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

Abstract

Two bottlenecks impeding the genetic analysis of complex traits in rodents are access to mapping populations able to deliver gene-level mapping resolution and the need for population-specific genotyping arrays and haplotype reference panels. Here we combine low-coverage (0.15×) sequencing with a new method to impute the ancestral haplotype space in 1,887 commercially available outbred mice. We mapped 156 unique quantitative trait loci for 92 phenotypes at a 5% false discovery rate. Gene-level mapping resolution was achieved at about one-fifth of the loci, implicating Unc13c and Pgc1a at loci for 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. These findings have implications for diverse areas of mammalian biology and demonstrate how genome-wide association studies can be extended via low-coverage sequencing to species with highly recombinant outbred populations.

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Figure 1: Sequence diversity of the CFW population.
Figure 2: Mapping resolution and effect size of QTLs.
Figure 3: Summary porcupine plot for 92 phenotypes.
Figure 4: Single-gene-resolution mapping at four loci using the entire set of SNPs (7.1 million).

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Acknowledgements

The authors wish to acknowledge excellent technical assistance from A. Kurioka, L. Swadling, C. de Lara, J. Ussher, R. Townsend, S. Lionikaite, A.S. Lionikiene, R. Wolswinkel and I. van der Made. We would like to thank T.M. Keane and A.G. Doran for their help in annotating variants and adding the FVB/NJ strain to the MGP. We thank the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics and the Wellcome Trust Sanger Institute for the generation of the sequencing data. This work was funded by Wellcome Trust grant 090532/Z/09/Z (J.F.). Primary phenotyping of the mice was supported by the Mary Lyon Centre and Mammalian Genetics Unit (Medical Research Council, UK Hub grant G0900747 91070 and Medical Research Council, UK grant MC U142684172). D.A.B. acknowledges support from NIH R01AR056280. The sleep work was supported by the state of Vaud (Switzerland) and the Swiss National Science Foundation (SNF 14694 and 136201 to P.F.). The ECG work was supported by the Netherlands CardioVascular Research Initiative (Dutch Heart Foundation, Dutch Federation of University Medical Centres, Netherlands Organization for Health Research and Development and the Royal Netherlands Academy of Sciences) PREDICT project, InterUniversity Cardiology Institute of the Netherlands (ICIN; 061.02; C.A.R. and C.R.B.). N.C. is supported by the Agency of Science, Technology and Research (A*STAR) Graduate Academy. R.W.D. is supported by a grant from the Wellcome Trust (097308/Z/11/Z).

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Authors and Affiliations

Authors

Contributions

J.N. and J.F. designed the study and experiments. J.N., B.K.Y. and N.C. processed data. C.C., R.E.M., N.B., A.B., P.H.-P., C.H., R.J., H.P., B.N., C.R. and T.H. phenotyped the mice and generated data. J.W. and A.W. developed bespoke Laboratory Information Management System (LIMS) and bioinformatics solutions for data collection. M.H. and M.F. managed importation and isolation procedures of mice into the Mary Lyon Centre. S.W., T.W. and S.D.M.B. provided infrastructure and staff, and established the phenotyping within the MLC. P.K.P. and J.N. managed the project. V.L., J.S.G. and R.M.A. quantified bone size and mineral content. D.A.B. and A.L. acquired skeletal muscle phenotypes. C.A.R., E.M.L., Y.M.P. and C.R.B. supervised cardiac data acquisition and analyzed the cardiac data. J.C. and J.-M.L. quantified serotonin. J.N., C.C., R.E.M., P.F., B.K.Y., D.J.A., P.K., N.P.T., P.A.R. and A.L. analyzed the phenotypic data. N.C. and L.G. processed the sequencing data. R.W.D. and L.G. performed genotype imputation. R.M., J.N., N.C. and J.F. performed the genetic analysis. J.N., R.W.D., N.C., R.M. and J.F. wrote the manuscript with input from co-authors.

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Correspondence to Richard Mott or Jonathan Flint.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–4, Supplementary Tables 2, 4, 6, and 7, and Supplementary Note. (PDF 2891 kb)

Supplementary Table 1

List of phenotypes measured in the outbred mice. (XLSX 43 kb)

Supplementary Table 3

Quality control data for genotypes derived from low-pass sequencing. (XLSX 43 kb)

Supplementary Table 5

List of 255 QTLs mapped in the outbred mice. (XLSX 90 kb)

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Nicod, J., Davies, R., Cai, N. et al. Genome-wide association of multiple complex traits in outbred mice by ultra-low-coverage sequencing. Nat Genet 48, 912–918 (2016). https://doi.org/10.1038/ng.3595

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