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Difficulties in fine-mapping quantitative trait loci (QTLs) are a major impediment to progress in the molecular dissection of complex traits in mice. Here we show that genome-wide high-resolution mapping of multiple phenotypes can be achieved using a stock of genetically heterogeneous mice. We developed a conservative and robust bootstrap analysis to map 843 QTLs with an average 95% confidence interval of 2.8 Mb. The QTLs contribute to variation in 97 traits, including models of human disease (asthma, type 2 diabetes mellitus, obesity and anxiety) as well as immunological, biochemical and hematological phenotypes. The genetic architecture of almost all phenotypes was complex, with many loci each contributing a small proportion to the total variance. Our data set, freely available at, provides an entry point to the functional characterization of genes involved in many complex traits.

Original publication




Journal article


Nat Genet

Publication Date





879 - 887


Animals, Breeding, Chromosome Mapping, Female, Genomics, Genotype, Humans, Male, Mice, Models, Genetic, Phenotype, Polymorphism, Single Nucleotide, Quantitative Trait Loci