Development of SNP markers for C57BL/6N-derived mouse inbred strains

C57BL/6N inbred mice are used as the genetic background for producing knockout mice inlarge-scale projects worldwide; however, the genetic divergence among C57BL/6N-derivedsubstrains has not been verified. Here, we identified novel single nucleotidepolymorphisms (SNPs) specific to the C57BL/6NJ strain and selected useful SNPs for thegenetic monitoring of C57BL/6N-derived substrains. Informative SNPs were selected from thepublic SNP database at the Wellcome Trust Sanger Institute by comparing sequence data fromC57BL/6NJ and C57BL/6J mice. A total of 1,361 candidate SNPs from the SNP database coulddistinguish the C57BL/6NJ strain from 12 other inbred strains. We confirmed 277C57BL/6NJ-specific SNPs including 10 nonsynonymous SNPs by direct sequencing, and selected100 useful SNPs that cover all of the chromosomes except Y. Genotyping of 11C57BL/6N-derived substrains at these 100 SNP loci demonstrated genetic differences amongthe substrains. This information will be useful for accurate genetic monitoring of mousestrains with a C57BL/6N-derived background.