Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNAseq analysis of Maize under nitrate limitation and recovery at different time points.

ABSTRACT: Nitrogen (N) is a key macronutrient required for plant growth, development, and yield. Improving nitrogen use efficiency (NUE) in maize is important for sustainable crop production and reducing fertilizer-associated environmental impacts. To investigate transcriptional responses to nitrate availability, we examined genome-wide gene expression dynamics in maize under nitrate-limiting, and nitrate-recovery conditions. This dataset captures rapid transcriptional shifts in both roots and leaves during nitrate deprivation and subsequent nitrate resupply.

ORGANISM(S): Zea mays

PROVIDER: GSE312408 | GEO | 2025/12/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Root gene expression profiles of two maize inbred lines (Lo5 and T250) in response to nitrate treatment

2014-05-19 | GSE49681 | GEO

RNAseq analysis of Sorghum under nitrate limitation and recovery at different time points.

Project description:Nitrogen availability strongly influences sorghum growth, physiology, and yield, making enhanced nitrogen use efficiency (NUE) critical for agricultural sustainability. To characterize transcriptional responses to nitrate availability in sorghum, we profiled genome-wide gene expression changes under nitrate-sufficient, nitrate-limiting, and nitrate-recovery conditions. This dataset provides temporal resolution of nitrate-responsive regulation in roots and leaves, enabling comparative insights into nitrogen signaling and assimilation.

2025-12-30 | GSE312411 | GEO

Root gene expression profiles of two maize inbred lines (Lo5 and T250) in response to nitrate treatment

Project description:Among the mineral elements necessary for plant growth, nitrogen (N) is the macronutrient required in larger amounts. The optimization of N use efficiency (NUE) in maize could be obtained through both genetic improvement and agronomic practices in order to enhance production and reduce the negative impact of the N fertilizer use on the environment. Physiological characterizations of inbred lines with different NUE are available in maize. Maize (Zea mays L.) seeds of two inbred lines (T250, Lo5) previously soaked in running water for 24 h, were allowed to germinate in the dark at 28M-BM-0C for 72 h over an aerated solution of 0.5 mM CaSO4. Half part of two-d-old seedlings was grown in a nutrient solution with 200 M-NM-<M of KNO3 (treated samples, +NO3-) and the other half with appropriate amounts of the corresponding chloride salt (KCl) (control samples, -NO3-). Three biological replicates were obtained by three independent experiments and collecting roots of treated (200 M-NM-<M NO3-) and not treated plants after 0, 1, 2 e 4 h for Lo5 inbred line and after 0, 5, 11 and 12 h for T250.

2014-05-19 | E-GEOD-49681 | biostudies-arrayexpress

ZmNRT1.1B (ZmNPF6.6) determines nitrogen use efficiency via regulation of nitrate transport and assimilation in maize

Project description:Nitrate (NO3-) is crucial for optimal plant growth and development and often limits crop productivity at the low availability. In comparison with model plant Arabidopsis, the molecular mechanisms underlying NO3- acquisition and utilization remain largely unclear in maize. In particular, only a few genes have been exploited to improve nitrogen use efficiency (NUE). Here, we demonstrated that NO3--inducible ZmNRT1.1B (ZmNPF6.6) positively regulated NO3--dependent growth and NUE in maize. We showed that the tandem duplicated proteoform ZmNRT1.1C is irrelevant to maize seedling growth under nitrate supply, however, loss-of-function of ZmNRT1.1B significantly weakened plant growth under adequate NO3- supply in both hydroponic and field conditions. 15N-labeled NO3- absorption assay indicated that ZmNRT1.1B mediated high-affinity NO3--transport and root-to-shoot NO3- translocation. Furthermore, upon NO3- supply, ZmNRT1.1B promotes cytoplasmic-to-nuclear shuttling of ZmNLP3.1 (ZmNLP8), which co-regulates the expression of genes involved in NO3- response, cytokinin biosynthesis and carbon metabolism. Remarkably, overexpression of ZmNRT1.1B in modern maize hybrids improved grain yield under nitrogen (N) limiting fields. Taken together, our study revealed a crucial role of ZmNRT1.1B in high-affinity NO3- transport and signaling and offers valuable genetic resource for breeding nitrogen use efficient high-yield cultivars.

2023-04-25 | GSE227472 | GEO

Root gene expression profiles of two maize inbred lines (Lo5 and T250) showing different nitrogen use efficiency (NUE) in response to the growth without N.

Project description:Among the mineral elements necessary for plant growth, nitrogen (N) is the macronutrient required in larger amounts. Maize genotypic-specific responses to N shortage could provide more information useful to improve NUE.

