Figure 1

Alignment of the potato chromosome 5 genetic, cytogenetic and sequence maps. A. Chr-5 genetic map of genotype RH [16]. The map is divided in 78 bin segments of which the gray scale intensity corresponds to the number of AFLP markers per bin. Bin 46 has the highest marker density (174 markers) and contains the centromere. B. Digitally stretched cytogenetic map of RH pachytene Chr-5. Intense DAPI staining (white) marks the pericentromeric heterochromatin. Coloured foci mark the FISH positions of 35 BAC clones from the RH sequence tiling paths. For selected BAC clones, the connections are shown to the RH genetic (A) and sequence (C) maps. C. Alignment of the RH and DM genomic sequences. Positions of RH BAC tiling path sequences of haplotypes {0} and {1}, are shown as green and red blocks respectively, along the DM pseudomolecule sequence map (dark violet) of Chr-5. In the central heterochromatin, RH BAC MTPs of which the exact position is unknown are placed in arbitrary order and are shown in lighter colours. Likewise, DM sequence scaffolds without alignment to the RH sequences are shown in a lighter colour. The DM superscaffold sequences are marked only by their ID numbers, e.g. sequence block 103 at the start of Chr-5 is superscaffold PGSC0003DMB000000103 [18]. D. Model for the distribution of homozygous and polymorphic regions on RH Chr-5. E. Classification of sequence collinearity in overlap regions between RH and DM sequences. RH {0} vs RH {1} is the comparison between both sequence haplotypes in RH. RH {0) vs DM and RH {1} vs DM are comparisons of RH haplotype {0} and {1} sequences with the DM reference sequence.