QGene generates graphical chromosome maps useful for a variety
of purposes; the one above shows a map generated by the simulator.
Aside from viewing and exporting sets of chromosome plots, you
can interact with the display to determine linkages and apply
selection weights to individual marker loci. If you don't have
marker or trait data, or even a population, you can still view
and export a map graphic by preparing a map file in the usual
way, and clicking on the map icon in the File/New map dialog
to open your map file. QGene will draw the map, and you will also
be able to simulate a population from it if desired.
If the map is associated with a population, you can double-click on a locus name to get a list of the loci most closely linked to it. In QGene, you'll click or drag to highlight the current locus. Command-click on names of loci to place weights on them for a selection index; the colored bands in the map graphic above represent loci with various weights on one or other of their alleles.
The plot at right schematically displays the allele array in the population sorted upon its genotypic score for the loci selected in the map figure above. Each double horizontal row of pixels represents a single BC1 individual; black represents recurrent-parent homozygote, green the heterozygote, and cyan the loci at which genotype data were missing. Notice the density of the respective genotype color around the selected loci, depending on which allele is under selection. The two bars at left indicate that only two individuals (in this simulated population of 100) carry the entire array of 5 selected alleles.
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