Fig. 4.

The genetic basis of CGA level of tuber flesh in diploid potatoes. (A) Manhattan plot of GWAS analysis for the CGA content of tuber flesh using the mixed linear model. The red line represents the significant threshold (adjusted by the Bonferroni method). 18 loci exceeding the threshold were identified in this analysis. The Quantile-Quantile plot of the p value shown in Supplementary Fig. 5. The regions containing significant polymorphisms were further restricted into three blocks (indicated by the dotted red line) by LD analysis. (B) Zoom in of the Manhattan plots and the local LD heatmap in chromosomal region Chr4:45.2–46.2 Mb (pvalue < 0.001), Chr8:42.6–43 (pvalue < 0.001). Mb, and Chr10:50.8–52.8 Mb (pvalue < 0.0001). Pairwise LD between the SNPs was estimated with r2 statistics. The pairwise LD r2 value from 0 to 1 is colored with white and dark red, respectively. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)