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Background  Nonalcoholic fatty liver disease (NAFLD) is a multifactorial disease caused by interactions between environmental and genetic factors. The SMXA-5 mouse is a high-fat diet-induced fatty liver model established from SM/J and A/J strains. We have previously identified  Fl1sa , a quantitative trait locus (QTL) for fatty liver on chromosome 12 (centromere-53.06 Mb) of SMXA-5 mice. However, the chromosomal region containing  Fl1sa  was too broad. The aim of this study was to narrow the  Fl1sa  region by genetic dissection using novel congenic mice and to identify candidate genes within the narrowed  Fl1sa  region.    Results  We established two congenic strains, R2 and R3, from parental A/J-12 SM  and A/J strains. R2 and R3 strains have genomic intervals of centromere-29.20 Mb and 29.20–46.75 Mb of chromosome 12 derived from SM/J, respectively. Liver triglyceride content in R2 and R3 mice was significantly lower than that in A/J mice fed with a high-fat diet for 7 weeks. This result suggests that at least one of the genes responsible for fatty liver exists within the two chromosomal regions centromere-29.20 Mb (R2) and 29.20–46.75 Mb (R3). We found that liver triglyceride accumulation is inversely correlated with epididymal fat weight among the parental and congenic strains. Therefore, the ectopic fat accumulation in the liver may be due to organ-organ interactions between the liver and epididymal fat. To identify candidate genes in  Fl1sa , we performed a DNA microarray analysis using the liver and epididymal fat in A/J and A/J-12 SM  mice fed with a high-fat diet for 7 weeks. In epididymal fat, mRNA levels of  Zfp125  (in R2) and  Nrcam  (in R3) were significantly different in A/J-12 SM  mice from those in A/J mice. In the liver, mRNA levels of  Iah1  (in R2) and  Rrm2  (in R2) were significantly different in A/J-12 SM  mice from those in A/J mice.    Conclusions  In this study, using congenic mice analysis, we narrowed the chromosomal region containing  Fl1sa  to two regions of mouse chromosome 12. We then identified 4 candidate genes in  Fl1sa :  Iah1  and  Rrm2  from the liver and  Zfp125  and  Nrcam  from epididymal fat.    Electronic supplementary material  The online version of this article (doi:10.1186/s12863-016-0453-7) contains supplementary material, which is available to authorized users.

Genetic dissection of the fatty liver QTL Fl1sa by using congenic mice and identification of candidate genes in the liver and epididymal fat