Intramuscular fat content and water-holding capacity are important traits in livestock. To identify genomic regions affecting them, the progeny of two inbred lines of the Berlin Muscle Mouse (BMMI816 and BMMI806), which have high muscle mass, were used as a QTL research model for livestock. These two strains were crossed reciprocally to generate F1, F2, and G3 intercross populations. Multiple related phenotypes have been measured and this is the data of G3 population. The linkage analyses with G3 animals revealed QTL on chromsome 7 and 2. For detailed protocols, see Karst et al 2011.