Outbred laboratory mouse populations are widely used in biomedical research. inexpensive, robust and readily available outbred population commonly used in toxicology and cancer research [1], [2], [3]. They have also been widely used for mouse transgenesis experiments, principally due to efficient breeding and large litter sizes. Although spontaneous mutations have arisen in CD-1 mice, very few have been mapped. The mutations that have been identified in CD-1 mice involved commonly used inbred mouse mapping strategies, including complementation testing of candidate genes or mapping by outcrossing to a genetically characterized inbred strain [4], [5]. However, CD-1 mice are applicable to a broad range of genetic studies. While many large-scale examinations of the genetic architecture of inbred mice have been completed [6], [7], [8], [9], [10], [11], no comparable evaluations of commercially available outbred strains, including CD-1 mice, have been reported. This lack of genome-wide evaluation has created a significant obstacle to realizing the utility of CD-1 mice for genetic research. Surprisingly little is known about the degree of heterogeneity that has survived within the various strains of outbred laboratory mice during their extended period of captive breeding, despite the reasonably well-documented historical relationship among both inbred and outbred laboratory mice [3], [12]. In fact, warnings against the use of commercially available outbred mice in genetic research have appeared in the literature due to the presumption that genetic variation within outbred mice cannot be easily maintained and may be highly variable across breeders and over time [13], [14], [15]. These warnings question whether outbred mice are actually genetically diverse mouse populations. Most outbred stocks are derived from a small number of mice that were imported to the US by Clara J. Lynch in 1926 and are collectively known as Swiss mice [3]. Reports examining allelic variation affecting enzymatic activity in outbred CD-1 mice and its inbred Pitavastatin calcium derivatives concluded that random fixation, but not inbreeding or population bottlenecks, accounted for slight losses in genetic variation among outbred mouse colonies [1], [2]. Although outbred mice are commonly cited as models for outbred human populations [1], [2], [3], based on their histories, it is Pitavastatin calcium more likely that outbred mice reflect human founder populations rather than outbred human populations. Large-scale evaluation of the genetic variation within commercially available outbred mice would resolve whether these mice are outbred and how they compare to human populations. Currently, the mouse quantitative trait loci (QTL) mapping community is focused on creating novel inbred-based mouse populations to increase recombination events and thereby reduce linkage disequilibrium (LD) to facilitate fine-mapping studies. This initiative has culminated in the ongoing Collaborative Cross (CC) [16], [17], [18], [19], [20]. Several existing mouse populations, including outbred and wild-caught mice, also represent attractive alternatives to inbred mice for association mapping. In wild-caught mice from Arizona, LD decays at a rate favorable for high resolution association studies [21]. However, many standard phenotyping procedures for laboratory mice are extremely challenging to perform in wild-derived inbred strains [18], [22], and are likely to prove to be similarly difficult to carry out in wild-caught mice. In contrast, outbred mice are readily available, relatively inexpensive and standard phenotyping protocols can be used without modification. Currently, MF1 is the only outbred strain Rabbit Polyclonal to HTR7 that has been utilized for QTL mapping [23], [24]. CD-1 mice have been used to examine the inherent genetic variability among common laboratory phenotypes such as discrimination learning [25], lever pressing, and locomotion [26], as well as phenotypic traits that model features of common complex human phenotypes, including stress reactivity [27], lithium response [28], and ingestion [29], [30], [31]. Pitavastatin calcium Despite this extensive, documented phenotypic variation, only one QTL has been reported in CD-1 mice and this was identified through a candidate gene approach [32]. The usefulness of CD-1 mice for identifying.