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Background  Mouse chromosome 2 is linked to growth and body fat phenotypes in many mouse crosses. With the goal to identify the underlying genes regulating growth and body fat on mouse chromosome 2, we developed five overlapping subcongenic strains that contained CAST/EiJ donor regions in a C57BL/6J  hg/hg   background ( hg  is a spontaneous deletion of 500 Kb on mouse chromosome 10). To fine map QTL on distal mouse chromosome 2 a total of 1,712 F2 mice from the five subcongenic strains, plus 278 F2 mice from the HG2D founder congenic strain were phenotyped and analyzed. Interval mapping (IM) and composite IM (CIM) were performed on body weight and body fat traits on a combination of SNP and microsatellite markers, which generated a high-density genotyping panel.    Results  Phenotypic analysis and interval mapping of total fat mass identified two QTL on distal mouse chromosome 2. One QTL between 150 and 161 Mb,  Fatq2a , and the second between 173.3 and 175.6 Mb,  Fatq2b . The two QTL reside in different congenic strains with significant total fat differences between homozygous  cast/cast  and  b6/b6  littermates. Both of these QTL were previously identified only as a single QTL affecting body fat,  Fatq2 . Furthermore, through a novel approach referred here as replicated CIM,  Fatq2b  was mapped to the  Gnas  imprinted locus.    Conclusions  The integration of subcongenic strains, high-density genotyping, and CIM succesfully partitioned two previously linked QTL 20 Mb apart, and the strongest QTL,  Fatq2b,  was fine mapped to a ~2.3 Mb region interval encompassing the  Gnas  imprinted locus.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-014-1191-8) contains supplementary material, which is available to authorized users.

Overlapping mouse subcongenic strains successfully separate two linked body fat QTL on distal MMU 2