Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome analysis of two near-isogenic lines with different NUE under normal nitrogen conditions in wheat

ABSTRACT: Transcriptome analysis of two near-isogenic lines with different NUE under normal nitrogen conditions in wheat

PROVIDER: PRJNA742655 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR14999754_1.fastq.gz	Fastqsanger.gz
	SRR14999754_2.fastq.gz	Fastqsanger.gz
	SRR14999755_1.fastq.gz	Fastqsanger.gz
	SRR14999755_2.fastq.gz	Fastqsanger.gz
	SRR14999756_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 24

Similar Datasets

Transcriptome analysis of two near-isogenic lines with different NUE under normal nitrogen conditions in wheat

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

2021-08-31 | GSE179179 | GEO

Transcriptome Analysis of Two Near-Isogenic Lines with Different NUE under Normal Nitrogen Conditions in Wheat.

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 N application rate. Nevertheless, little has been known about the molecular mechanisms of differences in NUE among genotypes of wheat. In this study, we used RNA-Sequencing (RNA-Seq) to compare the transcriptome profiling of flag leaves at the stage of anthesis in wheat NILs (1Y, high-NUE, and 1W, low-NUE) under normal nitrogen conditions (300 kg N ha-1, corresponding to 1.6 g N pot-1). We identified 7023 DEGs (4738 upregulated and 2285 downregulated) in the comparison between lines 1Y and 1W. The responses of 1Y and 1W to normal N differed in the transcriptional regulatory mechanisms. Several genes belonging to the GS and GOGAT gene families were upregulated 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.

| S-EPMC8389668 | biostudies-literature

Transcription profiling of Zea mays leafs of MON810 (Helen Bt) and near-isogenic commercial varieties (Helen) gorwn in low nitrogen conditions

Project description:Comparison of the transcriptome profiles of a widely commercialized maize MON810 variety and its non-GM near-isogenic counterpart subjected to low N fertilization farming practices

2010-09-21 | E-MEXP-2364 | biostudies-arrayexpress

Expression data in wheat (T. aestivum L.) near isogenic lines in response to powdery mildew infection

Project description:We used two wheat genotypes, the susceptible wheat cultivar ‘8866 ’(S) and its near isogenic line with single powdery mildew resistance gene ‘pm30’ (R), to investigate gene expression changes in response to powdery mildew infection by using Wheat Genome Array wheat young leveas of near isogenic lines before or 12 hours after powdery mildew infection were selected for RNA extraction and hybridization on Affymetrix microarrays.The leaf samples were harvested from three independent biological replicates, and the leaves without inoculation were regarded as control.

2011-02-15 | E-GEOD-27320 | biostudies-arrayexpress

Expression data in wheat (T. aestivum L.) near isogenic lines in response to powdery mildew infection

2011-02-15 | GSE27320 | GEO

Crown transcriptome analysis of Norstar (NO), Manitou (MA), and the near-isogenic lines (NIL) spring Norstar (SN) and winter Manitou (WM) under field conditions

Project description:To explore transcriptional regulations in common wheat cultivars Norstar (NO), Manitou (MA), and the near-isogenic lines (NIL) spring Norstar (SN) and winter Manitou (WM) during seasonal cold acclimation.

2018-03-30 | GSE101118 | GEO

Phaseolus vulgaris cultivar:Near isogenic lines

Project description:Phaseolus vulgaris cultivar:Near isogenic lines Transcriptome or Gene expression

| PRJNA342420 | ENA

RNA sequencing of the Hordeum vulgare near-isogenic line mnd1.a

Project description:RNA sequencing of the near-isogenic line mnd1.a in cv. Bowman background, compared to cv. Mesa and cv. Bowman Purpose: Expression analysis and variant calling.

2020-04-23 | GSE149110 | GEO

Transcriptome Analysis Reveals Different Responsive Patterns to Nitrogen Deficiency in Two Wheat Near-Isogenic Lines Contrasting for Nitrogen Use Efficiency.

Project description:The development of crop cultivars with high nitrogen use efficiency (NUE) under low-N fertilizer inputs is imperative for sustainable agriculture. However, there has been little research on the molecular mechanisms underlying enhanced resilience to low N in high-NUE plants. The comparison of the transcriptional responses of genotypes contrasting for NUE will facilitate an understanding of the key molecular mechanism of wheat resilience to low-N stress. In the current study, the RNA sequencing (RNA-seq) technique was employed to investigate the genotypic difference in response to N deficiency between two wheat NILs (1Y, high-NUE, and 1W, low-NUE). In our research, high- and low-NUE wheat NILs showed different patterns of gene expression under N-deficient conditions, and these N-responsive genes were classified into two major classes, including "frontloaded genes" and "relatively upregulated genes". In total, 103 and 45 genes were identified as frontloaded genes in high-NUE and low-NUE wheat, respectively. In summary, our study might provide potential directions for further understanding the molecular mechanism of high-NUE genotypes adapting to low-N stress.

| S-EPMC8614915 | biostudies-literature

Comparative proteomic analysis of near isogenic lines for qDSI.4B.1 QTL on short arm of chromosome 4B conferring drought tolerance in wheat

Project description:This study conducted isobaric tags for relative and absolute quantitation (iTRAQ) proteomic analysis on near-isogenic lines (NILs) to shed light on the drought tolerance conferring qDSI.4B.1 QTL on short arm of chromosome 4B.

2023-05-24 | PXD036534 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data