Thoday's Method³

Suppose there is a locus, $Q$, influencing the expression of a quantitative trait situated between two known marker loci, $A$ and $B$.⁴ If we have inbred lines with different phenotypes, we can assume that one line has the genotype $AQB/AQB$ and the other has the genotype $aqb/aqb$. The procedure for detecting the presence of $Q$ is as follows:

1. Cross the inbred lines to form an $F_1$. The genotype of all $F_1$ progeny will be $AQB/aqb$.

2. Intercross the $F_1$'s to form an $F_2$ and look at the progeny with recombinant genotypes, e.g., $aB/ab$.

3. If $Q$ lies between $A$ and $B$
   1. The phenotypes of progeny will fall into two distinct classes corresponding with the genotypes: $aqB/aqb$ and $aQB/aqb$.⁵

   2. The recombination fraction between $A$ and $Q$ is related to the proportion of $qq$ and $Qq$ genotypes among the progeny.

Notice that in this last step we actually have a criterion for determining whether $Q$ lies between $A$ and $B$. Namely, if $A$ and $B$ are close enough in the linkage map that there is essentially no chance of double recombination between them, then we'll get the two phenotype classes referred to in recombinants between $A$ and $B$. If $Q$ lies outside this region,⁶ we'll get only one phenotypic class among progeny with recombinant genotypes.