ArticlePlant physiology2009
Defining core metabolic and transcriptomic responses to oxygen availability in rice embryos and young seedlings.
Article in Plant physiology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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Who cites it
69 citing papers in PubMed, 161 citations in OpenAlex.
- Integrated Multi-Omics Analysis Reveals the Survival Strategy of Dongxiang Wild Rice (DXWR,Plants (Basel, Switzerland) · 2025Article
- ERFVIIs as transducers of oxygen-sensing in the evolution of land plant response to hypoxia.Molecular plant · 2025Article
- Comparative transcriptomic and proteomic analyses of hypoxia response in wild and cultivated tomato roots.BMC genomics · 2025Article
- The transcriptome landscape of Kumrogarh, a unique rice landrace showing the simultaneous presence of3 Biotech · 2025Article
- Genetic factors underlying anaerobic germination in rice: Genome-wide association study and transcriptomic analysis.The plant genome · 2024Article
- Article
- Plant Life with and without Oxygen: A Metabolomics Approach.International journal of molecular sciences · 2023Review
- GWAS Combined with WGCNA of Transcriptome and Metabolome to Excavate Key Candidate Genes for Rice Anaerobic Germination.Rice (New York, N.Y.) · 2023Article
- Characterization and in silico analysis of the domain unknown function DUF568-containing gene family in rice (Oryza sativa L.).BMC genomics · 2023Article
- Role of Gamma-Aminobutyric Acid in Plant Defense Response.Metabolites · 2023Review
- Genome-wide association study reveals novel genetic loci involved in anaerobic germination tolerance inMolecular breeding : new strategies in plant improvement · 2023Article
- The small subunit of Rubisco and its potential as an engineering target.Journal of experimental botany · 2023Review
- The Role of Alternative Oxidase in the Interplay between Nitric Oxide, Reactive Oxygen Species, and Ethylene in Tobacco (International journal of molecular sciences · 2022Article
- Try or Die: Dynamics of Plant Respiration and How to Survive Low Oxygen Conditions.Plants (Basel, Switzerland) · 2022Review
- Mapping QTLs for anaerobic tolerance at germination and bud stages using new high density genetic map of rice.Frontiers in plant science · 2022Article
- Multi-Omics Approaches Unravel Specific Features of Embryo and Endosperm in Rice Seed Germination.Frontiers in plant science · 2022Article
- Enriched-GWAS and Transcriptome Analysis to Refine and Characterize a Major QTL for Anaerobic Germination Tolerance in Rice.International journal of molecular sciences · 2021Article
- Promoter Architecture and Transcriptional Regulation of Genes Upregulated in Germination and Coleoptile Elongation of Diverse Rice Genotypes Tolerant to Submergence.Frontiers in genetics · 2021Article
- Nitric Oxide Turnover Under Hypoxia Results in the Rapid Increased Expression of the Plastid-Localized Phosphorylated Pathway of Serine Biosynthesis.Frontiers in plant science · 2021Article
- Metabolic signatures provide novel insights to Picrorhiza kurroa adaptation along the altitude in Himalayan region.Metabolomics : Official journal of the Metabolomic Society · 2020Article
9 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Analysis reveals that there is limited overlap in the sets of transcripts that show significant changes in abundance during anaerobiosis in different plant species. This may be due to the fact that a combination of primary effects, changes due to the presence or absence of oxygen, and secondary effects, responses to primary changes or tissue and developmental responses, are measured together and not differentiated from each other. In order to dissect out these responses, the effect of the presence or absence of oxygen was investigated using three different experimental designs using rice (Oryza sativa) as a model system. A total of 110 metabolites and 9,596 transcripts were found to change significantly in response to oxygen availability in at least one experiment. However, only one-quarter of these showed complementary responses to oxygen in all three experiments, allowing the core response to oxygen availability to be defined. A total of 10 metabolites and 1,136 genes could be defined as aerobic responders (up-regulated in the presence of oxygen and down-regulated in its absence), and 13 metabolites and 730 genes could be defined as anaerobic responders (up-regulated in the absence of oxygen and down-regulated in its presence). Defining core sets of transcripts that were sensitive to oxygen provided insights into alterations in metabolism, specifically carbohydrate and lipid metabolism and the putative regulatory mechanisms that allow rice to grow under anaerobic conditions. Transcript abundance of a specific set of transcription factors was sensitive to oxygen availability during all of the different experiments conducted, putatively identifying primary regulators of gene expression under anaerobic conditions. Combined with the possibility of selective transcript degradation, these transcriptional processes are involved in the core response of rice to anaerobiosis.
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Registered trials
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