title: Development of SNP markers for C57BL/6N-derived mouse inbred strains.
abstract: C57BL/6N inbred mice are used as the genetic background for producing knockout mice in large-scale projects worldwide; however, the genetic divergence among C57BL/6N-derived substrains has not been verified. Here, we identified novel single nucleotide polymorphisms (SNPs) specific to the C57BL/6NJ strain and selected useful SNPs for the genetic monitoring of C57BL/6N-derived substrains. Informative SNPs were selected from the public SNP database at the Wellcome Trust Sanger Institute by comparing sequence data from C57BL/6NJ and C57BL/6J mice. A total of 1,361 candidate SNPs from the SNP database could distinguish the C57BL/6NJ strain from 12 other inbred strains. We confirmed 277 C57BL/6NJ-specific SNPs including 10 nonsynonymous SNPs by direct sequencing, and selected 100 useful SNPs that cover all of the chromosomes except Y. Genotyping of 11 C57BL/6N-derived substrains at these 100 SNP loci demonstrated genetic differences among the substrains. This information will be useful for accurate genetic monitoring of mouse strains with a C57BL/6N-derived background.
authors.affiliation: Experimental Animal Division, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan.
authors.forename: Kazuyuki
authors.initials: K
authors.lastname: Mekada
authors.forename: Mayu
authors.initials: M
authors.lastname: Hirose
authors.forename: Ayumi
authors.initials: A
authors.lastname: Murakami
authors.forename: Atsushi
authors.initials: A
authors.lastname: Yoshiki
mesh_terms: D000818:Animals; D002875:Chromosomes / Q000235:genetics; D005819:Genetic Markers; D060005:Genotyping Techniques; D008810:Mice, Inbred C57BL / Q000235:genetics*; D008815:Mice, Inbred Strains / Q000235:genetics*; D018345:Mice, Knockout; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D005819:Genetic Markers