Analysis of Global Gene Expression in Brachypodium distachyon Reveals Extensive Network Plasticity in Response to Abiotic Stress

Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules which were up-regulated by each abiotic stress fell into diverse and unique gene ontology GO categories. This study provides genomics resources and improves our understanding of abiotic stress responses of Brachypodium.

• Publication year

  2014

• Venue

  PLoS ONE

• Publication date

  2014-01-29

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1371/journal.pone.0087499PMID 24489928PMCID 3906199
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Stress-mediated alterations in chromatin architecture correlate with down-regulation of a gene encoding 60S rpL32 in rice.

  2013cited by this paper
• Maximizing capture of gene co-expression relationships through pre-clustering of input expression samples: an Arabidopsis case study

  2013cited by this paper
• Structure, Function and Networks of Transcription Factors Involved in Abiotic Stress Responses

  2013cited by this paper
• Arabidopsis ubiquitin ligase MIEL1 mediates degradation of the transcription factor MYB30 weakening plant defence

  2013cited by this paper
• Coexpression network analysis associated with call of rice seedlings for encountering heat stress

  2013cited by this paper
• Reference genome sequence of the model plant Setaria

  2012cited by this paper
• Fast R Functions for Robust Correlations and Hierarchical Clustering.

  2012cited by this paper
• Comparative analyses reveal potential uses of Brachypodium distachyon as a model for cold stress responses in temperate grasses

  2012cited by this paper
• Phytozome: a comparative platform for green plant genomics

  2011cited by this paper
• Global Landscape of a Co-Expressed Gene Network in Barley and its Application to Gene Discovery in Triticeae Crops

  2011cited by this paper
• The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

  2011cited by this paper
• Transcriptional responses of winter barley to cold indicate nucleosome remodelling as a specific feature of crown tissues

  2011cited by this paper
• Epigenetic control of gene regulation in plants.

  2011cited by this paper
• Mutations in MYB3R1 and MYB3R4 Cause Pleiotropic Developmental Defects and Preferential Down-Regulation of Multiple G2/M-Specific Genes in Arabidopsis1[C][W]

  2011influential reference
• Abiotic Stress Response in Plants - Physiological, Biochemical and Genetic Perspectives

  2011cited by this paper
• ABA-mediated transcriptional regulation in response to osmotic stress in plants

  2011influential reference
• A stress-free walk from Arabidopsis to crops.

  2011cited by this paper
• Plant abiotic stress: insights from the genomics era

  2011cited by this paper
• Freezing Tolerance in Plants Requires Lipid Remodeling at the Outer Chloroplast Membrane

  2010cited by this paper
• Linking the Salt Transcriptome with Physiological Responses of a Salt-Resistant Populus Species as a Strategy to Identify Genes Important for Stress Acclimation1[W][OA]

  2010influential reference
• Plant physiology and proteomics reveals the leaf response to drought in alfalfa (Medicago sativa L.)

  2010cited by this paper
• Gene regulation by nucleosome positioning.

  2010cited by this paper
• Genome-wide mapping of alternative splicing in Arabidopsis thaliana.

  2010cited by this paper
• Plant responses to cold: Transcriptome analysis of wheat.

  2010cited by this paper
• Artemisia L. species recognized by the local community of the northern areas of Pakistan as folk therapeutic plants

  2010cited by this paper
• Research on plant abiotic stress responses in the post-genome era: past, present and future.

  2010cited by this paper
• agriGO: a GO analysis toolkit for the agricultural community

  2010cited by this paper
• Genome sequencing and analysis of the model grass Brachypodium distachyon

  2010cited by this paper
• Genome sequence of the palaeopolyploid soybean

  2010cited by this paper
• Cytoscape 2.8: new features for data integration and network visualization

  2010cited by this paper
• Altered expression of pyrophosphate: Fructose-6-phosphate 1-phosphotransferase affects the growth of transgenic Arabidopsis plants

  2009cited by this paper
• The B73 Maize Genome: Complexity, Diversity, and Dynamics

  2009cited by this paper
• DNA-methylation changes induced by salt stress in wheat Triticum aestivum

  2009cited by this paper
• Roles for Arabidopsis CAMTA Transcription Factors in Cold-Regulated Gene Expression and Freezing Tolerance[W][OA]

  2009influential reference
• Photosynthesis under drought and salt stress: regulation mechanisms from whole plant to cell.

