In this chapter, we describe how to perform GWAS in
A. thaliana, starting with obtaining raw data on genotypes and
phenotypes of candidate genes involved in the phenotype of interest from the perspective of data analysis. We will describe how to
prepare and evaluate data with PLINK [18], infer associations with
EMMAX, plot results with R package qqman [19], and augment
GWAS signals via integration with functional gene network information using the araGWAB web application [13].
2 Materials
2.1 Arabidopsis
Ecotype Accessions
Arabidopsis natural accessions for phenotyping can be obtained
from the Arabidopsis Biological Resource Center (ABRC). Orders
can be placed online at https://abrc.osu.edu/catalog (see Notes 1
and 2).
2.2 Basic
Computational
Requirements
1. Access to the Internet to download data and use analysis
software.
2. UNIX-based operating system. In this protocol, we will only
describe how to perform GWAS under a LINUX environment.
3. At least 135 GB of free disk space and 8 GB of RAM are
required to handle data from the 1001 Genome Project.
2.3 Software for
GWAS Analysis
1. PLINK (version 1.9 or higher), which is downloadable from
https://www.cog-genomics.org/plink2, will be used to format
input data for GWAS.
2. EMMAX (Mixed-Model Association Mapping Tool), which
accounts for population structure during statistical association
analysis, can be obtained from http://csg.sph.umich.edu//
kang/emmax/download/.
3. R is a free software environment widely used for data analysis.
Use of an R version higher than 3.4 is recommended. R is
available at https://www.r-project.org/.
4. For plotting Manhattan plots, R-package qqman needs to be
obtained from https://cran.r-project.org/web/packages/
qqman/.
3 Methods
The lines that begin with $ and with > are command lines that need
to be executed in your computer terminal and in R, respectively.
The whole process of GWAS analysis is summarized in Fig. 1.
Genome-Wide Association Studies in Arabidopsis
189
A. thaliana, starting with obtaining raw data on genotypes and
phenotypes of candidate genes involved in the phenotype of interest from the perspective of data analysis. We will describe how to
prepare and evaluate data with PLINK [18], infer associations with
EMMAX, plot results with R package qqman [19], and augment
GWAS signals via integration with functional gene network information using the araGWAB web application [13].
2 Materials
2.1 Arabidopsis
Ecotype Accessions
Arabidopsis natural accessions for phenotyping can be obtained
from the Arabidopsis Biological Resource Center (ABRC). Orders
can be placed online at https://abrc.osu.edu/catalog (see Notes 1
and 2).
2.2 Basic
Computational
Requirements
1. Access to the Internet to download data and use analysis
software.
2. UNIX-based operating system. In this protocol, we will only
describe how to perform GWAS under a LINUX environment.
3. At least 135 GB of free disk space and 8 GB of RAM are
required to handle data from the 1001 Genome Project.
2.3 Software for
GWAS Analysis
1. PLINK (version 1.9 or higher), which is downloadable from
https://www.cog-genomics.org/plink2, will be used to format
input data for GWAS.
2. EMMAX (Mixed-Model Association Mapping Tool), which
accounts for population structure during statistical association
analysis, can be obtained from http://csg.sph.umich.edu//
kang/emmax/download/.
3. R is a free software environment widely used for data analysis.
Use of an R version higher than 3.4 is recommended. R is
available at https://www.r-project.org/.
4. For plotting Manhattan plots, R-package qqman needs to be
obtained from https://cran.r-project.org/web/packages/
qqman/.
3 Methods
The lines that begin with $ and with > are command lines that need
to be executed in your computer terminal and in R, respectively.
The whole process of GWAS analysis is summarized in Fig. 1.
Genome-Wide Association Studies in Arabidopsis
189