Extensive linkage disequilibrium among classical laboratory strains represents an obstacle in the high-resolution haplotype mapping of mouse quantitative trait loci (QTL). To determine the potential of wild-derived mouse strains for fine QTL mapping, we constructed a haplotype map of a 250-kb region of the t-complex on chromosome 17 containing the Hybrid sterility 1 (Hst1) gene. We resequenced 33 loci from up to 80 chromosomes of five mouse (sub)species. Trans-species single-nucleotide polymorphisms (SNPs) were rare between Mus m. musculus (Mmmu) and Mus m. domesticus (Mmd). The haplotypes in Mmmu and Mmd differed and therefore strains from these subspecies should not be combined for haplotype-associated mapping. The haplotypes of t-chromosomes differed from all non-t Mmmu and Mmd haplotypes. Half of the SNPs and SN indels but only one of seven longer rearrangements found in classical laboratory strains were useful for haplotype mapping in the wild-derived M. m. domesticus. The largest Mmd haplotype block contained three genes of a highly conserved synteny. The lengths of the haplotype blocks deduced from 36 domesticus chromosomes were in tens of kilobases, suggesting that the wild-derived Mmd strains are suitable for fine interval-specific mapping.

Department of Mouse Molecular Genetics Institute of Molecular Genetics Academy of Sciences of the Czech Republic 14220 Prague Czech Republic

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Abe, K., H. Noguchi, K. Tagawa, M. Yuzuriha, A. Toyoda PubMed PMC

Artzt, K., D. Barlow, W. F. Dove, K. Fischer-Lindahl, J. Klein PubMed

Barrett, J. C., B. Fry, J. Maller and M. J. Daly, 2005. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21 263–265. PubMed

Barski, A., S. Cuddapah, K. Cui, T. Y. Roh, D. E. Schones PubMed

Chistiakov, D. A., Y. A. Seryogin, R. I. Turakulov, K. V. Savost'anov, E. V. Titovich PubMed

Cutler, G., L. A. Marshall, N. Chin, H. Baribault and P. D. Kassner, 2007. Significant gene content variation characterizes the genomes of inbred mouse strains. Genome Res. 17 1743–1754. PubMed PMC

Dipetrillo, K., X. Wang, I. M. Stylianou and B. Paigen, 2005. Bioinformatics toolbox for narrowing rodent quantitative trait loci. Trends Genet. 21 683–692. PubMed

Eberle, M. A., M. J. Rieder, L. Kruglyak and D. A. Nickerson, 2006. Allele frequency matching between SNPs reveals an excess of linkage disequilibrium in genic regions of the human genome. PLoS Genet. 2 e142. PubMed PMC

Egan, C. M., S. Sridhar, M. Wigler and I. M. Hall, 2007. Recurrent DNA copy number variation in the laboratory mouse. Nat. Genet. 39 1384–1389. PubMed

Forejt, J., and P. Ivanyi, 1975. Genetic studies on male sterility of hybrids between laboratory and wild mice ( PubMed

Forejt, J., S. Gregorova and P. Jansa, 1988. Three new t-haplotypes of Mus musculus reveal structural similarities to PubMed

Frazer, K. A., C. M. Wade, D. A. Hinds, N. Patil, D. R. Cox PubMed PMC

Frazer, K. A., E. Eskin, H. M. Kang, M. A. Bogue, D. A. Hinds PubMed

Gabriel, S. B., S. F. Schaffner, H. Nguyen, J. M. Moore, J. Roy PubMed

Galtier, N., M. Gouy and C. Gautier, 1996. SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput. Appl. Biosci. 12 543–548. PubMed

Gregorova, S., and J. Forejt, 2000. PWD/Ph and PWK/Ph inbred mouse strains of PubMed

Gregorova, S., M. Mnukova-Fajdelova, Z. Trachtulec, J. Capkova, M. Loudova PubMed

Grupe, A., S. Germer, J. Usuka, D. Aud, J. K. Belknap PubMed

Guenet, J. L., and F. Bonhomme, 2003. Wild mice: an ever-increasing contribution to a popular mammalian model. Trends Genet. 19 24–31. PubMed

Guryev, V., B. M. Smits, J. Van De Belt, M. Verheul, N. Hubner PubMed PMC

Herrmann, B., M. Bucan, P. E. Mains, A. M. Frischauf, L. M. Silver PubMed

Ideraabdullah, F. Y., E. De La Casa-Esperon, T. A. Bell, D. A. Detwiler, T. Magnuson PubMed PMC

International HapMap Consortium, 2007. A second generation human haplotype map of over 3.1 million SNPs. Nature 449 851–861. PubMed PMC

Jansa, P., P. Divina and J. Forejt, 2005. Construction and characterization of a genomic BAC library for the PubMed PMC

