AraQTL – workbench and archive for systems genetics in Arabidopsis thaliana

Genetical genomics studies uncover genome-wide genetic interactions between genes and their transcriptional regulators. High-throughput measurement of gene expression in recombinant inbred line populations has enabled investigation of the genetic architecture of variation in gene expression. This has the potential to enrich our understanding of the molecular mechanisms affected by and underlying natural variation. Moreover, it contributes to the systems biology of natural variation, as a substantial number of experiments have resulted in a valuable amount of interconnectable phenotypic, molecular and genotypic data. A number of genetical genomics studies have been published for Arabidopsis thaliana, uncovering many expression quantitative trait loci (eQTLs). However, these complex data are not easily accessible to the plant research community, leaving most of the valuable genetic interactions unexplored as cross-analysis of these studies is a major effort. We address this problem with AraQTL (http://www.bioinformatics.nl/Ara QTL/), an easily accessible workbench and database for comparative analysis and meta-analysis of all published Arabidopsis eQTL datasets. AraQTL provides a workbench for comparing, re-using and extending upon the results of these experiments. For example, one can easily screen a physical region for specific local eQTLs that could harbour candidate genes for phenotypic QTLs, or detect gene-by-environment interactions by comparing eQTLs under different conditions.

• Publication year

  2017

• Venue

  The Plant Journal

• Publication date

  2017-03-01

• Fields of study

  Biology, Medicine, Computer Science, Environmental Science

• Identifiers
  DOI 10.1111/tpj.13457PMID 27995664
• 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.

• 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

  2016cited by this paper
• Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions.

  2016cited by this paper
• Allelic differences in a vacuolar invertase affect Arabidopsis growth at early plant development.

  2016cited by this paper
• The Glucosinolate Biosynthetic Gene AOP2 Mediates Feed-back Regulation of Jasmonic Acid Signaling in Arabidopsis.

  2015cited by this paper
• Natural genetic variation in Arabidopsis thaliana defense metabolism genes modulates field fitness

  2015cited by this paper
• Developmental progress and current status of the Animal QTLdb

  2015cited by this paper
• Investigation of the multifunctional gene AOP3 expands the regulatory network fine-tuning glucosinolate production in Arabidopsis

  2015cited by this paper
• Natural variation in cross-talk between glucosinolates and onset of flowering in Arabidopsis

  2015cited by this paper
• R/qtlcharts: Interactive Graphics for Quantitative Trait Locus Mapping

  2014cited by this paper
• Meta-analysis of metabolome QTLs in Arabidopsis: trying to estimate the network size controlling genetic variation of the metabolome

  2014influential reference
• An Arabidopsis Gene Regulatory Network for Secondary Cell Wall Synthesis

  2014cited by this paper
• Cryptic genetic variation: evolution's hidden substrate

  2014cited by this paper
• Exploiting natural variation in Arabidopsis.

  2014cited by this paper
• Worm variation made accessible

  2014cited by this paper
• Network types and their application in natural variation studies in plants.

  2014cited by this paper
• Interaction between parental environment and genotype affects plant and seed performance in Arabidopsis

  2014cited by this paper
• The AT-hook motif-encoding gene METABOLIC NETWORK MODULATOR 1 underlies natural variation in Arabidopsis primary metabolism

  2014cited by this paper
• Genetic resources for quantitative trait analysis: novelty and efficiency in design from an Arabidopsis perspective.

  2014cited by this paper
• Extensive cis-Regulatory Variation Robust to Environmental Perturbation in Arabidopsis[W]

  2014cited by this paper
• The genetic structure of Arabidopsis thaliana in the south-western Mediterranean range reveals a shared history between North Africa and southern Europe

  2014cited by this paper
• Identifying Genotype-by-Environment Interactions in the Metabolism of Germinating Arabidopsis Seeds Using Generalized Genetical Genomics 1[C][W][OA]

  2013influential reference
• Expression Quantitative Trait Locus Mapping across Water Availability Environments Reveals Contrasting Associations with Genomic Features in Arabidopsis[C][W][OPEN]

  2013influential reference
• WormQTLHD—a web database for linking human disease to natural variation data in C. elegans

  2013cited by this paper
• Systems genetics approaches to understand complex traits

  2013cited by this paper
• Genetical Genomics Reveals Large Scale Genotype-By-Environment Interactions in Arabidopsis thaliana

  2013influential reference
• WormQTL—public archive and analysis web portal for natural variation data in Caenorhabditis spp

  2012cited by this paper
• University of Groningen Identifying Genotype-by-Environment Interactions in the Metabolism of Germinating Arabidopsis Seeds Using Generalized Genetical Genomics

  2012influential reference
• Expression variation in connected recombinant populations of Arabidopsis thaliana highlights distinct transcriptome architectures

  2012influential reference
• Redefining plant systems biology: from cell to ecosystem.

  2011cited by this paper
• Natural Variation in Arabidopsis: From Molecular Genetics to Ecological Genomics1[W][OA]

  2011cited by this paper
• Ensembl BioMarts: a hub for data retrieval across taxonomic space

  2011cited by this paper
• Multiple reference genomes and transcriptomes for Arabidopsis thaliana

  2011cited by this paper
• Network Quantitative Trait Loci Mapping of Circadian Clock Outputs Identifies Metabolic Pathway-to-Clock Linkages in Arabidopsis[C][W]

  2011influential reference
• Combining Genome-Wide Association Mapping and Transcriptional Networks to Identify Novel Genes Controlling Glucosinolates in Arabidopsis thaliana

  2011cited by this paper
• What does Arabidopsis natural variation teach us (and does not teach us) about adaptation in plants?

