List of SNPs showing significant associations with total skin anthocyanin (TSA) concentration, pulp colour (PC) and skin and pulp colour together (SPC).

This table shows significant nominal P-values obtained under Models A and B (P<0.01). Significance was confirmed by 10 000 permutations for Model A. SNPs significant after Bonferroni correction for 15 genes are marked with *. Some SNPs that were not significant for TSA concentration, PC and SPC but were associated with other phenotypes are shown on Tables S3 and S4. Table S8 shows location, MAF, Hardy Weinberg chi-squared and missing data for all the SNPs genotyped.