Ontology highlight
ABSTRACT:
PROVIDER: PRJNA925925 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23171728_1.fastq.gz | Fastqsanger.gz | |||
| SRR23171728_2.fastq.gz | Fastqsanger.gz | |||
| SRR23171729_1.fastq.gz | Fastqsanger.gz | |||
| SRR23171729_2.fastq.gz | Fastqsanger.gz | |||
| SRR23171730_1.fastq.gz | Fastqsanger.gz |
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Project description:The development of crop genotypes with high nitrogen utilization efficiency (NUE) under low nitrogen (LN) conditions is of great significance for ensuring food security worldwide. However, different crops have different responses to LN stress, and the regulatory mechanisms involved remain unclear. Comparative transcriptomic of wheat genotypes with contrasting NUE is a strategy to reveal the genetic mechanism of wheat in response to LN stress. In this study, we employed RNA-sequencing (RNA-seq) to investigate the difference between the transcriptome profiles of two wheat genotypes differing in NUE under different N treatments. The results indicated that wheat with high and low NUE genotypes exhibited different gene expression patterns under LN conditions. To identify potential key genes, we classify these N-responsive genes into two major categories: pre-expressed genes and stress-expressed genes. In total, the pre-expressed genes identified in the genotypes with high NUE were 2.97 times that of wheat with low NUE. In summary, the identified candidate genes may provide new insights into comprehensive understanding of the genotypic difference and improving NUE in wheat.
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Project description:For analysis of ABA and nitrogen treated transcriptome, wild-type wheat JW1 at 3 days after germination was removed endosperm and cultured on wheat nutrient culture medium containing 2 mM nitrate for 3 days, and then transferred to a nitrogen-free wheat nutrient culture medium for an additional 2 days. Following this, the wheat seedlings were exposed to wheat nutrient culture medium containing 2 mM KCl or 2 mM KNO3, and/or ABA for 3 hours. The roots of wheat were collected and subjected to total RNA extraction using the TriZol RNA extraction kit (TransGen Biotech).
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Project description:For analysis of ABA and nitrogen treated transcriptome, wild-type wheat JW1 at 3 days after germination was removed endosperm and cultured on wheat nutrient culture medium containing 2 mM nitrate for 3 days, and then transferred to a nitrogen-free wheat nutrient culture medium for an additional 2 days. Following this, the wheat seedlings were exposed to wheat nutrient culture medium containing 2 mM KCl or 2 mM KNO3, and/or ABA for 3 hours. The roots of wheat were collected and subjected to total RNA extraction using the TriZol RNA extraction kit (TransGen Biotech).
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Project description:The transcriptome profile was examined in four wheat genotypes in roots and shoots under nitrogen stressed condition which indicates genotype specific transcript data-set apart from the common transcripts. Unique genes was identified for nitrogen uptake and utilization process. We used microarrays to detail the gene expression and identify the candidate genes related to uptake and utilization of nitrogen in root and shoot tissues of wheat genotypes.