  2011cited by this paper
• Gene Regulatory Network Reconstruction Using Bayesian Networks, the Dantzig Selector, the Lasso and Their Meta-Analysis

  2011cited by this paper
• Whole-genome sequencing of multiple Arabidopsis thaliana populations

  2011cited by this paper
• Temporal variation in genetic diversity and effective population size of Mediterranean and subalpine Arabidopsis thaliana populations

  2011cited by this paper
• Regulatory networks of glucosinolates shape Arabidopsis thaliana fitness.

  2010cited by this paper
• The development of Arabidopsis as a model plant.

  2010cited by this paper
• Network Analysis Identifies ELF3 as a QTL for the Shade Avoidance Response in Arabidopsis

  2010cited by this paper
• Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana

  2010influential reference
• agriGO: a GO analysis toolkit for the agricultural community

  2010cited by this paper
• Regulatory Network Identification by Genetical Genomics: Signaling Downstream of the Arabidopsis Receptor-Like Kinase ERECTA1[W][OA]

  2010influential reference
• System-wide molecular evidence for phenotypic buffering in Arabidopsis

  2009cited by this paper
• Metabolic Networks: How to Identify Key Components in the Regulation of Metabolism and Growth1

  2009cited by this paper
• The many functions of ERECTA.

  2009cited by this paper
• Advances in Genetical Genomics of Plants

  2009cited by this paper
• Gene Expression Analysis, Proteomics, and Network Discovery1

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

  2009cited by this paper
• Genetical metabolomics: closing in on phenotypes.

  2009cited by this paper
• Integrative analyses of genetic variation in enzyme activities of primary carbohydrate metabolism reveal distinct modes of regulation in Arabidopsis thaliana

  2008cited by this paper
• Genetical Genomics: Spotlight on QTL Hotspots

  2008cited by this paper
• Quantitative genetics in the age of omics.

  2008cited by this paper
• Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks

  2008cited by this paper
• Sequence Polymorphisms Cause Many False cis eQTLs

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

  2007influential reference
• Global eQTL Mapping Reveals the Complex Genetic Architecture of Transcript-Level Variation in Arabidopsis

  2007influential reference
• Genetics of global gene expression

  2006cited by this paper
• The genetics of plant metabolism

  2006cited by this paper
• Identification of QTLs controlling gene expression networks defined a priori

  2006cited by this paper
• High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis.

  2006cited by this paper
• GeneNetwork: an interactive tool for reconstruction of genetic networks using microarray data

  2004cited by this paper
• Studying complex biological systems using multifactorial perturbation

  2003cited by this paper
• Genetical genomics: the added value from segregation.

  2001cited by this paper
• Naturally occurring variation in Arabidopsis: an underexploited resource for plant genetics.

  2000cited by this paper

• Making use of naturally occurring variation within the Arabidopsis thaliana

  2023influential citation
• Integration of eQTL and GWAS analysis uncovers a genetic regulation of natural ionomic variation in Arabidopsis

  2023cites this paper
• Modulation of quantitative trait loci for Arabidopsis thaliana seed performance by the maternal and germination environment

  2023influential citation
• Prioritizing candidate eQTL causal genes in Arabidopsis using RANDOM FORESTS

  2022cites this paper
• Prior Biological Knowledge Improves Genomic Prediction of Growth-Related Traits in Arabidopsis thaliana

  2021cites this paper
• The genetics of gene expression in a C. elegans multi parental recombinant inbred line population

  2021cites this paper
• Plasticity of maternal environment-dependent expression-QTLs of tomato seeds

  2021influential citation
• Using precision phenotyping to inform de novo domestication

  2021cites this paper
• Effects of Natural Variations on Biofortification

  2021cites this paper
• The genetics of gene expression in a Caenorhabditis elegans multiparental recombinant inbred line population

  2021cites this paper
• Network Analysis Prioritizes DEWAX and ICE1 as the Candidate Genes for Major eQTL Hotspots in Seed Germination of Arabidopsis thaliana

  2020cites this paper
• Network Analysis Prioritizes DEWAX and ICE1 as the Candidate Genes for Major eQTL Hotspots in Seed Germination

  2020cites this paper
• Molecular Mapping of Grapevine Genes

  2019cites this paper
• Computational aspects underlying genome to phenome analysis in plants

  2019cites this paper
• WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans

  2019cites this paper
• The complex genetic architecture of shoot growth natural variation in Arabidopsis thaliana

  2018cites this paper
• Environmental tuning of the genetic control of seed performance : a systems genetics approach

  2018influential citation
• Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population

  2017cites this paper
• Genetic Dissection of Morphometric Traits Reveals That Phytochrome B Affects Nucleus Size and Heterochromatin Organization in Arabidopsis thaliana

  2017cites this paper
• Bioinformatics Group - Thesis projects

  year unknowncites this paper
• Bioinformatics Group - Thesis projects

  year unknowncites this paper