The use of STSB has many advantages, including the ability to rapidly detect whether a particular phenotype is heritable, providing a strategy for confirming QTLs detected by some other independent experiment, and the ability to produce essentially unlimited numbers of animals that can be used for gene-expression analyses (see, e.g., Palmer et al. 2005). The major disadvantage of STSB is genetic drift and the stochastic fixation of some alleles that have no relevance to the phenotype of interest. Thus, one expects that many of the QTLs detected in STSB experiments will be false positives. To some extent, this problem can be dealt with by adjusting the LOD threshold (upward) for a significant QTL. However, this adjustment will always be an estimate and may well in some cases underestimate the needed correction. One common solution to this problem is to have a replicate selection—the idea here being that the chance of randomly fixing the same alleles in two independent selections is very small. The experimental design used in the current study extends this design by using two independent selections, which were
