GWAPP: A Web Application for Genome-Wide Association Mapping in Arabidopsis.

Bjarni J. Vilhjálmsson (1, 2, 3) , Matthew W. Horton (1, 2, 4) , Dazhe Meng (1, 2, 3) , Petar Forai (1, 2) , Yu S. Huang (5, 6) , Quan Long (1, 2) , Vincent Segura (7) , Magnus Nordborg (1, 2, 3)

1 GMI - Gregor Mendel Institute of Molecular Plant Biology
2 OeAW - Austrian Academy of Sciences
3 Molecular and Computational Biology
4 Department of Ecology and Evolution [Chicago]
5 Center for Neurobehavioral Genetics, Semel Institute
6 Center for Neurobehavioral Genetics
7 AGPF - Unité de recherche Amélioration, Génétique et Physiologie Forestières

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.

Mots clés: genome-wide; association study; web application; linear mixed model; data analysis; association mapping

Domaines: Biologie végétale

Bjarni J. Vilhjálmsson, Matthew W. Horton, Dazhe Meng, Petar Forai, Yu S. Huang, et al.. GWAPP: A Web Application for Genome-Wide Association Mapping in Arabidopsis.. The Plant cell, 2012, 24 (12), pp.4793-4805. ⟨10.1105/tpc.112.108068⟩. ⟨hal-01267853⟩