  2009cited by this paper
• PlnTFDB: updated content and new features of the plant transcription factor database

  2009cited by this paper
• Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays.

  2009cited by this paper
• Structuring and extracting knowledge for the support of hypothesis generation in molecular biology

  2009influential reference
• The Sorghum bicolor genome and the diversification of grasses

  2009cited by this paper
• Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array.

  2008cited by this paper
• Heat stress-responsive transcriptome analysis in heat susceptible and tolerant wheat (Triticum aestivum L.) by using Wheat Genome Array

  2008cited by this paper
• WGCNA: an R package for weighted correlation network analysis

  2008cited by this paper
• FactoMineR: An R Package for Multivariate Analysis

  2008cited by this paper
• Breeding for abiotic stresses for sustainable agriculture

  2008cited by this paper
• Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle

  2007cited by this paper
• Mechanisms of high salinity tolerance in plants.

  2007cited by this paper
• Calcium Signaling via Phospholipase C Is Essential for Proline Accumulation upon Ionic But Not Nonionic Hyperosmotic Stresses in Arabidopsis1

  2007cited by this paper
• Network Discovery Pipeline Elucidates Conserved Time-of-Day–Specific cis-Regulatory Modules

  2007influential reference
• Rapid variations of mesophyll conductance in response to changes in CO2 concentration around leaves.

  2007cited by this paper
• The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses.

  2007cited by this paper
• The TIGR Rice Genome Annotation Resource: improvements and new features

  2006cited by this paper
• Temperature dependence of photosynthesis in Arabidopsis plants with modifications in Rubisco activase and membrane fluidity.

  2005cited by this paper
• Effects of winter cold stress on photosynthesis and photochemical efficiency of PSII of the Mediterranean Cistus albidus L. and Quercus ilex L.

  2005cited by this paper
• Cold, salinity and drought stresses: an overview.

  2005influential reference
• Role of calcium ion in protection against heat and high irradiance stress-induced oxidative damage to photosynthesis of wheat leaves

  2005cited by this paper
• Theoretical and practical advances in genome halving

  2004cited by this paper
• Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis.

  2004cited by this paper
• Calmodulin Is Involved in Heat Shock Signal Transduction in Wheat1

  2003cited by this paper
• Exploration, normalization, and summaries of high density oligonucleotide array probe level data.

  2003influential reference
• Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance

  2003cited by this paper
• CBL1, a Calcium Sensor That Differentially Regulates Salt, Drought, and Cold Responses in Arabidopsis Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.012393.

  2003cited by this paper
• Plant breeding and drought in C3 cereals: what should we breed for?

  2002cited by this paper
• PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences

  2002cited by this paper
• InterProScan - an integration platform for the signature-recognition methods in InterPro

  2001influential reference
• Exceptional sensitivity of Rubisco activase to thermal denaturation in vitro and in vivo.

  2001cited by this paper
• In silico prediction of protein-protein interactions in human macrophages

  2001influential reference
• Cell signaling under salt, water and cold stresses.

  2001cited by this paper
• Characterization of two glutamate decarboxylase cDNA clones from Arabidopsis.

  1998cited by this paper
• Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit.

  1997cited by this paper
• Cold calcium signaling in Arabidopsis involves two cellular pools and a change in calcium signature after acclimation.

  1996cited by this paper
• A novel cis-acting element in an Arabidopsis gene is involved in responsiveness to drought, low-temperature, or high-salt stress.

  1994cited by this paper
• Stomatal Closure in Conifer Seedlings in Response to Leaf Moisture Stress

  1969cited by this paper
• Statistical Tables for Biological, Agricultural and Medical Research

  1956cited by this paper
• Statistical Tables for Biological, Agricultural and Medical Research.

