One note on picking which genotype should be represented by the male and female, respectively, should depend on the selectable marker of the male, or in other words, whatever selectable marker is associated with the gene being crossed into the female background. This acts as the experiment and as an internal positive control for the cross itself. For example, if the female is a mutant line that does not harbor a resistance marker, it would be advantageous to use a male that has a robust resistance marker associated with its transgene. A couple of examples of robust molecular plant markers would be BASTA (a herbicidal resistance gene), Kanamycin, or hygromycin. If the male parent is homozygous for the BASTA resistance marker, one can harbor seeds from the cross, plant F1s, and spray these plants with BASTA. Whatever lives should represent a productive cross that is heterozygous for the male transgene.
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