Anchoring of linkage groups to chromosomes by fluorescent in situ hybridization. The black and stippled regions show the heterochromatin (C-banded regions) on the seven autosomes and two sex chromosomes, the vertical lines on chromosome 2 show the rDNA, and the ruler is marked in 1 Mb increments. The chromosomal regions to which bacterial artificial chromosomes (BACs) hybridize are marked. All fluorescent in situ hybridization (FISH)-mapped BACs shown hybridize uniquely to a single position in the genome and BLAST match to scaffolds from which the microsatellite markers were designed (see Additional data file 4 for the BLAST matched markers for each BAC). The green BACs are congruent with linkage mapping results both in terms of chromosome and relative marker order. Hence the number of green markers provides a visual impression of the strength of support anchoring each linkage group. Black BACs are congruent with linkage mapping results for chromosome, but the ordering of markers is incongruent by a large distance (compare Figure 2 and Additional data file 4). Red BACS are incongruent (that is, the linkage mapping results and FISH identify different chromosomes). Red BACs on the same chromosome always matched to markers from different linkage groups, thus displaying a random pattern of mismatching. The blue BACs 15A15.TJ and 11A15, 15B18 indicate potential positions for the orphan markers sc117 and LG8 that were not incorporated into the linkage groups. BACs followed by TJ or TV indicate that only 1 BAC end matched correctly. TJ and TV refer to the two different BAC ends that could be sequenced and follow the naming convention given in GenBank. The BACs followed by a (Z) on chromosome Z indicate BACs that match to Z-specific scaffolds. The assignment of LG9 to chromosome 5 is tentative as there was only one congruent and one incongruent marker. The inset figure illustrates 1 of 16 scaffolds where markers on the same scaffold mapped to different linkage groups. The schematic of Smp_scaff000004 (2.21 Mb) shows the relative positions of two FISH markers (BAC 11C10 and Smox1) and two linkage markers (sc3 and sc3b). Both sets of markers suggest that this scaffold was incorrectly assembled (see Figure 2 for the FISH result of Smox1).