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GWAPP: a web application for genome-wide association mapping in Arabidopsis
- Source :
- Plant Cell, Plant Cell, American Society of Plant Biologists, 2012, 24 (12), pp.4793-4805. ⟨10.1105/tpc.112.108068⟩, The Plant cell, The Plant cell, American Society of Plant Biologists (ASPB), 2012, 24 (12), pp.4793-4805. ⟨10.1105/tpc.112.108068⟩, The Plant Cell, Plant Cell 12 (24), 4793-4805. (2012)
- Publication Year :
- 2013
-
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.
- Subjects :
- 0106 biological sciences
analyse de données
Linkage disequilibrium
cartographie génomique
genome-wide
association study
web application
linear mixed model
data analysis
association mapping
Arabidopsis
modèle linéaire mixte
Genome-wide association study
Plant Science
Computational biology
polymorphisme
01 natural sciences
Linkage Disequilibrium
03 medical and health sciences
User-Computer Interface
Arabidopsis thaliana
[SDV.BV]Life Sciences [q-bio]/Vegetal Biology
application web
Large-Scale Biology Article
Association mapping
Genome size
030304 developmental biology
Genetic association
Genetics
0303 health sciences
Internet
Vegetal Biology
biology
génome
arabidopsis thaliana
Cell Biology
Replicate
biology.organism_classification
étude d'association
Biologie végétale
Software
010606 plant biology & botany
Genome-Wide Association Study
Subjects
Details
- ISSN :
- 1532298X and 10404651
- Volume :
- 24
- Issue :
- 12
- Database :
- OpenAIRE
- Journal :
- The Plant cell
- Accession number :
- edsair.doi.dedup.....5bbf84007cf590ebb2e2c9126b5302da