ArticleBMC genomics2022
Gene-coexpression network analysis identifies specific modules and hub genes related to cold stress in rice.
Article in BMC genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28 citing papers in PubMed, 42 citations in OpenAlex.
- Transcriptomic and Physiological Profiling Elucidates Differential Salt Stress Responses in Tolerant 'SO4' and Sensitive 'Beida' Grapevine Rootstocks.International journal of molecular sciences · 2026Article
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- ROS-Centered Transcriptomic Regulatory Networks Linking Salinity Stress, Antioxidant Defense and Processability Traits inCurrent issues in molecular biology · 2026Review
- Genome-wide identification and expression analysis of the UGT gene family in honeysuckle.BMC plant biology · 2026Article
- Transcriptome analysis and characterization of cathepsin B-like protein inMolecular breeding : new strategies in plant improvement · 2026Article
- Autophagy-Mediated Adaptation: Revealing the Role of Autophagy in Plant Responses to Abiotic Stress.Genes · 2025Review
- Gene Editing of a Susceptibility LncRNA Enhances Broad-Spectrum Disease Resistance in Rice without Developmental Trade-Offs.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- A multi-layered systems biology framework reveals dual-phased regulators and hormonal crosstalk underlying soybean cold tolerance.Plant cell reports · 2025Article
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- Isolation and identification of core-genes in barley roots under low phosphorus stress.Molecular biology reports · 2025Article
- WGCNA analysis and identification of key genes in tobacco in response to different nitrogen levels.BMC plant biology · 2025Article
- 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
- Time-course transcriptome analysis reveals gene co-expression networks and transposable element responses to cold stress in cotton.BMC genomics · 2025Article
- Genome-Wide Identification and Analysis of Phospholipase C Gene Family Reveals Orthologs, Co-Expression Networks, and Expression Profiling Under Abiotic Stress inPlants (Basel, Switzerland) · 2024Article
- In-silico analysis predicts disruption of normal angiogenesis as a causative factor in osteoporosis pathogenesis.BMC genomic data · 2024Article
- Identification and core gene-mining of Weighted Gene Co-expression Network Analysis-based co-expression modules related to flood resistance in quinoa seedlings.BMC genomics · 2024Article
- Comparison of Transcriptome Differences between Two Rice Cultivars Differing in Cadmium Translocation from Spike-Neck to Grain.International journal of molecular sciences · 2024Article
- Transcriptome analysis of high- and low-selenium genotypes identifies genes responsible for selenium absorption, translocation, and accumulation.Frontiers in plant science · 2024Article
- Detection of locally adapted genomic regions in wild rice (Oryza rufipogon) using environmental association analysis.G3 (Bethesda, Md.) · 2023Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWhen plants are subjected to cold stress, they undergo a series of molecular and physiological changes to protect themselves from injury. Indica cultivars can usually withstand only mild cold stress in a relatively short period. Hormone-mediated defence response plays an important role in cold stress. Weighted gene co-expression network analysis (WGCNA) is a very useful tool for studying the correlation between genes, identifying modules with high phenotype correlation, and identifying Hub genes in different modules. Many studies have elucidated the molecular mechanisms of cold tolerance in different plants, but little information about the recovery process after cold stress is available.
resultsTo understand the molecular mechanism of cold tolerance in rice, we performed comprehensive transcriptome analyses during cold treatment and recovery stage in two cultivars of near-isogenic lines (9311 and DC907). Twelve transcriptomes in two rice cultivars were determined. A total of 2509 new genes were predicted by fragment splicing and assembly, and 7506 differentially expressed genes were identified by pairwise comparison. A total of 26 modules were obtained by expression-network analysis, 12 of which were highly correlated with cold stress or recovery treatment. We further identified candidate Hub genes associated with specific modules and analysed their regulatory relationships based on coexpression data. Results showed that various plant-hormone regulatory genes acted together to protect plants from physiological damage under short-term low-temperature stress. We speculated that this may be common in rice. Under long-term cold stress, rice improved the tolerance to low-temperature stress by promoting autophagy, sugar synthesis, and metabolism.
conclusionThrough WGCNA analysis at the transcriptome level, we provided a potential regulatory mechanism for the cold stress and recovery of rice cultivars and identified candidate central genes. Our findings provided an important reference for the future cultivation of rice strains with good tolerance.
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