The primary goal of the current study was to determine if reciprocal QTLs could be found in the selectively bred lines formed by short-term selective breeding from HS4. The advantage of detecting QTLs in HS animals is that it is possible to extract a more detailed haplotype signature for the QTL. The importance of extracting a more detailed haplotype signature can be seen in the following example. Consider that we have detected a HS4 QTL, but the only information available is that the genetic marker or markers differentiate the B6 and D2 strains; if the B6 strain has the A allele and the D2 strain has the B allele, the haplotype is simply AB. If we now add information about the C and LP strains, the QTL could have not one but four possible haplotypes (ABAA, ABBBB, ABAB, and ABBA). This increased information makes it possible to narrow the QTL interval and the number of candidate genes generated from gene expression and sequence databases (see, e.g., Hitzemann et al. 2003).
