Fine haplotype structure of a chromosome 17 region in the laboratory and wild mouse

Extensive linkage disequilibrium among classical laboratory strains represents an obstacle in the high-resolution haplotype snapping of mouse quantitative trait loci (QTL). To determine the potential of wild-derived mouse strains for fine QTL mapping, we constructed a haplotype snap of a 250-kb region of the l-complex on chromosome 17 containing the Hybrid sterility 1 (Hsi1) gene. We resequenced 33 loci from tip 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 its Mmmu and Mind differed and therefore strains from these subspecies should not be combined for haplotype-associated snapping. The haplotypes of l-chromosomes differed from all non-l, Mmmu and Mind 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 Mind 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 Mind strains are suitable for fine interval-specific mapping.