Comparison of two methods of building combined microsatellite and SNP maps. (A) The maps created by the conventional method. (B) Maps created by the method where the SNP markers are mapped before the microsatellites. The maps produced by the 'SNPs preceding microsatellites' are more similar to the physical order of the markers in the genome assembly, which are shown in the centre. The microsatellite markers are highlighted in red and the markers positioned at a LOD ≥ 3 are in bold, underlined font. To aid clarity, the markers on the linkage maps are shown at equidistant positions along the chromosomes, although the total map lengths are shown on the same scale, illustrating the inflated lengths of the conventional build process.