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).