A sequence-based variation map of 8.27 million SNPs in inbred mouse strains.
A dense map of genetic variation in the laboratory mouse genome will provide insights into the evolutionary history of the species and lead to an improved understanding of the relationship between inter-strain genotypic and phenotypic differences. Here we resequence the genomes of four wild-derived and eleven classical strains. We identify 8.27 million high-quality single nucleotide polymorphisms (SNPs) densely distributed across the genome, and determine the locations of the high (divergent subspecies ancestry) and low (common subspecies ancestry) SNP-rate intervals for every pairwise combination of classical strains. Using these data, we generate a genome-wide haplotype map containing 40,898 segments, each with an average of three distinct ancestral haplotypes. For the haplotypes in the classical strains that are unequivocally assigned ancestry, the genetic contributions of the Mus musculus subspecies--M. m. domesticus, M. m. musculus, M. m. castaneus and the hybrid M. m. molossinus--are 68%, 6%, 3% and 10%, respectively; the remaining 13% of haplotypes are of unknown ancestral origin. The considerable regional redundancy of the SNP data will facilitate imputation of the majority of these genotypes in less-densely typed classical inbred strains to provide a complete view of variation in additional strains.
Perlegen Sciences, 2021 Stierlin Court, Mountain View, California 94043, USA. frazer.kelly@scrippshealth.org
Kelly A
KA
Frazer
Eleazar
E
Eskin
Hyun Min
HM
Kang
Molly A
MA
Bogue
David A
DA
Hinds
Erica J
EJ
Beilharz
Robert V
RV
Gupta
Julie
J
Montgomery
Matt M
MM
Morenzoni
Geoffrey B
GB
Nilsen
Charit L
CL
Pethiyagoda
Laura L
LL
Stuve
Frank M
FM
Johnson
Mark J
MJ
Daly
Claire M
CM
Wade
David R
DR
Cox
D000818:Animals; D033481:Chromosomes, Mammalian / Q000235:genetics; D004252:DNA Mutational Analysis; D030541:Databases, Genetic; D016678:Genome / Q000235:genetics; D023281:Genomics; D006239:Haplotypes / Q000235:genetics; D051379:Mice; D008810:Mice, Inbred C57BL; D008815:Mice, Inbred Strains / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*