ArticleBMC plant biology2019
Genes, pathways and transcription factors involved in seedling stage chilling stress tolerance in indica rice through RNA-Seq analysis.
Article in BMC plant biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers, 1 of them a synthesis that pooled it.
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60 citing papers in PubMed, 1 synthesis or guideline pooled it, 146 citations in OpenAlex.
- Genome-wide lncRNAs identification and association analysis for cold-responsive genes at the booting stage in rice (Oryza sativa L.).The plant genome · 2020Pooled it
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- Whole Genome Sequencing of the Moruga Hill Rice (Biotech (Basel (Switzerland)) · 2026Article
- Natural variation in WRKY53 confers cold tolerance at the booting stage between japonica and indica rice.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Transcriptomic profiling reveals stage-specific responses to cold stress in rice seedlings.BMC plant biology · 2026Article
- Genome-wide association studies for identification of QTLs and key candidate genes to improve grain quality in rice (Food chemistry. Molecular sciences · 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
- Comparative Transcriptomic Analyses Reveal Key Pathways in Response to Cold Stress at the Germination Stage of Quinoa (Plants (Basel, Switzerland) · 2025Article
- Natural variation of CTB5 confers cold adaptation in plateau japonica rice.Nature communications · 2025Article
- Subtilisin-like protease 4 regulates cold tolerance through cell wall modification in rice.Scientific reports · 2025Article
- Mycorrhizal helper bacteria further promote mycorrhizal fungi to improve cold tolerance in rice seedlings: evidence from oxidative stress, osmoregulation, photosynthesis, and related genes in rice.Frontiers in plant science · 2025Article
- Physiological and molecular mechanisms of leaf response to high-temperature stress in high-temperature-resistant soybean varieties.BMC genomics · 2024Article
- Genetic Adaptations of Soybean to Cold Stress Reveal Key Insights Through Transcriptomic Analysis.Biology · 2024Article
- Article
- Identification of candidate genes controlling cold tolerance at the early seedling stage from Dongxiang wild rice by QTL mapping, BSA-Seq and RNA-Seq.BMC plant biology · 2024Article
- NIN-like proteins (NLPs) as crucial nitrate sensors: an overview of their roles in nitrogen signaling, symbiosis, abiotic stress, and beyond.Physiology and molecular biology of plants : an international journal of functional plant biology · 2024Review
- Identification of Key Genes and Pathways for Anaerobic Germination Tolerance in Rice Using Weighted Gene Co-Expression Network Analysis (WGCNA) in Association with Quantitative Trait Locus (QTL) Mapping.Rice (New York, N.Y.) · 2024Article
- Integrated transcriptomic and metabolomic analysis provides insights into cold tolerance in lettuce (Lactuca sativa L.).BMC plant biology · 2024Article
- Discovering the regulators of heat stress tolerance inPhysiology and molecular biology of plants : an international journal of functional plant biology · 2024Article
- Meta-QTL and ortho analysis unravels the genetic architecture and key candidate genes for cold tolerance at seedling stage in rice.Physiology and molecular biology of plants : an international journal of functional plant biology · 2024Article
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5 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundRice plants show yellowing, stunting, withering, reduced tillering and utimately low productivity in susceptible varieties under low temperature stress. Comparative transcriptome analysis was performed to identify novel transcripts, gain new insights into different gene expression and pathways involved in cold tolerance in rice.
resultsComparative transcriptome analyses of 5 treatments based on chilling stress exposure revealed more down regulated genes in susceptible and higher up regulated genes in tolerant genotypes. A total of 13930 and 10599 differentially expressed genes (DEGs) were detected in cold susceptible variety (CSV) and cold tolerant variety (CTV), respectively. A continuous increase in DEGs at 6, 12, 24 and 48 h exposure of cold stress was detected in both the genotypes. Gene ontology (GO) analysis revealed 18 CSV and 28 CTV term significantly involved in molecular function, cellular component and biological process. GO classification showed a significant role of transcription regulation, oxygen, lipid binding, catalytic and hydrolase activity for tolerance response. Absence of photosynthesis related genes, storage products like starch and synthesis of other classes of molecules like fatty acids and terpenes during the stress were noticed in susceptible genotype. However, biological regulations, generation of precursor metabolites, signal transduction, photosynthesis, regulation of cellular process, energy and carbohydrate metabolism were seen in tolerant genotype during the stress. KEGG pathway annotation revealed more number of genes regulating different pathways resulting in more tolerant. During early response phase, 24 and 11 DEGs were enriched in CTV and CSV, respectively in energy metabolism pathways. Among the 1583 DEG transcription factors (TF) genes, 69 WRKY, 46 bZIP, 41 NAC, 40 ERF, 31/14 MYB/MYB-related, 22 bHLH, 17 Nin-like 7 HSF and 4C3H were involved during early response phase. Late response phase showed 30 bHLH, 65 NAC, 30 ERF, 26/20 MYB/MYB-related, 11 C3H, 12 HSF, 86 Nin-like, 41 AP2/ERF, 55 bZIP and 98 WRKY members TF genes. The recovery phase included 18 bHLH, 50 NAC, 31 ERF, 24/13 MYB/MYB-related, 4 C3H, 4 HSF, 14 Nin-like, 31 bZIP and 114 WRKY TF genes.
conclusionsTranscriptome analysis of contrasting genotypes for cold tolerance detected the genes, pathways and transcription factors involved in the stress tolerance.
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