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Table 9.6 Derivation of the expected phenotypic value for two genetic marker genotypes when QTL mapping with pairs of marker loci that flank a QTL. There are a total of nine genetic marker genotypes possible with two genetic marker loci. Like QTL mapping based on a single genetic marker, the phenotypic value of the a1a1b1b1 marker genotype is a function of both the additive and dominance effects of the QTL. In contrast, the expected phenotypic value of the a1a2b1b2 marker genotype is a function only of d. Therefore, the a1a2b1b2 marker class mean value provides an estimate of the dominance coefficient independent of a. The gametes and expected gamete frequencies are given in Fig. 9.16.

Marker genotype

Marker genotype frequency

F2 genotype

F2 genotype frequency

F2 genotypic value

Frequency-weighted F2 genotypic value

4 a1q1b1

a1q1b1

a1q2b1 a1q2b1 a1q2b1

rpop _aQ-rA)20-rB)2 , 2drArBQ-rA)Ç\-rB) | -arjr2 44*,*, "4 4 4

a1q1b1

a2q2b2 a1q1b2 a2q2b1 a2q1b1 a1q1b2 a1q2b1

A2Q!B2 a1q1b1 A2Q!B2

a2q2b2

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