As an initial step, growth and carcass composition QTL were identified in a cross between CAST/EiJ (CAST) and HG [24]. In the F2, mice homozygous for the hg deletion (hg/hg) and wild type (+/+) were assayed and hg modifier QTL were defined as those either absent in +/+ mice and segregating in hg/hg or loci with altered gene action dependent on background. Four hg modifier QTL (Wg2 on MMU2, Carfhg2 on MMU9, Carp2 on MMU11 and Feml3 on MMU17) were identified, along with 12 additional QTL (Q1Ucd1 on MMU1 (which only reached a suggestive level of statistical significance), Wg1, Carp1, Cara1 and Feml1 on MMU2, Carfhg1 on MMU5, Wg3 on MMU8, Feml2 on MMU9, Wg4 and Cara2 on MMU11 and Carp3 and Cara3 on MMU17) whose expression was independent of the hg locus.