  1939cited by this paper

• Genome-Wide Identification of SRS Gene Family in Wheat and Expression Analysis Under Abiotic Stress

  2025cites this paper
• Plant growth-promoting endophytic consortium improved artemisinin biosynthesis via modulating antioxidants, gene expression, and transcriptional profile in Artemisia annua (L.) under stressed environments

  2025cites this paper
• Unraveling the occurrence of hyperhydricity in oil palm somatic embryos during somatic embryogenesis process

  2024cites this paper
• Selection on genome‐wide gene expression plasticity of rice in wet and dry field environments

  2024cites this paper
• Heat Stress Effects on Legumes: Challenges, Management Strategies and Future Insights

  2024cites this paper
• Transcriptomic and co-expression network analyses on diverse wheat landraces identifies candidate master regulators of the response to early drought

  2023cites this paper
• Bio Prospecting of Endophytes and PGPRs in Artemisinin Production for the Socio-economic Advancement

  2023cites this paper
• Plasma-activated water regulated transcriptome gene expression leading to high germination and growth of mung beans

  2023cites this paper
• Comparative Analysis of Fruits and Vegetables Quality Using AI Assisted Technologies: A Review

  2023cites this paper
• Patterns of pan‐genome occupancy and gene coexpression under water‐deficit in Brachypodium distachyon

  2022cites this paper
• Targeted and Untargeted Metabolomic Analyses Reveal Organ Specificity of Specialized Metabolites in the Model Grass Brachypodium distachyon

  2022cites this paper
• Photosynthetic Carbon Fixation and Sucrose Metabolism Supplemented by Weighted Gene Co-expression Network Analysis in Response to Water Stress in Rice With Overlapping Growth Stages

  2022cites this paper
• A stress-inducible protein regulates drought tolerance and flowering time in Brachypodium and Arabidopsis

  2022cites this paper
• An integrative computational approach to predict stress-specific candidate and shared genes in multiple plant stresses

  2022cites this paper
• Local diversity of drought resistance and resilience in Populus accessions correlates with the variation of DNA methylation.

  2022cites this paper
• Testing the chilling‐ before drought‐tolerance hypothesis in Pooideae grasses

  2022cites this paper
• Comparative time-course transcriptome analysis of two contrasting alfalfa (Medicago sativa L.) genotypes reveals tolerance mechanisms to salt stress

  2022cites this paper
• A Proteome-Level Investigation Into Plasmodiophora brassicae Resistance in Brassica napus Canola

  2022cites this paper
• Parallel adaptation to lower altitudes is associated with enhanced plasticity in Heliosperma pusillum (Caryophyllaceae)

  2022cites this paper
• Comparative transcriptome sequencing analysis and functional identification of a NAM-2-like gene in jute (Corchorus capsularis L.).

  2021cites this paper
• A review on applications of plant network biology to understand the drought stress response in economically important cereal crops

  2021cites this paper
• Linking Plants Functioning to Adaptive Responses Under Heat Stress Conditions: A Mechanistic Review

  2021cites this paper
• Patterns of gene co-expression under water-deficit treatments and pan-genome occupancy in Brachypodium distachyon

  2021cites this paper
• Allotetraploidization in Brachypodium May Have Led to the Dominance of One Parent’s Metabolome in Germinating Seeds

  2021cites this paper
• Physiological and transcriptome analysis of Poa pratensis var. anceps cv. Qinghai in response to cold stress

  2020cites this paper
• A critical review on computer vision and artificial intelligence in food industry

  2020cites this paper
• Dynamics of Global Gene Expression and Regulatory Elements in Growing Brachypodium Root System

  2020cites this paper
• Comparative time-course transcriptome analysis in contrasting Carex rigescens genotypes in response to high environmental salinity.

