Table 9.5 Derivation of the expected phenotypic value for the three marker-locus genotypes when QTL mapping with a single marker locus associated with a single QTL. The three genetic marker genotypes may be associated with any of the three possible QTL genotypes because of recombination during the formation of F2 gametes. The difference between the M1/M1 and M2/M2 marker class means (expressions in the Marker-class mean value column) is equal to 2d. The phenotypic value of each marker locus genotype is a function of both the additive and dominance effects of the QTL (a and d) as well as the recombination rate (r). So unless there is no dominance and no recombination, estimates of QTL effects from single-marker-locus mapping are always minimum estimates. The gametes and expected gamete frequencies are given in Fig. 9.15.

Gametes F2 Genotype genotype frequency

Genotypic Frequency- Marker value weighted genotype genotypic value

Marker-class contribution to F2 population mean value

Marker genotype frequency in F2 population

Marker-class mean value c/c c/r r/r c/c r/r c/r r/c c/c c/r r/r


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