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Recombinant

Figure 9.15 The F2 or recombinant inbred line design for OTL mapping assuming one OTL (Q) and one genetic marker locus (M). The top phenotypic distribution represents the variance in value in the population that is subject to OTL mapping. Individuals at the edges of this phenotypic distribution are then sampled to start lines to be inbred for five (self-fertilization) to 10 (sib mating) generations to achieve high homozygosity. Individuals are then sampled from inbred lines with diverged phenotypes to form the P1 generation. The progeny of the P1 individuals are all double heterozygotes and form the F1 generation. Gamete frequencies produced by F1 individuals depend on recombination rates between loci. Random mating among F1 individuals produces the F2 individuals which are genotyped for the marker loci and measured for their phenotypic values.

random mating to their progeny in the F2 generation. Notice now that recombination between the OTL and the marker locus does influence gamete frequencies and thereby the genotype frequencies in the F2 generation. The OTL mapping analysis is based on two types of data for all F2 individuals: that is, (i) the marker locus genotype is known and (ii) the phenotypic value is known.

The 10 unique two-locus genotypes in the F2 population are shown in Table 9.5, grouped into three classes based on the marker-locus genotype.

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