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Protocols

GWAPP specifications

Information


Unique identifier OMICS_08630
Name GWAPP
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Taxon


  • Plants and Fungi
    • Arabidopsis thaliana

Versioning


No version available

Maintainer


  • person_outline Magnus Nordborg

Information


Unique identifier OMICS_08630
Name GWAPP
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Plants and Fungi
    • Arabidopsis thaliana

Maintainer


  • person_outline Magnus Nordborg

Publication for GWAPP

GWAPP citations

 (11)
library_books

Natural allelic variation of the AZI1 gene controls root growth under zinc limiting condition

2018
PLoS Genet
PMCID: 5897037
PMID: 29608565
DOI: 10.1371/journal.pgen.1007304

[…] For GWAS, mean total root length values of 231 natural accessions were used ( and Tables). The GWA analysis was performed in the GWAPP web interface using the mixed model algorithm (AMM) that accounts for population structure [] and using the SNP data from the RegMap panel [, ] []. Only SNPs with minor allele counts greater or […]

call_split

LPCAT1 controls phosphate homeostasis in a zinc dependent manner

2018
eLife
PMCID: 5826268
PMID: 29453864
DOI: 10.7554/eLife.32077.021
call_split See protocol

[…] ermined using the molybdate assay as previously described by . The shoot Pi concentrations across the analysed accessions was used as phenotype for GWA analysis. The GWA analysis was performed in the GWAPP web interface using the mixed model algorithm (AMM) that accounts for population structure () and using the SNP data from the RegMap panel (; ; ). Only SNPs with minor allele counts greater or e […]

library_books

Parallel evolution of the POQR prolyl oligo peptidase gene conferring plant quantitative disease resistance

2017
PLoS Genet
PMCID: 5757927
PMID: 29272270
DOI: 10.1371/journal.pgen.1007143

[…] the database to include only SNPs with a minor allele frequency greater than 0.10, which left 158,054 SNPs for mapping. The analysis was conducted using the Accelerated Mixed Model (AMM) approach in GWAPP []. To account for multiple simultaneous tests we calculated genome-wide FDR (q-values). For this, observed phenotype values were randomly assigned to Arabidopsis accession in 100 bootstrap repl […]

library_books

Natural Genetic Variation of Seed Micronutrients of Arabidopsis thaliana Grown in Zinc Deficient and Zinc Amended Soil

2016
Front Plant Sci
PMCID: 4960235
PMID: 27507976
DOI: 10.3389/fpls.2016.01070

[…] To uncover the underlying genetics of seed nutrients accumulation and the response to -Zn, we carried out GWA using GWAPP, a user-friendly web application (). GWAPP has already included about 206,000 SNPs and 1386 individuals for analysis. As several accessions in this study were not included in GWAPP, the GWAS was […]

library_books

Extensive Natural Variation in Arabidopsis Seed Mucilage Structure

2016
Front Plant Sci
PMCID: 4894908
PMID: 27375657
DOI: 10.3389/fpls.2016.00803

[…] t for population structure and relatedness (Eu-ahsunthornwattana et al., ), we first performed GWAS analysis using FaST-LMM (Supplemental Figure ). As we obtained qualitatively similar results in the GWAPP web application (http://gwapp.gmi.oeaw.ac.at; Seren et al., ), which can be conveniently accessed by other users, we then used in this tool for further data visualization. Figure shows a summar […]

library_books

Genome Wide Association Mapping for the Tolerance to the Polyamine Oxidase Inhibitor Guazatine in Arabidopsis thaliana

2016
Front Plant Sci
PMCID: 4820465
PMID: 27092150
DOI: 10.3389/fpls.2016.00401

[…] GWAS was performed using the GWAPP web interface (Seren et al., ). Mean chlorophyll values of 107 Arabidopsis accessions grown under control and guazatine conditions (as indicated above), were transformed using the square root. G […]

Citations

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GWAPP institution(s)
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria

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