it is then possible to estimate the values of a and d for the linked QTL. We will need to make a distinction between the true values of a and d and the estimated values of a and O since recombination between the marker and QTL will cause a ^ a and d ^ O. The difference between the two most extreme phenotypic values in the F2 population defines the genotypic scale from +a to -a as in Fig. 9.15. Therefore, the difference between the M1/M1 and M2/M2 marker class means is equal to 2 a. In an equation this can be stated as

2a = gm1m1 gm2m2

Substituting the definitions of GM M and GM M from Table 9.5 gives

The expected degree of dominance of the QTL is also obtained using the definition of d from the geno-typic scale of measurement as the difference between the heterozygote genotypic value and the midpoint between +a and -a. For QTL mapping data, the value of the midpoint is half the difference between the M1M1 and M2M2 marker class mean values and the heterozygote genotypic value is the M1M2 marker class mean value. The estimated degree of dominance is therefore

gm1m1 + gm2m2 2

Using the definitions of Gmm and Gmm from Table 9.5 yields

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