Natural Variation of Transcriptional Auxin Response Networks in Arabidopsis thaliana[C][W][OA]

In this study, physiological, comparative transcriptomic, and network analysis approaches identify extensive natural variation of auxin responses among A. thaliana accessions. Expression level variation in auxin signaling genes is hypothesized to contribute to downstream variation in large auxin-regulated gene clusters. Natural variation has been observed for various traits in Arabidopsis thaliana. Here, we investigated natural variation in the context of physiological and transcriptional responses to the phytohormone auxin, a key regulator of plant development. A survey of the general extent of natural variation to auxin stimuli revealed significant physiological variation among 20 genetically diverse natural accessions. Moreover, we observed dramatic variation on the global transcriptome level after induction of auxin responses in seven accessions. Although we detect isolated cases of major-effect polymorphisms, sequencing of signaling genes revealed sequence conservation, making selective pressures that favor functionally different protein variants among accessions unlikely. However, coexpression analyses of a priori defined auxin signaling networks identified variations in the transcriptional equilibrium of signaling components. In agreement with this, cluster analyses of genome-wide expression profiles followed by analyses of a posteriori defined gene networks revealed accession-specific auxin responses. We hypothesize that quantitative distortions in the ratios of interacting signaling components contribute to the detected transcriptional variation, resulting in physiological variation of auxin responses among accessions.

• Publication year

  2010

• Venue

  The Plant Cell

• Publication date

  2010-07-01

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1105/tpc.110.073957PMID 20622145PMCID PMC2929100
• 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.

• RRS1 and RPS4 provide a dual Resistance-gene system against fungal and bacterial pathogens.

  2009cited by this paper
• What Has Natural Variation Taught Us about Plant Development, Physiology, and Adaptation?

  2009cited by this paper
• Growth and development: a broad view of fine detail.

  2009cited by this paper
• Hormonal regulation of temperature-induced growth in Arabidopsis.

  2009cited by this paper
• Auxin enters the matrix--assembly of response machineries for specific outputs.

  2009cited by this paper
• A gain-of-function mutation in IAA18 alters Arabidopsis embryonic apical patterning

  2009cited by this paper
• Complex regulation of the TIR1/AFB family of auxin receptors

  2009cited by this paper
• Complex regulation of the TIR 1 / AFB family of auxin receptors

  2009cited by this paper
• Arabidopsis IAR4 Modulates Auxin Response by Regulating Auxin Homeostasis1[OA]

  2009cited by this paper
• DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

  2009influential reference
• Mechanism of auxin-regulated gene expression in plants.

  2009cited by this paper
• System-wide molecular evidence for phenotypic buffering in Arabidopsis

  2009cited by this paper
• The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access.

  2008cited by this paper
• Auxin dynamics: the dazzling complexity of a small molecule’s message

  2008cited by this paper
• Complex Genetics Control Natural Variation in Arabidopsis thaliana Resistance to Botrytis cinerea

  2008cited by this paper
• Phosphate Availability Alters Lateral Root Development in Arabidopsis by Modulating Auxin Sensitivity via a Mechanism Involving the TIR1 Auxin Receptor[C][W][OA]

  2008cited by this paper
• Comprehensive transcriptome analysis of auxin responses in Arabidopsis.

  2008influential reference
• Global Analysis of Genetic, Epigenetic and Transcriptional Polymorphisms in Arabidopsis thaliana Using Whole Genome Tiling Arrays

  2008cited by this paper
• Degradation of the auxin response factor ARF1.

  2007influential reference
• Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana

  2007cited by this paper
• Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci

  2007cited by this paper
• Natural Variation in RPS2-Mediated Resistance among Arabidopsis Accessions: Correlation between Gene Expression Profiles and Phenotypic Responses[W]

  2007cited by this paper
• The Circadian Clock Regulates Auxin Signaling and Responses in Arabidopsis

  2007cited by this paper
• Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana

  2007influential reference
• Natural Variation among Arabidopsis thaliana Accessions for Transcriptome Response to Exogenous Salicylic Acid[W][OA]

  2007cited by this paper
• Development of series of gateway binary vectors, pGWBs, for realizing efficient construction of fusion genes for plant transformation.

