ArticleFrontiers in plant science2023
Weighted gene co-expression network analysis of nitrogen (N)-responsive genes and the putative role of G-quadruplexes in N use efficiency (NUE) in rice.
Article in Frontiers in plant science, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed, 5 citations in OpenAlex.
- Machine Learning-Guided Stress Atlases Reveal Co-Expression Rewiring and Divergent Cellular Deployment of Abiotic Stress Programs in Rice and Wheat.International journal of molecular sciences · 2026Article
- Variations in Ecological Locations Induce Soybean Seed Wrinkles by Disrupting Source-Sink Relationship and Energy Metabolism at the Grain-Filling Stage.Plants (Basel, Switzerland) · 2026Article
- Identification of Gene Regulatory Network for Nitrogen-Promoted Tiller Regrowth in Perennial Rice.Rice (New York, N.Y.) · 2026Article
- Accelerating crop improvement via integration of transcriptome-based network biology and genome editing.Planta · 2025Review
- Identification and validation of hub genes associated with biotic and abiotic stresses by modular gene co-expression analysis in Oryza sativa L.Scientific reports · 2025Article
- Phenotypic, Physiological, and Gene Expression Analysis for Nitrogen and Phosphorus Use Efficienies in Three Popular Genotypes of Rice (Plants (Basel, Switzerland) · 2024Article
- Genome-Wide Identification and Co-Expression Networks ofPlants (Basel, Switzerland) · 2024Article
- An integrated transcriptome and physiological analysis of nitrogen use efficiency in rice (Frontiers in genetics · 2024Article
- Integrative Multi-Scale Analysis Identifies the Hub Gene TRE1 Associating Trehalose Metabolism With Salinity Tolerance in Rice.Physiologia plantarumArticle
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5 authors at 2 institutions in 1 country.
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Abstract
Rice is an important target to improve crop nitrogen (N) use efficiency (NUE), and the identification and shortlisting of the candidate genes are still in progress. We analyzed data from 16 published N-responsive transcriptomes/microarrays to identify, eight datasets that contained the maximum number of 3020 common genes, referred to as N-responsive genes. These include different classes of transcription factors, transporters, miRNA targets, kinases and events of post-translational modifications. A Weighted gene co-expression network analysis (WGCNA) with all the 3020 N-responsive genes revealed 15 co-expression modules and their annotated biological roles. Protein-protein interaction network analysis of the main module revealed the hub genes and their functional annotation revealed their involvement in the ubiquitin process. Further, the occurrences of G-quadruplex sequences were examined, which are known to play important roles in epigenetic regulation but are hitherto unknown in N-response/NUE. Out of the 3020 N-responsive genes studied, 2298 contained G-quadruplex sequences. We compared these N-responsive genes containing G-quadruplex sequences with the 3601 genes we previously identified as NUE-related (for being both N-responsive and yield-associated). This analysis revealed 389 (17%) NUE-related genes containing G-quadruplex sequences. These genes may be involved in the epigenetic regulation of NUE, while the rest of the 83% (1811) genes may regulate NUE through genetic mechanisms and/or other epigenetic means besides G-quadruplexes. A few potentially important genes/processes identified as associated with NUE were experimentally validated in a pair of rice genotypes contrasting for NUE. The results from the WGCNA and G4 sequence analysis of N-responsive genes helped identify and shortlist six genes as candidates to improve NUE. Further, the hitherto unavailable segregation of genetic and epigenetic gene targets could aid in informed interventions through genetic and epigenetic means of crop improvement.
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