Figure 4 Conditional GWAS and statistical analyses reveal an association between  MYB52  and  PHT1;1.  Manhattan plots of GWAS analyses performed using AMM (A, no conditioning )  or modified AMM in which the most significant SNP located at Chr5 (the red arrowhead in A) was included as a cofactor (B, conditioning )  in GWAPP; a further SNP peak on Chr1 became evident (the red arrowhead in B). The 5% false discovery rate threshold is plotted as a dashed horizontal line. C, List of candidate accessions used for examination of the epistatic relationship between Chr1 and Chr5. Asterisks indicate the SNPs that were corrected after re-sequencing. Analyses of the relationship between SNP locus 1 and SNP locus 2 by two-way ANOVA based on average gene expression levels of  MYB52  (2 −△CT  × 1,000) (D) and  PHT1;1  (2 −△CT  ×100) (E). The letters in blue and red shown in (C), (D), and (E) indicate SNP locus 1 and SNP locus 2, respectively.