  2007cited by this paper
• Genomic Survey of Gene Expression Diversity in Arabidopsis thaliana

  2006cited by this paper
• Auxin receptors: a new role for F-box proteins.

  2006cited by this paper
• Auxin signaling

  2006cited by this paper
• Different plant hormones regulate similar processes through largely nonoverlapping transcriptional responses.

  2006cited by this paper
• Auxin in action: signalling, transport and the control of plant growth and development

  2006cited by this paper
• Auxin signaling.

  2006cited by this paper
• A Plant miRNA Contributes to Antibacterial Resistance by Repressing Auxin Signaling

  2006cited by this paper
• Faculty Opinions recommendation of Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis.

  2006cited by this paper
• The Arabidopsis F-box protein TIR1 is an auxin receptor

  2005cited by this paper
• Functional Genomic Analysis of the AUXIN RESPONSE FACTOR Gene Family Members in Arabidopsis thaliana: Unique and Overlapping Functions of ARF7 and ARF19w⃞

  2005cited by this paper
• Genome-Wide Identification and Testing of Superior Reference Genes for Transcript Normalization in Arabidopsis1[w]

  2005cited by this paper
• The Pattern of Polymorphism in Arabidopsis thaliana

  2005cited by this paper
• Statistical Applications in Genetics and Molecular Biology

  2005cited by this paper
• Functional Genomic Analysis of the AUXIN/INDOLE-3-ACETIC ACID Gene Family Members in Arabidopsis thaliana[W]

  2005cited by this paper
• Plant Development Is Regulated by a Family of Auxin Receptor F Box Proteins

  2005cited by this paper
• Plant development is regulated by a family of auxin receptor F box proteins.

  2005cited by this paper
• The F-box protein TIR1 is an auxin receptor

  2005cited by this paper
• Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes.

  2004influential reference
• Derivative Estimation and Testing in Generalized Additive Models

  2003cited by this paper
• The Roles of Auxin Response Factor Domains in Auxin-Responsive Transcription Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.008417.

  2003cited by this paper
• Local Context Finder (LCF) reveals multidimensional relationships among mRNA expression profiles of Arabidopsis responding to pathogen infection

  2003influential reference
• A fluorimetric method for the estimation of G+C mol% content in microorganisms by thermal denaturation temperature.

  2002cited by this paper
• Natural variation in light sensitivity of Arabidopsis

  2001cited by this paper
• Auxin modulates the degradation rate of Aux/IAA proteins

  2001cited by this paper
• Rapid Degradation of Auxin/Indoleacetic Acid Proteins Requires Conserved Amino Acids of Domain II and Is Proteasome Dependent

  2001cited by this paper
• Methods to detect selection in populations with applications to the human.

  2000cited by this paper
• AXR2 encodes a member of the Aux/IAA protein family.

  2000influential reference
• Control of auxin-regulated root development by the Arabidopsis thaliana SHY2/IAA3 gene.

  1999cited by this paper
• BIOEDIT: A USER-FRIENDLY BIOLOGICAL SEQUENCE ALIGNMENT EDITOR AND ANALYSIS PROGRAM FOR WINDOWS 95/98/ NT

  1999influential reference
• Activation and repression of transcription by auxin-response factors.

  1999cited by this paper
• The TIR1 protein of Arabidopsis functions in auxin response and is related to human SKP2 and yeast grr1p.

  1998cited by this paper
• The TIR 1 protein of Arabidopsis functions in auxin response and is related to human SKP 2 and yeast Grr 1 p

  1998cited by this paper
• The ARF family of transcription factors and their role in plant hormone-responsive transcription

  1998cited by this paper
• High temperature promotes auxin-mediated hypocotyl elongation in Arabidopsis.

