Genome-wide association of multiple complex traits in outbred mice by ultra low-coverage sequencing

Two bottlenecks that have impeded the genetic analysis of complex traits in inbred strain crosses and populations derived from them, are the lack of gene level mapping resolution and the need for population specific genotyping arrays and haplotype reference panels. To address these problems we mapped multiple complex traits at high resolution in a highly recombinant commercially-available outbred mouse population, using imputed genotypes from 0.15x whole genome sequencing. By simultaneously imputing the ancestral haplotype space comprising 5,766,828 single nucleotide polymorphisms and the genomes of the mapping population at 359,559 tagging variants, we mapped 255 quantitative trait loci representing 156 unique regions in 1,887 mice for 92 phenotypes. Linkage disequilibrium decays fast enough to provide gene-level mapping resolution at about a fifth of loci. Our results implicate Unc13c and Pgc1-alpha at loci affecting the quality of sleep, Adarb2 for home cage activity, Rtkn2 for intensity of reaction to startle, Bmp2 for wound healing, Il15 and Id2 for several T-cell measures and Prkca for bone mineral content. Six diverse phenotypes map over the Met gene: muscle weight, startle response, serum albumin, calcium, protein and cholesterol levels, suggesting this is an important pleiotropic locus. These findings have implications for diverse areas of mammalian biology and demonstrate how GWAS can be extended via low-coverage sequencing to species with large highly recombinant outbred populations.