Jeffreys, A. J., L. Kauppi and R. Neumann, 2001. Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat. Genet. 29 217–222. PubMed

Laurie, C. C., D. A. Nickerson, A. D. Anderson, B. S. Weir, R. J. Livingston PubMed PMC

Lisitsyn, N., and M. Wigler, 1993. Cloning the differences between two complex genomes. Science 259 946–951. PubMed

Liu, P., H. Vikis, Y. Lu, D. Wang and M. You, 2007. Large-scale PubMed PMC

Lyon, M. F., 2003. Transmission ratio distortion in mice. Annu. Rev. Genet. 37 393–408. PubMed

Mihola, O., J. Forejt and Z. Trachtulec, 2007. Conserved alternative and antisense transcripts at the programmed cell death 2 locus. BMC Genomics 8 20. PubMed PMC

Mikkelsen, T. S., M. Ku, D. B. Jaffe, B. Issac, E. Lieberman PubMed PMC

Mural, R. J., M. D. Adams, E. W. Myers, H. O. Smith, G. L. Miklos PubMed

Payne, F., D. J. Smyth, R. Pask, J. D. Cooper, J. Masters PubMed

Payseur, B. A., and M. Place, 2007. Prospects for association mapping in classical inbred mouse strains. Genetics 175 1999–2008. PubMed PMC

Pialek, J., M. Vyskocilova, B. Bimova, D. Havelkova, J. Pialkova PubMed

Pletcher, M. T., P. McClurg, S. Batalov, A. I. Su, S. W. Barnes PubMed PMC

Ptak, S. E., D. A. Hinds, K. Koehler, B. Nickel, N. Patil PubMed

Schimenti, J., 2000. Segregation distortion of mouse PubMed

Trachtulec, Z., and J. Forejt, 1999. Transcription and RNA processing of mammalian genes in PubMed PMC

Trachtulec, Z., and J. Forejt, 2001. Synteny of orthologous genes conserved in mammals, snake, fly, nematode, and fission yeast. Mamm. Genome 12 227–231. PubMed

Trachtulec, Z., V. Vincek, R. M. Hamvas, J. Forejt, H. Lehrach PubMed

Trachtulec, Z., R. M. Hamvas, J. Forejt, H. R. Lehrach, V. Vincek PubMed

Trachtulec, Z., M. Mnukova-Fajdelova, R. M. Hamvas, S. Gregorova, W. E. Mayer PubMed

Trachtulec, Z., C. Vlcek, O. Mihola and J. Forejt, 2004. Comparative analysis of the PDCD2-TBP-PSMB1 region in vertebrates. Gene 335 151–157. PubMed

Trachtulec, Z., O. Mihola, C. Vlcek, H. Himmelbauer, V. Paces

Vincek, V., J. Sertic, Z. Zaleska-Rutzynska, F. Figueroa and J. Klein, 1990. Characterization of PubMed

Vyskocilova, J., Z. Trachtulec, J. Forejt and J. Pialek, 2005. Does geography matter in hybrid sterility in house mice? Biol. J. Linn. Soc. Lond. 84 663–674.

Wade, C. M., E. J. Kulbokas, III, A. W. Kirby, M. C. Zody, J. C. Mullikin PubMed

Wang, N., J. M. Akey, K. Zhang, R. Chakraborty and L. Jin, 2002. Distribution of recombination crossovers and the origin of haplotype blocks: the interplay of population history, recombination, and mutation. Am. J. Hum. Genet. 71 1227–1234. PubMed PMC

Waterston, R. H., K. Lindblad-Toh, E. Birney, J. Rogers, J. F. Abril PubMed

Wiltshire, T., M. T. Pletcher, S. Batalov, S. W. Barnes, L. M. Tarantino PubMed PMC

Winckler, W., S. R. Myers, D. J. Richter, R. C. Onofrio, G. J. McDonald PubMed

Yalcin, B., J. Fullerton, S. Miller, D. A. Keays, S. Brady PubMed PMC

Yang, H., T. A. Bell, G. A. Churchill and F. Pardo-Manuel De Villena, 2007. On the subspecific origin of the laboratory mouse. Nat. Genet. 39 1100–1107. PubMed

Zhang, K., Z. S. Qin, J. S. Liu, T. Chen, M. S. Waterman PubMed PMC

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Copy-number variation introduced by long transgenes compromises mouse male fertility independently of pachytene checkpoints

Prdm9 incompatibility controls oligospermia and delayed fertility but no selfish transmission in mouse intersubspecific hybrids

X chromosome control of meiotic chromosome synapsis in mouse inter-subspecific hybrids

Interallelic and intergenic incompatibilities of the Prdm9 (Hst1) gene in mouse hybrid sterility

Polymorphism in hybrid male sterility in wild-derived Mus musculus musculus strains on proximal chromosome 17