Fig. 1.—

Schematic of MapComp using a reference genome to pair markers. MapComp compares genetic maps from two different species (e.g. Coho Salmon and Brook Charr) by mapping marker sequences against a reference genome (e.g. Rainbow Trout), then retaining high quality mappings (i.e. single alignment with MAPQ ≥10). The closest two markers, one from each species, are paired if they align to the same contig/scaffold. This method captures homologous markers (e.g. the white star in image) and nonidentical but nearby markers (e.g. gray stars). In this example, the closest marker from Coho Salmon and Brook Charr are paired, and the second closest marker from Coho Salmon is discarded (shown with an X) because each marker is paired without replacement. After pairing is complete, the cM position of the marker from each species’ linkage group is plotted in an Oxford grid. The position on the contig is not carried over to the Oxford grid, only that from the linkage maps. Note that the marker names and contig ID in the schematic are for demonstration purposes only and do not reflect actual pairings.