3.1 Obtaining and
Preprocessing
Genotype Data
3.1.1 Download
Genotype Data for
Arabidopsis Accessions
The genotype data for Arabidopsis natural accessions can be downloaded from the 1001 Genomes Project website (http://
1001genomes.org/data/) under directory GMI-MPI/releases/
v3.1. The data used here are based on the latest releases as of
April 2019. Download and unzip the variant call format (vcf) file
“1001genomes_snp-short-indel_only_ACGTN.vcf.gz.” The file
size is large, so you will need to have sufficient disk space and a
stable Internet connection until the data download is finished.
3.1.2 Download PLINK
Software
1. Download the latest version of PLINK and unzip it. PLINK
has binaries that are precompiled, so no further installation
steps are required.
Fig. 1 Workflow of genome-wide association study (GWAS) in Arabidopsis. First,
genotype data are obtained from the 1001 Genomes Project database. Then, the
genotype data are preprocessed with PLINK and subsequently used for accession selection. Selected accessions are subjected to phenotyping. The preprocessed genotype and phenotype data are analyzed using EMMAX to identify
statistical association between genotypes and the phenotype. Using R package
qqman, GWAS results are visualized and evaluated with Q–Q plot and Manhattan
plot. Further improvements of the results can be made with network-based
augmentation using the araGWAB web application
190
Tak Lee and Insuk Lee
Preprocessing
Genotype Data
3.1.1 Download
Genotype Data for
Arabidopsis Accessions
The genotype data for Arabidopsis natural accessions can be downloaded from the 1001 Genomes Project website (http://
1001genomes.org/data/) under directory GMI-MPI/releases/
v3.1. The data used here are based on the latest releases as of
April 2019. Download and unzip the variant call format (vcf) file
“1001genomes_snp-short-indel_only_ACGTN.vcf.gz.” The file
size is large, so you will need to have sufficient disk space and a
stable Internet connection until the data download is finished.
3.1.2 Download PLINK
Software
1. Download the latest version of PLINK and unzip it. PLINK
has binaries that are precompiled, so no further installation
steps are required.
Fig. 1 Workflow of genome-wide association study (GWAS) in Arabidopsis. First,
genotype data are obtained from the 1001 Genomes Project database. Then, the
genotype data are preprocessed with PLINK and subsequently used for accession selection. Selected accessions are subjected to phenotyping. The preprocessed genotype and phenotype data are analyzed using EMMAX to identify
statistical association between genotypes and the phenotype. Using R package
qqman, GWAS results are visualized and evaluated with Q–Q plot and Manhattan
plot. Further improvements of the results can be made with network-based
augmentation using the araGWAB web application
190
Tak Lee and Insuk Lee