Figure 3

Subgenome assignment of BACs. All 57 putative BACs that were identified with the six SNP assays surrounded by the box are shown as rectangles. SNP assays were ordered according to their sequence in the Brassica rapa genome. Two slashes indicate that one or more of the SNP assays used in this study map in the Brassica rapa genome between the ones shown. PCR experiments revealed which of the putative BACs truly map to the regions of interest. Black font marks confirmed BACs, whereas BAC coordinates that were not verified to map to the homoeologous regions of interest are shown in red font. Red, dark blue and black boxes indicate SNP scores that were confirmed by PCR analyses, whereas dotted outlines mark false positive SNP scores. Pink or pale blue boxes correspond to scores that were only revealed by PCR but not by Illumina’s GoldenGate® Genotyping Assay. Red or pink colour represent the A subgenome, C subgenome sequences are displayed in dark or pale blue. Scores of assays for which only one of the assay nucleotides revealed putative BACs are shown as black boxes.