Pilot studies for high throughput analysis of Arabidopsis GWAS

在这项研究中，我们尝试使用基因组序列已公布的拟南芥80份材料进行GWAS定位(曹等人，2011)。从基因组序列中制备了DNA多态性数据，提取了1.5M个SNPs。在表型方面，用光抑制作为抗性的参数来测定其对环境胁迫的抗性。使用流苏(Bradbury等人，2007)和结构(Pritchard等人，2000)进行关联图谱绘制。对所获得的GWAS信号的研究发现，这些信号在峰高和分布上与人类的不同，这种差异可能是由于人类和拟南芥的种群结构不同所致。这些差异将被考虑到修改人类GWA计算方法，以适应拟南芥的研究。正如预期的那样，在我们的GWAS计算中观察到了假阳性的GWAS信号，并且可以通过从计算中删除少数SNP基因座来消除这些信号。

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.