A panel of chromosome substitution strains (CSS) was generated [11] by a "marker-assisted" breeding program where the progeny of a B6 × A/J cross were successively backcrossed to the B6 mice. Genetic markers were used to identify homozygosity in the background (B6) and the individual A/J chromosome. These strains have one chromosome from A/J mice in a B6 background. This allows the identification of a trait in one or more CSS and implies that at least one QTL resides on this chromosome. Use of this panel requires fewer mice to determine the QTL than does a genome-wide scan. Another advantage is the ability for detection of QTL in the presence of other QTL. In addition, initial screens with the CSS simplify the fine-mapping of QTL. Several studies of this CSS panel, B6 Chr1-19, X, YA/J, have been reported for behavior [12], weight gain [13], sterols [13], and plasma amino acids levels [13,14], and have identified many more QTL than studies of the same traits using a genome-wide scan.