Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A DUF630 and 632 Domains-containing Protein, ZmNRL1, Acts as a Positive Regulator of Nitrogen Stress Response in Maize

ABSTRACT: Nitrogen (N) is a key macronutrient whose availability often determines maize growth and productivity. Improving nitrogen use efficiency (NUE) is critical to increase maize yield while reducing N input, and more importantly, alleviating environmental pollution. However, only a few genes have been exploited for maize NUE improvement thus far. Here, we evaluate NUE-related traits in 296 maize inbred lines. A total of 87 genetic variants, resolved to a total of 44 candidate genes, were found to associated with NUE-related traits through a genome-wide association study. We further found that the natural variations in ZmNRL1, encoding a DUF630 and DUF632 domains-containing protein, strongly associated with chlorophyll content under N starvation. Loss of ZmNRL1 function causes accelerated leaf senescence and reduces biomass, nitrate content and nitrate reductase activity under N limitation, while overexpression of ZmNRL1 enhanced N stress tolerance. Comparative transcriptome analysis revealed that ZmNRL1 has a broad impact on the expression of many N utilization and signaling genes. Furthermore, heterologous expression of ZmNRL1 in Arabidopsis also improved the growth and yield under N-limiting conditions. Thus, ZmNRL1 plays a key role in regulating maize adaptation to N limitation and could be a potential target for breeding high-yield maize with enhanced NUE.

ORGANISM(S): Zea mays

PROVIDER: GSE252822 | GEO | 2026/01/07

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

Project description: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.

2025-12-30 | GSE312408 | GEO

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

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

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

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

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.

2014-05-19 | GSE49681 | GEO

Zea mays Transcriptome or Gene expression

Project description:Development of crop varieties with high nitrogen use efficiency (NUE) is crucial for minimizing N loss, reducing environmental pollution and decreasing input cost. Maize is one of the most important crops cultivated worldwide and its productivity is closely linked to the amount of fertilizer used. A survey of the transcriptomes of shoot and root tissues of a maize hybrid line and its two parental inbred lines grown under sufficient and limiting N conditions by mRNA-Seq has been conducted to have a better understanding of how different maize genotypes respond to N limitation.

2014-01-09 | E-MTAB-4410 | biostudies-arrayexpress

Genomic basis of rice geographic adaptation to soil nitrogen

Project description:Intensive application of inorganic nitrogen underlies marked increase in crop production yet imposes detrimental impact on ecosystems, hence it is crucial for future sustainable agriculture to improve nitrogen-use efficiency (NUE). Here we report the genetic basis of NUE associated with the local soil adaptation in rice. With a diverse rice germplasm panel collected from different ecogeographic regions, we performed genome-wide association study on tillering response to nitrogen (TRN), the most correlated trait with NUE of rice, and identified OsTCP19 as a modulator of TRN via transcriptionally responding to nitrogen and targeting to Dwarf and Low-Tillering (DLT), a tiller-promoting gene. A 29-bp InDel in OsTCP19 promoter confers differential transcription response to nitrogen and TRN variation among rice varieties. The high-TRN allele of OsTCP19 (OsTCP19-H) is prevalent in wild rice population, but largely lost in modern cultivars correlating with increased local soil nitrogen content, suggesting that it might have contributed to geographic adaptation in rice. Introgression of OsTCP19-H into modern rice cultivars boosts grain yield and NUE under low or moderate nitrogen levels, demonstrating its enormous potential for rice breeding and environment amelioration through reducing nitrogen application.

2020-11-12 | GSE161265 | GEO

Model-to-crop conserved NUE Regulons enhance machine learning predictions of nitrogen use efficiency

Project description:In this data-rich era, the promise of systems biology is to learn gene regulatory networks controlling key agricultural traits. However, validating these networks in crops remains challenging. By integrating gene regulatory network and machine learning, we functionally validated network regulons predicting nitrogen use efficiency (NUE) in Arabidopsis and maize. Our time-course nitrogen response transcriptome analysis uncovered a conserved N-response cascade between maize and Arabidopsis. Using Dynamic Factor Graph, we inferred N-regulated gene regulatory networks (N-GRNs) in maize and validated TF-target interactions for 23 maize TFs with the TARGET, a cell-based TF-perturbation assay. We pruned the N-GRNs by Precision-Recall analysis. Combining these data, we uncovered a previously unknown role for KNOTTED1 in the dynamic N-signaling network. We learned gene-to-NUE trait models across 16 maize varieties using XGBoost trained on N-response genes conserved model-to-crop. Integrating NUE importance scores within our GRN, we ranked maize TFs by their NUENet scores. In a model-to-crop approach, we validated orthologous N-regulated TF-targets for the top-ranked maize NUENet TFs (MYB34/R424 targets) and the orthologous Arabidopsis TF (AtDIV123 targets) using the cell-based TARGET assay. The genes in this orthologous model-to-crop NUENet regulons were superior at predicting NUE traits in XGBoost models learned in both maize and Arabidopsis. Thus, our model-to-crop approach combining GRNs, machine learning, and orthologous network modules offers a strategic framework for crop trait improvement.

2025-05-09 | GSE280345 | GEO

Model-to-crop conserved NUE Regulons enhance machine learning predictions of nitrogen use efficiency

2025-05-09 | GSE280344 | GEO