  2020cites this paper
• The Role of FLOWERING LOCUS C Relatives in Cereals

  2020cites this paper
• Exploring Core Response Mechanisms to Multiple Environmental Stressors Via A Genome‐Wide Study in the Brown Alga Saccharina japonica (Laminariales, Phaeophyceae)

  2020cites this paper
• Transcriptional memories mediate the plasticity of cold stress responses to enable morphological acclimation in Brachypodium distachyon

  2020cites this paper
• Genetic and Methylome Variation in Turkish Brachypodium Distachyon Accessions Differentiate Two Geographically Distinct Subpopulations

  2020cites this paper
• Biochemical characterization of recombinant UDP-sugar pyrophosphorylase and galactinol synthase from Brachypodium distachyon

  2020cites this paper
• Partial defoliation of Brachypodium distachyon plants grown in petri dishes under low light increases P and other nutrient levels concomitantly with transcriptional changes in the roots

  2019influential citation
• Hydroxyproline-Rich Glycoproteins as Markers of Temperature Stress in the Leaves of Brachypodium distachyon

  2019cites this paper
• Transcriptional and Metabolomic Analyses Indicate that Cell Wall Properties are Associated with Drought Tolerance in Brachypodium distachyon

  2019cites this paper
• Depicting the Core Transcriptome Modulating Multiple Abiotic Stresses Responses in Sesame (Sesamum indicum L.)

  2019cites this paper
• Unraveling Field Crops Sensitivity to Heat Stress：Mechanisms, Approaches, and Future Prospects

  2018cites this paper
• R(NA)‐tistic expression: The art of matching unknown mRNA and proteins to environmental response in ecological genomics

  2018cites this paper
• Transcriptome Sequencing of Two Kentucky Bluegrass (Poa pratensis L.) Genotypes in Response to Heat Stress

  2018cites this paper
• Transcriptome changes induced by abiotic stresses in Artemisia annua

  2018cites this paper
• Successive evolutionary steps drove Pooideae grasses from tropical to temperate regions.

  2018cites this paper
• Brachypodium: A Monocot Grass Model Genus for Plant Biology[OPEN]

  2018influential citation
• Regulation of cell wall development in Brachypodium distachyon in vitro as affected by cytokinin and gas exchange

  2018cites this paper
• Brachypodium distachyon seedling growth visualization under osmotic stress and overexpression of MIR7757 to increase drought tolerance

  2018cites this paper
• Integrated “omics” approaches to sustain global productivity of major grain legumes under heat stress

  2017cites this paper
• Interactive effects of water limitation and elevated temperature on the physiology, development and fitness of diverse accessions of Brachypodium distachyon.

  2017cites this paper
• Temporal network analysis identifies early physiological and transcriptomic indicators of mild drought in Brassica rapa

  2017cites this paper
• Expression atlas and comparative coexpression network analyses reveal important genes involved in the formation of lignified cell wall in Brachypodium distachyon.

  2017cites this paper
• Unique Physiological and Transcriptional Shifts under Combinations of Salinity, Drought, and Heat1[OPEN]

  2017cites this paper
• Differentially Regulated Orthologs in Sorghum and the Subgenomes of Maize[OPEN]

  2017cites this paper
• Heat Stress Regulates the Expression of Genes at Transcriptional and Post-Transcriptional Levels, Revealed by RNA-seq in Brachypodium distachyon

  2017cites this paper
• Microarray meta-analysis to explore abiotic stress-specific gene expression patterns in Arabidopsis

  2017cites this paper
• Genome-Wide Analysis and Expression Profiles of the MYB Genes in Brachypodium distachyon

  2017cites this paper
• Brachypodium distachyon BdPP2CA6 Interacts with BdPYLs and BdSnRK2 and Positively Regulates Salt Tolerance in Transgenic Arabidopsis

  2017cites this paper
• Food Legumes and Rising Temperatures: Effects, Adaptive Functional Mechanisms Specific to Reproductive Growth Stage and Strategies to Improve Heat Tolerance

  2017cites this paper
• Genome-wide survey of heat shock factors and heat shock protein 70s and their regulatory network under abiotic stresses in Brachypodium distachyon

  2017cites this paper
• Seed desiccation mechanisms co-opted for vegetative desiccation in the resurrection grass Oropetium thomaeum.