  1998cited by this paper
• Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana.

  1998cited by this paper
• Aux/IAA proteins repress expression of reporter genes containing natural and highly active synthetic auxin response elements.

  1997cited by this paper
• Histochemical localization of β-glucuronidase.

  1992cited by this paper
• Growth and development of the axr1 mutants of Arabidopsis.

  1990cited by this paper
• Molecular Evolutionary Genetics

  1987influential reference
• Mathematical model for studying genetic variation in terms of restriction endonucleases.

  1979cited by this paper

• Advancing ecological and evolutionary research in Arabidopsis: Extending insights into model and nonmodel plants

  2025cites this paper
• Computational Reconstruction of the Transcription Factor Regulatory Network Induced by Auxin in Arabidopsis thaliana L.

  2024cites this paper
• InterTransViewer: a comparative description of differential gene expression profiles from different experiments

  2023cites this paper
• In silico analysis of cis-elements and identification of transcription factors putatively involved in the regulation of the OAS cluster genes SDI1 and SDI2

  2021cites this paper
• Differences in the Seed Germination of Leymus chinensis (Poaceae) Ecotypes Reveal Distinct Strategies for Coping With Salinity Stress: A Common Garden Experiment

  2021cites this paper
• Heterologous Expression of Arabidopsis rty Enhances Drought Tolerance in Strawberry (Fragaria × ananassa Duch.)

  2020cites this paper
• The CEP5 Peptide Promotes Abiotic Stress Tolerance, As Revealed by Quantitative Proteomics, and Attenuates the AUX/IAA Equilibrium in Arabidopsis

  2020cites this paper
• Natural Variation in Plant Pluripotency and Regeneration

  2020cites this paper
• Heterologous expression of Arabidopsis thaliana rty gene in strawberry (Fragaria × ananassa Duch.) improves drought tolerance

  2020cites this paper
• Transcriptional variation analysis of Arabidopsis ecotypes in response to drought and salt stresses dissects commonly regulated networks.

  2020cites this paper
• Genetic analysis of the Arabidopsis TIR1/AFB auxin receptors reveals both overlapping and specialized functions

  2019cites this paper
• Emerging Advances in Computational Omics Tools for Systems Analysis of Gramineae Family Grass Species and Their Abiotic Stress Responsive Functions

  2019cites this paper
• Members of the Arabidopsis auxin receptor gene family are essential early in embryogenesis and have broadly overlapping functions

  2019cites this paper
• Systems, variation, individuality and plant hormones.

  2019cites this paper
• BAŞKENT UNIVERSITY INSTITUTE OF SCIENCE AND ENGINEERING EXPERIMENT RETRIEVAL IN GENOMIC DATABASES

  2019cites this paper
• Auxin‐induced actin cytoskeleton rearrangements require AUX1

  2019cites this paper
• Advancement in Sustainable Agriculture: Computational and Bioinformatics Tools

  2019cites this paper
• Genetic analysis of phosphite sensitivity in Arabidopsis thaliana

  2018cites this paper
• Natural variation of hormone levels in Arabidopsis roots and correlations with complex root architecture

  2018cites this paper
• Type III Secretion-Dependent and -Independent Phenotypes Caused by Ralstonia solanacearum in Arabidopsis Roots.

  2018cites this paper
• Natural genetic variation shapes root system responses to phytohormones in Arabidopsis

  2018influential citation
• Cotyledons contribute to plant growth and hybrid vigor in Arabidopsis

  2018cites this paper
• Accelerating structure‐function mapping using the ViVa webtool to mine natural variation

  2018cites this paper
• Transcriptomic variation among six Arabidopsis thaliana accessions identified several novel genes controlling aluminium tolerance.

