Abstract Background: The p53 tumor suppressor gene plays a key role in sporadic and inherited breast cancers. Spontaneous mammary tumors develop in ~55% of female BALB/c-Trp53+/- mice providing a model for breast cancer in Li-Fraumeni Syndrome. In contrast, C57BL/6J-Trp53+/- females are devoid of mammary tumors. This strain difference offers a dramatic example of variable penetrance and tools to define genes contributing to the risk of mammary tumors. Methods: Genome-wide linkage analysis of the mammary tumor incidence was performed in F1 and N2 backcross mice. The C57BL/6J alleles of SM1 locus were introgressed into the BALB/c genetic background through 10 backcrosses to generate SM1-Trp53+/- mice. Radiation sensitivity, DNA double-strand break repair, processitivity of DNA replication and expression of DNA repair genes in SM1-Trp53+/- mice were compared with BALB/c-Trp53+/- and C57BL/6J-Trp53+/-. Results: Genome-wide linkage analysis identified a major modifier locus on chromosome 7 (designated SM1) and another on chromosome 2 with an overall LOD score of 6.1 using a multigenic model of inheritance. The SM1 locus does not undergo loss of heterozygosity in mammary tumors consistent with dominant-acting risk alleles from BALB/c mice. Mammary epithelial cells (MMEC) of SM1 mice, having C57BL/6 alleles of SM1 in BALB/c background, were sensitive to radiation as were BALB/c MMEC. Functional assays of DNA double-strand break repair (1) demonstrate error-prone repair through the single strand annealing (SSA) pathway level in SM1 embryo fibroblasts (MEF) was similar to that in C57BL/6 MEF, which was 2.8-fold higher in BALB/c-Trp53+/- MEF and 2.5-fold higher in [BALB.B6]F1-Trp53+/-. Similarly, DNA fiber assays showed that processivity of DNA replication was significantly decreased in BALB/c and F1 MEF with median fork length (MFL) 6.4µM but increased in C57BL/6 and complemented in SM1 MEF (MFL ~8.2µM). In addition, gene expression profile of at least 5 DNA repair proteins (Ercc5, Rev1, Rev3l, Trex2, Rdm1) that are differentially expressed in C57BL/6 and BALB/c were complemented by SM1 locus. Conclusions: Gene(s) within the 20Mb SM1 locus impair movement of replications forks. Stalling of replication may precipitate fork collapse and DNA double strand breaks resulting in the loss of heterozygosity for Trp53 through recombination observed in 90% of mammary tumors.