Pilot studies for high throughput analysis of Arabidopsis GWAS

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In this study, we tried GWAS mapping using Arabidopsis 80 accessions whose genome sequences have been published (Cao et al, 2011). DNA polymorphism data has been prepared from the genome sequences, and 1.5 M SNPs have been extracted. As for the phenotyping, environmental stress resistance has been measured using photoinhibition as a parameter of resistance. Association mapping was done using TASSEL (Bradbury et al, 2007) and STRUCTURE (Pritchard et al, 2000). Survey of the obtained GWAS signals revealed some differences from human GWAS signals in the peak height and distribution, and the differences are suggested to be due to different population structures between human and Arabidopsis. These differences are to be considered for modification of the human GWAS calculation methods to fit with Arabidopsis studies. As expected, false-positive GWAS signals were observed in our GWAS calculations, and they could be removed by deletion of minority SNP loci from the calculation.