Accordingly, we detected five cQTLs for the gonadal fat mass trait on Chromosomes 1, 3, 5, 11, and 19. The detection of all five cQTLs was “driven” by the larger effect in females, with significant improvement by the incorporation of sex*additive and sex*dominant parameters. QTLs associated with obesity, gonadal fat, and abdominal fat have been reported before overlapping with cQTLs on Chromosomes 1 [26–28], 5 [26,29], and 11 [19,29] reported here, whereas the cQTL on Chromosome 3 represents a novel QTL for this trait. The Chromosome 19 cQTL for fat mass was recently reported by us [5] in the BXD intercross F2 progeny from the strains B6 and DBA (which shares the same haplotype at this region as the C3H strain used in this study). Interestingly, significant heritability and genetic regulation was seen in this F2 population despite the hyperlipidemic, proinflammatory ApoE−/− background and the high-fat Western diet. This background possesses several advantages, such as allowing the modeling of human-like disease states. The predominantly female-driven effects of the five cQTLs likely reflect the significant effect of differential gonadal hormone secretions on the genetic regulation of this complex trait.