluble at pH below 5.5. The presented transcriptome analysis may help to find potential targets for breeding barley plants more tolerant to such conditions.
2021-02-23 | GSE167271 | GEO