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Background  Familial adenomatous polyposis is an inherited genetic disease, characterized by colorectal polyps. It is caused by inactivating mutations in the  Adenomatous polyposis coli  ( Apc ) gene. Mice carrying a nonsense mutation in the  Apc  gene at R850, which is designated  Apc   Min/+   ( Multiple intestinal neoplasia ), develop intestinal adenomas. Several genetic modifier loci of  Min  ( Mom ) were previously mapped, but so far, most of the underlying genes have not been identified. To identify novel modifier loci associated with  Apc   Min/+  , we performed quantitative trait loci (QTL) analysis for polyp development using 49 F1 crosses between different Collaborative Cross (CC) lines and C57BL/6 J- Apc   Min/+  mice. The CC population is a genetic reference panel of recombinant inbred lines, each line independently descended from eight genetically diverse founder strains. C57BL/6 J- Apc   Min/+   males were mated with females from 49 CC lines. F1 offspring were terminated at 23 weeks and polyp counts from three sub-regions (SB1–3) of small intestinal and colon were recorded.    Results  The number of polyps in all these sub-regions and colon varied significantly between the different CC lines. At 95% genome-wide significance, we mapped nine novel QTL for variation in polyp number, with distinct QTL associated with each intestinal sub-region. QTL confidence intervals varied in width between 2.63–17.79 Mb. We extracted all genes in the mapped QTL at 90 and 95% CI levels using the BioInfoMiner online platform to extract, significantly enriched pathways and key linker genes, that act as regulatory and orchestrators of the phenotypic landscape associated with the  Apc   Min/+   mutation.    Conclusions  Genomic structure of the CC lines has allowed us to identify novel modifiers and confirmed some of the previously mapped modifiers. Key genes involved mainly in metabolic and immunological processes were identified. Future steps in this analysis will be to identify regulatory elements – and possible epistatic effects – located in the mapped QTL.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07890-x.

bmc genomics

Genetic mapping of novel modifiers for ApcMin induced intestinal polyps’ development using the genetic architecture power of the collaborative cross mice