2020-06-30 | GSE116473 | GEO
Project description:Nitrogen (N) is an essential nutrient element for crop productivity. Unfortunately, the nitrogen use efficiency (NUE) of crop plants gradually decreases with the increase of the nitrogen application rate. Nevertheless, little has been known about the molecular mechanisms of differences in NUE among genotypes of wheat. The use of near-isogenic lines (NILs) in transcriptome analysis can reduce genetic background noise. In this study, we used RNA-Sequencing (RNA-Seq) to compare the transcriptome profiling in NILs (1Y, high-NUE, and 1W, low-NUE) under normal nitrogen conditions. The results showed that 7,023 DEGs (4,738 up-regulated and 2,285 down-regulated) were identified in the 1Y vs 1W comparison. The responses of 1Y and 1W to normal nitrogen differed significantly in the transcriptional regulation mechanisms. Several genes belonging to the GS and GOGAT gene families were up-regulated in 1Y compared with 1W, and the enhanced carbon metabolism might lead 1Y to produce more C skeletons, metabolic energy, and reductants for nitrogen metabolism. A subset of transcription factors (TFs) family members such as ERF, WRKY, NAC, and MYB were also identified. Collectively, these identified candidate genes provided new information for a further understanding of the genotypic difference in NUE
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Project description:Abiotic stress causes disturbances in the cellular homeostasis. Re-adjustment of balance in carbon, nitrogen and phosphorus metabolism therefore plays a central role in stress adaptation. However, it is currently unknown which parts of the primary cell metabolism follow common patterns under different stress conditions and which represent specific responses. To address these questions, changes in transcriptome, metabolome and ionome were analyzed in maize source leaves from plants suffering low temperature, low nitrogen (N) and low phosphorus (P) stress. The selection of maize as study object provided data directly from an important crop species and the so far underexplored C4 metabolism. Growth retardation was comparable under all tested stress conditions. The only primary metabolic pathway responding similar to all stresses was nitrate assimilation, which was down-regulated. The largest group of commonly regulated transcripts followed the expression pattern: down under low temperature and low N, but up under low P. Several members of this transcript cluster could be connected to P metabolism and correlated negatively to different phosphate concentration in the leaf tissue. Accumulation of starch under low temperature and low N stress, but decrease in starch levels under low under low P conditions indicated that only low P treated leaves suffered carbon starvation. In conclusion, maize employs very different strategies for management of nitrogen and phosphorus metabolism under stress. While nitrate assimilation was regulated depending on demand by growth processes, phosphate concentrations changed depending on availability, thus building up reserves under excess conditions. Carbon and energy metabolism of the C4 maize leaves were particularly sensitive to P starvation.
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Project description:Abiotic stress causes disturbances in the cellular homeostasis. Re-adjustment of balance in carbon, nitrogen and phosphorus metabolism therefore plays a central role in stress adaptation. However, it is currently unknown which parts of the primary cell metabolism follow common patterns under different stress conditions and which represent specific responses. To address these questions, changes in transcriptome, metabolome and ionome were analyzed in maize source leaves from plants suffering low temperature, low nitrogen (N) and low phosphorus (P) stress. The selection of maize as study object provided data directly from an important crop species and the so far underexplored C4 metabolism. Growth retardation was comparable under all tested stress conditions. The only primary metabolic pathway responding similar to all stresses was nitrate assimilation, which was down-regulated. The largest group of commonly regulated transcripts followed the expression pattern: down under low temperature and low N, but up under low P. Several members of this transcript cluster could be connected to P metabolism and correlated negatively to different phosphate concentration in the leaf tissue. Accumulation of starch under low temperature and low N stress, but decrease in starch levels under low under low P conditions indicated that only low P treated leaves suffered carbon starvation. In conclusion, maize employs very different strategies for management of nitrogen and phosphorus metabolism under stress. While nitrate assimilation was regulated depending on demand by growth processes, phosphate concentrations changed depending on availability, thus building up reserves under excess conditions. Carbon and energy metabolism of the C4 maize leaves were particularly sensitive to P starvation. Responses of maize source leaves to low temperature, low nitrogen and low phosphorus conditions were tested in independent single-stress experiments. Seedlings were cultivated in pots containing nutrient-poor peat soil under the controlled conditions of a growth chamber. The plants were fertilized with modified Hoagland solutions, containing 15mM KNO3 and 0.5mM KH2PO4 for control conditions; for low N and low P treatment, the nutrient concentrations were reduced to 0.15mM KNO3 and 0.1mM KH2PO4, respectively. Low temperature treated plants were always supplied with control nutrient solution. Plants from the nitrogen and phosphorus experiment as well as the control temperature plants were exposed to 28°C during the day and 20°C during the night. Low temperature treatment was limited to the night period and was reduced to 4°C for the 10h dark period. Source leaf lamina were harvested at day 20 (low temperature experiment) or day 30 after start of germination (low nitrogen and low phosphorus experiment) for parallel analysis of transcriptome, metabolome and ion profiles. The molecular data is further supplemented by phenotypic characterization of the maize seedlings under investigation.
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