Fig. 2.

Physical maps of potato chromosomes I to VI. The maps are based on the pseudomolecules version 4.03 [31], which are represented as vertical bars. Chromosomes a: to the left are shown as horizontal blue lines the positions of the genes detected by association of SolCAP SNPs with TSC in the PIN184 population (details in Additional file 9). To the right are shown as horizontal blue lines the positions of the genes tagged by SolCAP SNPs with differential allele frequency in the QUEST case-control population for TSC (details in Additional file 8). The length of the lines is proportional to the p value. The scale (− log10(p)) is shown on top of the chromosome maps. Chromosomes b: To the left are shown as horizontal red lines the positions of the genes tagged by SolCAP SNPs with differential allele frequency in the QUEST case-control population for TY. On the right are shown as horizontal green lines the positions of the genes tagged by SolCAP SNPs with differential allele frequency in the QUEST case-control population for TSY; otherwise as in chromosomes a (details in Additional file 8). The numbers between chromosomes a and b indicate the positions of the 46 genomic regions, where QTL for TSC detected by GWAS in the PIN184 population overlap with QTL for TSC, TY and TSY detected by differential SNPs in the QUEST case-control populations (details in Additional files 4 and 5). Chromosomes c: To the left is shown as horizontal purple lines the frequency distribution of 3144 genes with differential RADseq SNPs, at least one with FDR < 0.001 (Table 1), in the QUEST case-control populations. The scale (No. of genes per 0.5 Mbp) is shown on top of the chromosome maps (details in Additional files 4 and 5). To the right are shown the positions of 71 genes with RADseq SNPs differential in all three case-control populations and with unidirectional effect on TSC, TY and TSY (Table 2). They are identified by the last five digits of the PGSC0003DMG locus number. Included are here also the positions of the eleven candidate genes with differential SNPs that were tested for association in the whole QUEST population (indicated by *) (Table 3), and the positions of 14 candidate genes (underlined) associated with TSC, TY or TSY in previous association studies that were also detected in the QUEST case-control populations (Table 6). The approximate position of PHO1A on the short arm of chromosome III, which is not included in pseudomolecules version 4.03, is also shown