TY - JOUR T1 - High-Resolution Maps of Mouse Reference Populations JF - bioRxiv DO - 10.1101/155507 SP - 155507 AU - Petr Simecek AU - Jiri Forejt AU - Robert W. Williams AU - Toshihiko Shiroishi AU - Toyoyuki Takada AU - Lu Lu AU - Thomas E. Johnson AU - Beth Bennett AU - Christian F. Deschepper AU - Marie-Pier Scott-Boyer AU - Gary Churchill AU - Fernando Pardo-Manuel de Villena Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/06/26/155507.abstract N2 - 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 x DBA/2J, ILS/IbgTejJ x ISS/IbgTejJ, C57BL/6J x A/J) and chromosome substitution strain panels (C57BL/6J-Chr#<A/J>, C57BL/6J-Chr#<PWD/Ph>, C57BL/6JChr#<MSM/Ms>). We genotyped all samples using the Affymetrix Mouse Diversity Array with an average inter-marker spacing of 4.3kb. 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 21kb to 8.4Mb. 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 http://churchill-lab.jax.org/website/MDA. ER -