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Originally published as Genetics Published Articles Ahead of Print on February 3, 2008.

Genetics, Vol. 178, 1777-1784, March 2008, Copyright © 2008
doi:10.1534/genetics.107.082404

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Fine Haplotype Structure of a Chromosome 17 Region in the Laboratory and Wild Mouse

Zdenek Trachtulec*,{dagger},1, Cestmir Vlcek{dagger},{ddagger}, Ondrej Mihola*,{dagger}, Sona Gregorova*,{dagger}, Vladana Fotopulosova*,{dagger} and Jiri Forejt*,{dagger}

* Department of Mouse Molecular Genetics, {ddagger} Department of Genomics and Bioinformatics, and {dagger} Center for Applied Genomics, Institute of Molecular Genetics Academy of Sciences of the Czech Republic, 14220 Prague, Czech Republic

1 Corresponding author: Department of Mouse Molecular Genetics, Institute of Molecular Genetics Academy of Sciences of the Czech Republic, Videnska 1083, 14220 Prague, Czech Republic.
E-mail: trachtul{at}img.cas.cz

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.






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