ArticleThe Plant cell2012
GWAPP: a web application for genome-wide association mapping in Arabidopsis.
Article in The Plant cell, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers, 1 of them a synthesis that pooled it.
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Who cites it
90 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Genome-wide association studies meta-analysis uncovers NOJO and SGS3 novel genes involved in Arabidopsis thaliana primary root development and plasticity.Molecular biology reports · 2024Pooled it
- MYB59 is Linked to Natural Variation of Water-Use Associated With Warmer Temperatures inPlant-environment interactions (Hoboken, N.J.) · 2026Article
- CartograPlant: bridging genomic, phenotypic, and environmental data to advance plant resilience and eco-evolutionary insight.Genetics · 2026Article
- Identification of a novel link connecting indole-3-acetamide with abscisic acid biosynthesis and signaling.The New phytologist · 2026Article
- Rapid acquisition of ionomic and morphological data from plant seeds through fast X-ray fluorescence microscopy and computer vision.Plant phenomics (Washington, D.C.) · 2025Article
- A retrotransposon insertion upstream of Arabidopsis thaliana CRK8 receptor-like kinase modulates a trade-off between pathogen defense and salt tolerance.The Plant journal : for cell and molecular biology · 2025Article
- Gene body methylation regulates gene expression and mediates phenotypic diversity in natural Arabidopsis populations.Nature plants · 2025Article
- A Genome-Wide Association Screen for Genes Affecting Leaf Trichome Development and Epidermal Metal Accumulation in Arabidopsis.Plant, cell & environment · 2025Article
- Genome-wide association study identifies candidate genes contributing to flowering time variation inPlant biotechnology (Tokyo, Japan) · 2025Article
- Reducing herbivory in mixed planting by genomic prediction of neighbor effects in the field.Nature communications · 2024Article
- Arabinosylation of cell wall extensin is required for the directional response to salinity in roots.The Plant cell · 2024Article
- Natural variation of TBR confers plant zinc toxicity tolerance through root cell wall pectin methylesterification.Nature communications · 2024Article
- Cauliflower mosaic virus disease spectrum uncovers novel susceptibility factor NCED9 in Arabidopsis thaliana.Journal of experimental botany · 2023Article
- Extensive sequence duplication in Arabidopsis revealed by pseudo-heterozygosity.Genome biology · 2023Article
- Combined Approach of GWAS and Phylogenetic Analyses to Identify New Candidate Genes That Participate inPlants (Basel, Switzerland) · 2022Article
- Diversity of root hydrotropism among natural variants of Arabidopsis thaliana.Journal of plant research · 2022Article
- AIG2A and AIG2B limit the activation of salicylic acid-regulated defenses by tryptophan-derived secondary metabolism in Arabidopsis.The Plant cell · 2022Article
- Phosphate transporter PHT1;1 is a key determinant of phosphorus acquisition in Arabidopsis natural accessions.Plant physiology · 2022Article
- The receptor kinase SRF3 coordinates iron-level and flagellin dependent defense and growth responses in plants.Nature communications · 2022Article
- Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in Arabidopsis.Genome biology · 2022Article
30 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Arabidopsis thaliana is an important model organism for understanding the genetics and molecular biology of plants. Its highly selfing nature, small size, short generation time, small genome size, and wide geographic distribution make it an ideal model organism for understanding natural variation. Genome-wide association studies (GWAS) have proven a useful technique for identifying genetic loci responsible for natural variation in A. thaliana. Previously genotyped accessions (natural inbred lines) can be grown in replicate under different conditions and phenotyped for different traits. These important features greatly simplify association mapping of traits and allow for systematic dissection of the genetics of natural variation by the entire A. thaliana community. To facilitate this, we present GWAPP, an interactive Web-based application for conducting GWAS in A. thaliana. Using an efficient implementation of a linear mixed model, traits measured for a subset of 1386 publicly available ecotypes can be uploaded and mapped with a mixed model and other methods in just a couple of minutes. GWAPP features an extensive, interactive, and user-friendly interface that includes interactive Manhattan plots and linkage disequilibrium plots. It also facilitates exploratory data analysis by implementing features such as the inclusion of candidate polymorphisms in the model as cofactors.
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