  2017cites this paper
• Molecular Profiles of Contrasting Shade Response Strategies in Wild Plants: Differential Control of Immunity and Shoot Elongation[OPEN]

  2017cites this paper
• Diversity of cis-regulatory elements associated with auxin response in Arabidopsis thaliana

  2017cites this paper
• 1 Title 1 Natural Genetic Variation Shapes Root System Responses to Phytohormones in Arabidopsis 2 3 Authors 4

  2017influential citation
• Explorer Molecular and genetic control of plant thermomorphogenesis

  2017cites this paper
• Natural Genetic Variation Shapes Root System Responses to Phytohormones in Arabidopsis

  2017cites this paper
• Type III secretion-dependent and-independent phenotypes caused by Ralstonia 1 solanacearum in Arabidopsis roots 2 3

  2017cites this paper
• Insights into the Evolution and Function of Auxin Signaling F-Box Proteins in Arabidopsis thaliana Through Synthetic Analysis of Natural Variants

  2017cites this paper
• Divergent regulation of Arabidopsis SAUR genes: a focus on the SAUR10-clade

  2017cites this paper
• Synthetic analysis of natural variants yields insights into the evolution and function of auxin signaling F-box proteins in Arabidopsis thaliana

  2017cites this paper
• Developmental and phenotypic plasticity of Arabidopsis thaliana accessions across an ambient temperature range Running title : Arabidopsis thermomorphogenesis

  2016cites this paper
• Free-Flow Electrophoresis of Plasma Membrane Vesicles Enriched by Two-Phase Partitioning Enhances the Quality of the Proteome from Arabidopsis Seedlings.

  2016cites this paper
• Auxin-induced expression divergence between Arabidopsis species likely originates within the TIR1/AFB-AUX/IAA-ARF signaling network running title: comparative transcriptomics of auxin-responses

  2016cites this paper
• Auxin-induced expression divergence between Arabidopsis species may originate within the TIR1/AFB–AUX/IAA–ARF module

  2016cites this paper
• Structural Biology of Nuclear Auxin Action.

  2016cites this paper
• Retrieving relevant time-course experiments: a study on Arabidopsis microarrays.

  2016cites this paper
• Genome Wide Association Mapping in Arabidopsis thaliana Identifies Novel Genes Involved in Linking Allyl Glucosinolate to Altered Biomass and Defense

  2016cites this paper
• Light and hormone interactions in the seed-to-seedling transition

  2016cites this paper
• Evolution of herbivore-induced early defense signaling was shaped by genome-wide duplications in Nicotiana

  2016cites this paper
• Leaf Growth Response to Mild Drought: Natural Variation in Arabidopsis Sheds Light on Trait Architecture[OPEN]

  2016cites this paper
• Molecular and genetic control of plant thermomorphogenesis

  2016cites this paper
• Auxin-induced expression divergence between Arabidopsis species likely originates within the TIR1/AFB-AUX/IAA-ARF module

  2016cites this paper
• Auxin-induced expression divergence between Arabidopsis species likely originates within the TIR 1 / AFB-AUX / IAA-ARF module running title : comparative transcriptomics of auxin responses

  2016cites this paper
• Natural Variants of ELF 3 Affect Thermomorphogenesis by Transcriptionally Modulating PIF 4-Dependent Auxin Responses

  2015cites this paper
• Ambient temperature and genotype differentially affect developmental and phenotypic plasticity in Arabidopsis thaliana

  2015cites this paper
• AtCAST3.0 update: a web-based tool for analysis of transcriptome data by searching similarities in gene expression profiles.

  2015influential citation
• Transcriptional regulatory networks in Arabidopsis thaliana during single and combined stresses

  2015cites this paper
• Developmental plasticity of Arabidopsis thaliana accessions across an ambient temperature range

  2015cites this paper
• Leaf Responses to Mild Drought Stress in Natural Variants of Arabidopsis1[OPEN]

  2015cites this paper
• Transcriptionally Modulating PIF4-Dependent Auxin Responses

  2015cites this paper
• Plant Physiomics: Photoelectrochemical and Molecular Retrograde Signalling in Plant Acclimatory and Defence Responses

  2015cites this paper
• Molecular mechanisms governing Arabidopsis iron uptake.

