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Figure 9.17 The difference in phenotypic mean values for each of 17 genetic marker loci versus the position of each marker locus on a chromosome. In this hypothetical example, there are two genetic markers that lie closest to QTLs indicated by two peak values for marker-class mean differences. The phenotypes of the homozygote classes for the marker loci at 33, 41, and 85 map units (or centimorgans, cM) differ by over one phenotypic standard deviation. The QTL near 33 cM increases the mean value while the QTL near 85 cM decreases the mean value. Marker-class mean value differences greater than ±1 phenotypic standard deviation (blue dashed lines) are considered statistically meaningful in this example. Marker-class mean differences smaller than one standard deviation could be different due to chance alone. The close proximity of these two QTLs with opposite effects on the trait would lead to reduced estimates of QTL effects at all marker loci. This occurs because each marker locus is partly linked to a QTL of both positive and negative effect, so the perceived marker class mean difference is the net effect of the two QTLs. Genetic marker locus positions are established by observed recombination rates. One map unit or centimorgan distance along a chromosome is equal to a 1% recombination rate. LOD score, log of odds score.

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