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G3 (Bethesda). 2017 Oct 5;7(10):3427-3434. doi: 10.1534/g3.117.300188.

High-Resolution Maps of Mouse Reference Populations.

Author information

The Jackson Laboratory, Bar Harbor, Maine 04609.
Division Biotechnology and Biomedicine Centre of the Academy of Sciences, Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic, Vestec, Prague 4, 142 20, Czech Republic.
Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, Tennessee 38163.
National Institute of Genetics, Mishima, 411-8540, Japan.
University of Colorado at Boulder, Colorado 80309.
Institut de Recherches Cliniques, Montreal, Quebec, H2W 1R7, Canada.
Institute for Behavioral Genetics, Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina 27599-7264
The Jackson Laboratory, Bar Harbor, Maine 04609


Genetic reference panels are widely used to map complex, quantitative traits in model organisms. We have generated new high-resolution genetic maps of 259 mouse inbred strains from recombinant inbred strain panels (C57BL/6J × DBA/2J, ILS/IbgTejJ × ISS/IbgTejJ, and C57BL/6J × A/J) and chromosome substitution strain panels (C57BL/6J-Chr#<A/J>, C57BL/6J-Chr#<PWD/Ph>, and C57BL/6J-Chr#<MSM/Ms>). We genotyped all samples using the Affymetrix Mouse Diversity Array with an average intermarker spacing of 4.3 kb. The new genetic maps provide increased precision in the localization of recombination breakpoints compared to the previous maps. Although the strains were presumed to be fully inbred, we found residual heterozygosity in 40% of individual mice from five of the six panels. We also identified de novo deletions and duplications, in homozygous or heterozygous state, ranging in size from 21 kb to 8.4 Mb. Almost two-thirds (46 out of 76) of these deletions overlap exons of protein coding genes and may have phenotypic consequences. Twenty-nine putative gene conversions were identified in the chromosome substitution strains. We find that gene conversions are more likely to occur in regions where the homologous chromosomes are more similar. The raw genotyping data and genetic maps of these strain panels are available at


chromosome substitution strains; gene conversions; mouse diversity genotyping array; recombinant inbred strains

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