2020-04-14 | GSE135613 | GEO

Morphophysiological and Proteomic Profiling Reveals Mechanisms Underlying Nitrogen Use Efficiency in Popcorn (Zea mays everta)

Project description:Nitrogen (N) is an essential macronutrient for agricultural production, and its excessive use causes not only economic but also environmental damage. However, improving nitrogen use efficiency (NUE) remains a complex task for achieving more productive crops under conditions of limited nitrogen availability. To the best of our knowledge, this is the first study aiming to integrate the morphophysiological responses and proteomic profiles of leaves and roots of popcorn (Zea mays everta). For this, two inbred lines contrasting for NUE, i.e., P2 (high NUE) and L80 (low NUE), were cultivated under high (100% of N supply) and low (10% of N supply) nitrogen conditions. Morphological and physiological traiits such as photochemical quenching (qP), non-photochemical quenching (NPQ), quantum yield of photosystem II (ΦPSII), and potential photosynthesis (Apot) were evaluated. P2 showed more pronounced vegetative growth under low N, as well as higher values of qP, NPQ, and ΦPSII. Comparative proteomic analysis of the leaves identified 215 differentially accumulated proteins (DAPs) in P2 and 168 DAPs in L80, while in roots, 127 DAPs were observed in P2 and 172 in L80. In leaves, DAPs involved in the response to oxidative stress, energy metabolism, and photosynthesis represented the main differences between P2 and L80. In roots, DAPs involved in nitrate transport, ammonium assimilation, and amino acid metabolism seem to have contributed to the improved NUE in P2. This study provides valuable insights into the molecular mechanisms underlying NUE and opens avenues for molecular breeding aimed at selecting superior genotypes for the development of a more sustainable agriculture.

2025-03-11 | PXD048990 | Pride

Diatom transcriptomics under nitrate limitation

Project description:Here, we examined the ramifications of between-species diversity by documenting the transcriptional response of three marine diatoms - Thalassiosira pseudonana, Fragilariopsis cylindrus, and Pseudo-nitzschia multiseries - to the onset of nitrate limitation of growth, a common limiting nutrient in the ocean. Less than 5% of orthologous genes, shared across the three diatoms, displayed the same transcriptional responses across species when growth was limited by nitrate availability. Orthologs, such as those involved in nitrogen uptake and assimilation, as well as carbon metabolism, were differently expressed across the three species. The two pennate diatoms, F. cylindrus and P. multiseries, shared 3,839 clusters without orthologs in the genome of the centric diatom T. pseudonana. A majority of these pennate-clustered genes, as well as the non-orthologous genes in each species, had minimal annotation information, but were often significantly differentially expressed under nitrate limitation, indicating their potential importance in the response to nitrogen availability. Despite these variations in the specific transcriptional response of each diatom, overall transcriptional patterns suggested that all three diatoms displayed a common physiological response to nitrate limitation that consisted of a general reduction in carbon fixation and carbohydrate and fatty acid metabolism and an increase in nitrogen recycling.

2014-03-25 | GSE56132 | GEO

Transcriptional characterization of maize roots in response to urea and nitrate

Project description:Although urea is the most used nitrogen fertilizer worldwide, little is known on the capacity of crop plants to use urea per se as a nitrogen source for development and growth. To date, the molecular and physiological bases of its transport have been investigated only in a limited number of species. In particular, up to date only one study reported the transcriptomic modulation induced by urea treatment in the model plant Arabidopsis (MM-CM-)rigout et al., 2008 doi: 10.1104/pp.108.119339). In maize, one of crops using huge amount of urea, only a physiological characterization of uptake and assimilation of the N-source has been conducted. General aim of the present work was the comprehension of the molecular basis of urea uptake and assimilation in maize plants, using a transcriptomic approach. In addition, the work focused on the possible interactions between the two main N-sources, conceivably occurring concomitantly in the soil, urea and nitrate. 5 dd-old maize plants were treated for 8 hours with nutrient solution containing nitrogen in form of urea; nitrate; urea and nitrate; or not exposed to any form of nitrogen. Three different biological replicates were used for each sample repeating the experiment three times. All samples were obtained pooling roots of six plants.

2015-03-02 | E-GEOD-53102 | biostudies-arrayexpress

CPK signaling orchestrates the plant nitrate regulatory network

Project description:Nitrate is the limiting nitrogen nutrient enabling photosynthetic plants to support the conversion of inorganic elements to organic biomass, which sustains all lives. Plants evolved multifaceted nitrate responses to modulate global gene expression, metabolism and developmental programs. However, primary nitrate signaling mechanisms remained elusive. Using an ultrasensitive Ca2+ biosensor, unique nitrate-induced Ca2+ signaling was illuminated in Arabidopsis cells and plants. Integrative functional genomic screens, chemical genetics, genome-wide transcript sequencing, and analyses of nitrate-associated traits uncovered the surprising roles of Ca2+ sensor protein kinases (CPKs) in orchestrating diverse primary and long-term nitrate responses. Nitrate specifies CPK signaling to reprogram transcriptome and govern N-assimilation, metabolism, transport, hormones, shoot growth, and root system architecture. CPKs may be targeted to enhance nitrogen-use-efficiency, reduce fertilizer demands, and alleviate ecosystem pollution.

2017-05-19 | GSE73437 | GEO

nitrate induction - nlp mutants-Nitrate induction - nlp mutants

Project description:bra-inra09-02_bioen_nitrogen - nitrate induction - nlp mutants - Short term nitrate induction kinetics in wildtype, nlp7-1, nlp7-3 and nlp6nlp7 - 10 days old seedling grown in liquid culture on 3mM nitrate wer starvec for N for 3 days and the kinetic for the resupply of nitrate was studied during a short kinetic (0,5, 10,20 minutes).

2012-12-01 | GSE39261 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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