  2015cites this paper
• Inherited phenotype instability of inflorescence and floral organ development in homeotic barley double mutants and its specific modification by auxin inhibitors and 2,4-D.

  2015cites this paper
• Peroxidase gene discovery from the horseradish transcriptome

  2014influential citation
• Microbe-associated molecular pattern-induced calcium signaling requires the receptor-like cytoplasmic kinases, PBL1 and BIK1

  2014cites this paper
• Target Identification of Biologically Active Small Molecules

  2013cites this paper
• Genome-scale cold stress response regulatory networks in ten Arabidopsis thalianaecotypes

  2013cites this paper
• Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes

  2013cites this paper
• Transcriptomic and Physiological Variations of Three Arabidopsis Ecotypes in Response to Salt Stress

  2013cites this paper
• Adventitious root induction in Arabidopsis thaliana as a model for in vitro root organogenesis.

  2013cites this paper
• A Major Facilitator Superfamily Transporter Plays a Dual Role in Polar Auxin Transport and Drought Stress Tolerance in Arabidopsis[W]

  2013cites this paper
• The Classical Arabinogalactan Protein AGP18 Mediates Megaspore Selection in Arabidopsis[W][OA]

  2013cites this paper
• Integrative systems approaches to study plant stress responses

  2013cites this paper
• Natural genetic variation in the expression regulation of chloroplast antioxidant system among A. thaliana accessions.

  2013cites this paper
• Physiological and cellular effects of TENin1, a novel small molecule inhibitor of endomembrane protein trafficking

  2013influential citation
• Lessons from eQTL mapping studies: non-coding regions and their role behind natural phenotypic variation in plants.

  2012cites this paper
• A comparison of transcriptome and epigenetic status between closely related species in the genus Arabidopsis.

  2012cites this paper
• Rosette iron deficiency transcript and microRNA profiling reveals links between copper and iron homeostasis in Arabidopsis thaliana

  2012cites this paper
• Defense-related calcium signaling mutants uncovered via a quantitative high-throughput screen in Arabidopsis thaliana.

  2012cites this paper
• Arabidopsis ribosomal proteins control developmental programs through translational regulation of auxin response factors

  2012cites this paper
• Physiological Genomics of Response to Soil Drying in Diverse Arabidopsis Accessions[W][OA]

  2012cites this paper
• Regulatory components involved in altering lateral root development in response to localized iron: Evidence for natural genetic variation

  2012cites this paper
• Mutant Analysis in Arabidopsis Provides Insight into the Molecular Mode of Action of the Auxinic Herbicide Dicamba

  2011cites this paper
• Molecular Evolution and Selection Patterns of Plant F-Box Proteins with C-Terminal Kelch Repeats 1 [ W ] [ OA ]

  2011cites this paper
• Advances in Omics and Bioinformatics Tools for Systems Analyses of Plant Functions

  2011cites this paper
• Einfluss von Gibberellin auf den Gravitropismus der Wurzel durch Regulation der PIN-Stabilität

  2011cites this paper
• Expression level polymorphisms: heritable traits shaping natural variation.

  2011cites this paper
• Einfluss von Gibberellin auf den Gravitropismus der Wurzel durch Regulation der PIN-Stabilität

  2011cites this paper
• The Genome Sequence of the North-European Cucumber (Cucumis sativus L.) Unravels Evolutionary Adaptation Mechanisms in Plants

  2011cites this paper
• Interplay between calcium signalling and early signalling elements during defence responses to microbe- or damage-associated molecular patterns.

  2011influential citation
• Molecular Evolution and Selection Patterns of Plant F-Box Proteins with C-Terminal Kelch Repeats1[W][OA]

  2010cites this paper
• Running head: Evolution and Selection Patterns of F-box Kelch Proteins For correspondence: Marcel Quint

  2010cites this paper