The Collaborative Cross uses the same robust principles for mapping genes as has been used with other recombinant inbred strains for decades. The various strains are tested for the trait of interest; in this example, those strains displaying the trait are indicated with a “+”. Comparing the inheritance pattern of an unknown gene (or trait) in a panel of RI strains with that of known genes and markers, the unknown gene can be integrated into the known map at the marker showing the same strain distribution pattern, or at the most similar marker minimizing crossovers in the new map.

 

In this example, the three positive strains only have in common the chromosomal region circled; they all share the same founder’s DNA at the position. None of the negative strains have the same founder’s DNA at this position. The actual analyses will of course be much more complicated, and will use sophisticated mapping software.