GWAS
Genome-wide association mapping was performed on measurements for 115 –
119 different natural accessions per phenotype. The phenotypic data are
available at the AraPheno database (Seren et al., 2016). The genotypic
data were based on whole-genome sequencing data (The 1001 Genomes
Consortium, 2016) and covered 4,314,718 SNPs for the 119 accessions.
GWAS was performed with a mixed model correcting for population
structure in a two-step procedure, where first all polymorphisms were
analyzed with a fast approximation (emmaX, Kang et al., 2010) and
afterwards the top 1000 polymorphisms were reanalyzed with the correct
full model. Only polymorphisms with a minor allele count greater than 5
are reported. The kinship structure has been calculated under the
assumption of the infinitesimal model using all sequence variants with a
minor allele frequency of more than 5% in the whole population. The
analysis was performed in R (R Core Team, 2016). The R scripts used are
available at https://github.com/arthurkorte/GWAS. The genotype data used
for GWAS are available at the 1001 Genomes Project
(www.1001genomes.org).