Conditional gene knockout is a popular approach in research involving mouse models. Often, loxP sites are inserted into the introns of a gene, say gene A, to create a floxed (fl) allele. Studies are often performed to mate mice with the Afl allele with another mouse stain containing a knock-in cre allele driven by gene B's promoter (referred to here as Bcre). Imagine that you hope to conduct experiments to define the phenotypes of mice with gene A knocked out in cells expressing gene B. Therefore, you obtained the Afl/flBcre/+ mice. In this nomenclature, fl/fl indicates that both gene A alleles are floxed. cre/+ means one of the gene B alleles contains cre, whereas the other allele is wildtype (wt, indicated by the + sign). Please describe (1) what are the genotypes for control mice that you have seen in the literature that the phenotypes of the Afl/flBcre/+ mice can be compared to? If there are more than two control genotypes that you have seen, you only need to list two of them. (2) For each of the genotypes in (1), what is the control genotype controlling for? What are the pros and cons? (3) In the ideal world (meaning you do not have to worry about the cost, labor, and the duration of the project), what genotype(s) are needed to convincingly demonstrate that the phenotypes of the Afl/flBcre/+ mice are due to the loss of gene A in cells expressing gene B? Please note that we assume that all mice and alleles are on the same pure genetic background (e.g. C57B6/J) and that backcrossing does not need to be considered.
