ArticleGenes2019
WGCNA Analysis of Salt-Responsive Core Transcriptome Identifies Novel Hub Genes in Rice.
Article in Genes, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed.
- Genome-Wide Identification and Characterization of the Annexin (ANN) Gene Family in Potato (Genes · 2026Article
- Integrated Transcriptomic and Metabolomic Analysis Reveals the Metabolic Basis and Regulatory Networks of Triterpenoid Biosynthesis inFoods (Basel, Switzerland) · 2026Article
- Molecular Mechanisms of Growth and Salt Tolerance in Diverse Rice Cultivars Balanced by Rhodobium marinum RH-AZ.Rice (New York, N.Y.) · 2026Article
- Aconserved salt-stress co-expression network in japonica rice reveals partially dissociated hub gene connectivity and transcriptional induction.Frontiers in plant science · 2026Article
- Comparative transcriptome analysis reveals the complex response mechanisms of soybean leaves and roots to salt stress.BMC plant biology · 2025Article
- Transcriptomic Meta-Analysis Reveals Hub Genes Integrating Multiple Abiotic Stress Responses in Wheat.Food science & nutrition · 2025Article
- Physiological Mechanisms and Core Genes in Response to Saline-Alkali Stress in Foxtail Millet (Biomolecules · 2025Article
- Weighted gene co-expression network analysis - based selection of hub genes related to phenolic and volatile compounds and seed coat color in sorghum.BMC plant biology · 2025Article
- Accelerating crop improvement via integration of transcriptome-based network biology and genome editing.Planta · 2025Review
- Transcriptome and Weighted Gene Co-Expression Network Analysis to Characterize the Expression of Genes Related to Yield Traits in Yunnan Hulled Wheat.International journal of molecular sciences · 2025Article
- ThePlants (Basel, Switzerland) · 2025Article
- Exploration of key genes and pathways in response to submergence stress in red clover (Trifolium pratense L.) by WGCNA.BMC plant biology · 2025Article
- Transcriptome and gene co-expression network analysis revealed a putative regulatory mechanism of low nitrogen response in rice seedlings.Frontiers in plant science · 2025Article
- Comparative transcriptomes and WGCNA reveal hub genes for spike germination in different quinoa lines.BMC genomics · 2024Article
- Comprehensive Genome-Wide Analysis of the Receptor-like Protein Gene Family and Functional Analysis ofPlants (Basel, Switzerland) · 2024Article
- Unveiling Salt Tolerance Mechanisms and Hub Genes in Alfalfa (Plants (Basel, Switzerland) · 2024Article
- Profiling of Key Hub Genes Using a Two-State Weighted Gene Co-Expression Network of 'Jao Khao' Rice under Soil Salinity Stress Based on Time-Series Transcriptome Data.International journal of molecular sciences · 2024Article
- Comprehensive Transcriptome and Proteome Analyses Reveal the Drought Responsive Gene Network in Potato Roots.Plants (Basel, Switzerland) · 2024Article
- Weighted gene co-expression network analysis reveals hub genes regulating response to salt stress in peanut.BMC plant biology · 2024Article
- Mining key circRNA-associated-ceRNA networks for milk fat metabolism in cows with varying milk fat percentages.BMC genomics · 2024Article
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Rice, being a major staple food crop and sensitive to salinity conditions, bears heavy yield losses due to saline soil. Although some salt responsive genes have been identified in rice, their applications in developing salt tolerant cultivars have resulted in limited achievements. Herein, we used bioinformatic approaches to perform a meta-analysis of three transcriptome datasets from salinity and control conditions in order to reveal novel genes and the molecular pathways underlying rice response to salt. From a total of 28,432 expressed genes, we identify 457 core differentially expressed genes (DEGs) constitutively responding to salt, regardless of the stress duration, genotype, or the tissue. Gene co-expression analysis divided the core DEGs into three different modules, each of them contributing to salt response in a unique metabolic pathway. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses highlighted key biological processes and metabolic pathways involved in the salt response. We identified important novel hub genes encoding proteins of different families including CAM, DUF630/632, DUF581, CHL27, PP2-13, LEA4-5, and transcription factors, which could be functionally characterized using reverse genetic experiments. This novel repertoire of candidate genes related to salt response in rice will be useful for engineering salt tolerant varieties.
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