One aim of using animal models for complex diseases is to detect the genetic basis of these diseases. With controllable environmental factors as well as the known genetic background, animal models are powerful tools to search for susceptibility genes for complex diseases, and have been intensively employed for that purpose. More than 27,000 QTL have been identified in the mouse genome since the first QTL was identified at the beginning of the 1990s [11]. By 2005, approximately 20 quantitative trait genes (QTGs) in the mouse genome had been identified [12,13]. Interestingly, most QTGs identified in animal models have the causal polymorphisms in the protein-coding region [14], which provoke protein structure changes or protein deficiency. This suggests, on the one hand, that small-effect QTL are difficult to identify with traditional strategies and, on the other hand, that the polymorphisms regulating gene expression might only slightly affect the quantitative traits, and thus are more difficult to identify.