  2017cites this paper
• Exploring the heat-responsive chaperones and microsatellite markers associated with terminal heat stress tolerance in developing wheat

  2017cites this paper
• Differentially regulated ortholog analysis demonstrates that early transcriptional responses to cold are more conserved in Andropogoneae

  2017cites this paper
• Comparative transcriptomics provides insight into the evolution of cold response in Pooideae

  2017cites this paper
• Transcriptomic and Epigenetic Responses to Environmental Stress in Marine Bivalves with a Focus on Harmful Algal Blooms

  2017cites this paper
• Genomics-Assisted Breeding for Improving Stress Tolerance of Graminaceous Crops to Biotic and Abiotic Stresses: Progress and Prospects

  2017cites this paper
• Differentially regulated ortholog analysis demonstrations that early transcriptional responses to cold have diverged slowly than downstream responses in panicoid grasses

  2017cites this paper
• Gene expression patterns of two dominant tallgrass prairie species differ in response to warming and altered precipitation

  2016cites this paper
• Development and Application of Comparative Gene Co-expression Network Methods in Brachypodium distachyon

  2016influential citation
• Genome-wide analysis of response to low sulfur (LSU) genes in grass species and expression profiling of model grass species Brachypodium distachyon under S deficiency

  2016cites this paper
• Advances in Plant Tolerance to Abiotic Stresses

  2016cites this paper
• Genetics and Genomics of Brachypodium

  2016cites this paper
• Artificial Microbiome-Selection to Engineer Microbiomes That Confer Salt-Tolerance to Plants

  2016cites this paper
• Molecular Cloning and Functional Characterization of Two Brachypodium distachyon UBC13 Genes Whose Products Promote K63-Linked Polyubiquitination

  2016cites this paper
• Drought stress and carbon assimilation in a warming climate: Reversible and irreversible impacts.

  2016cites this paper
• High-Throughput Sequencing Reveals H2O2 Stress-Associated MicroRNAs and a Potential Regulatory Network in Brachypodium distachyon Seedlings

  2016cites this paper
• Expansion and stress responses of AP2/EREBP superfamily in Brachypodium Distachyon

  2016cites this paper
• Small RNAs in Plant Responses to Abiotic Stresses: Regulatory Roles and Study Methods

  2015cites this paper
• Transcriptional networks-crops, clocks, and abiotic stress.

  2015cites this paper
• Brachypodium and the Abiotic Environment

  2015influential citation
• Stress-induced endogenous siRNAs targeting regulatory intron sequences in Brachypodium

  2015cites this paper
• Transcriptome analysis of hormone-induced gene expression in Brachypodium distachyon

  2015cites this paper
• Brachypodium distachyon as a Genetic Model System.

  2015cites this paper
• Genome-wide evolutionary characterization and analysis of bZIP transcription factors and their expression profiles in response to multiple abiotic stresses in Brachypodium distachyon

  2015cites this paper
• The Brachypodium distachyon Reference Genome

  2015cites this paper
• Brachypodium: A Model Temperate Grass

  2015cites this paper
• Comparative physiological and metabolomic responses of four Brachypodium distachyon varieties contrasting in drought stress resistance

  2015influential citation
• Cold Responsive Gene Expression Profiling of Sugarcane and Saccharum spontaneum with Functional Analysis of a Cold Inducible Saccharum Homolog of NOD26-Like Intrinsic Protein to Salt and Water Stress

  2015cites this paper
• Comparative transcriptome profiling of a desert evergreen shrub, Ammopiptanthus mongolicus, in response to drought and cold stresses

  2014influential citation
• Heat stress in crop plants: its nature, impacts and integrated breeding strategies to improve heat tolerance

  2014cites this paper
• Brachypodium: a promising hub between model species and cereals.

  2014cites this paper
• Détoxication des mycotoxines par les plantes : analyse de l'interaction entre Brachypodium distachyon et Fusarium graminearum

  2014cites this paper