Fig. 4
Manhattan plots and QQ plots. Describing marker-trait associations for absolute values of the onset of flowering (BOF-ABS) in the three divergent environments Gross Gerau, Rauischholzhausen (both Germany) and Temuco (Chile) in 2011. Associations were calculated using a mixed model with PC adjustment, using 21,623 single-copy, genome-wide SNP markers. The solid line represents the significance threshold (p = 0.1) for associations after Bonferroni correction, the dashed line represents the level considered as significant in this analysis (−log10(p) > 4), and the dotted line represents the threshold for suggestive associations(−log10(p) > 3). The A and C subgenomes are displayed in a slightly different color code (dark: A subgenome, bright: C subgenome)