Genome-wide association study of behavioral, physiological and gene expression traits in outbred CFW mice

Journal name:
Nature Genetics
Year published:
Published online


Although mice are the most widely used mammalian model organism, genetic studies have suffered from limited mapping resolution due to extensive linkage disequilibrium (LD) that is characteristic of crosses among inbred strains. Carworth Farms White (CFW) mice are a commercially available outbred mouse population that exhibit rapid LD decay in comparison to other available mouse populations. We performed a genome-wide association study (GWAS) of behavioral, physiological and gene expression phenotypes using 1,200 male CFW mice. We used genotyping by sequencing (GBS) to obtain genotypes at 92,734 SNPs. We also measured gene expression using RNA sequencing in three brain regions. Our study identified numerous behavioral, physiological and expression quantitative trait loci (QTLs). We integrated the behavioral QTL and eQTL results to implicate specific genes, including Azi2 in sensitivity to methamphetamine and Zmynd11 in anxiety-like behavior. The combination of CFW mice, GBS and RNA sequencing constitutes a powerful approach to GWAS in mice.

At a glance


  1. Components of the study.
    Figure 1: Components of the study.

    Our study consisted of four phases, including behavioral testing and measurement of physiological traits (phase A), GBS (phase B), measurement of gene expression in brain tissues using RNA-seq (phase C), and QTL mapping for physiological and behavioral traits and for gene expression (phase D). The red dotted line for phase D corresponds to P = 2 × 10−7.

  2. Genetic characteristics of the CFW mouse population.
    Figure 2: Genetic characteristics of the CFW mouse population.

    (a) Density of GBS SNPs on autosomal chromosomes. (b) Mean LD (r2) decay rates estimated using frequency-matched SNPs55, with MAF >20%, in a 34th-generation advanced intercross line (AIL) derived from LG/J and SM/J strains43, 46, heterogeneous stock (HS) mice bred for >50 generations49, HMDP83, a panel of 30 inbred laboratory strains14, 52, DO mice12 and CFW mice. (c) Treemix analysis summarizing the genetic relationship between CFW mice and inbred strains in the Wellcome Trust sequencing panel.

  3. QTLs for physiological and behavioral traits.
    Figure 3: QTLs for physiological and behavioral traits.

    (a) Minimum P values for association across all tested behavioral and physiological phenotypes (see Supplementary Tables 1 and 2 for details). FC, fear conditioning; gastroc., gastrocnemius. (b,c) Genome-wide scans for testis weight (b) and PPI in response to a 12-dB prepulse (c). (d) Association signal for testis weight near the QTL on chromosome 13. (e) Association signal for PPI near the QTL on chromosome 7. Dotted red lines correspond to significance thresholds (P < 0.1) estimated via permutation tests.

  4. Overview of eQTL mapping.
    Figure 4: Overview of eQTL mapping.

    (a) The color of each pixel in the matrix corresponds to the lowest P value among all eQTLs using a 10 Mb × 10 Mb window. (b) Overlap of genes with eQTLs in the three brain tissues, detected using the traditional cis-eQTL mapping method (not ASE). The permutation-based P-value threshold for each eQTL is 0.05. (c) Genome-wide scan for total locomotor activity on day 3 of the methamphetamine sensitivity tests. (d) Association signal for total locomotor activity in the QTL region on chromosome 9. (e) Association signal for expression of Azi2 in the striatum, in the same region as in d. Dotted red lines correspond to significance thresholds (P < 0.1) estimated via permutation tests.


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Author information

  1. These authors contributed equally to this work.

    • Clarissa C Parker,
    • Shyam Gopalakrishnan &
    • Peter Carbonetto


  1. Department of Human Genetics, University of Chicago, Chicago, Illinois, USA.

    • Clarissa C Parker,
    • Shyam Gopalakrishnan,
    • Peter Carbonetto,
    • Natalia M Gonzales,
    • Emily Leung,
    • Yeonhee J Park,
    • Emmanuel Aryee,
    • Joe Davis &
    • Abraham A Palmer
  2. Department of Psychology, Middlebury College, Middlebury, Vermont, USA.

    • Clarissa C Parker
  3. Program in Neuroscience, Middlebury College, Middlebury, Vermont, USA.

    • Clarissa C Parker
  4. Natural History Museum of Denmark, Copenhagen University, Copenhagen, Denmark.

    • Shyam Gopalakrishnan
  5. AncestryDNA, San Francisco, California, USA.

    • Peter Carbonetto
  6. Department of Biobehavioral Health, Pennsylvania State University, University Park, Pennsylvania, USA.

    • David A Blizard
  7. Center for Musculoskeletal Research, University of Rochester, Rochester, New York, USA.

    • Cheryl L Ackert-Bicknell
  8. Department of Orthopedics and Rehabilitation, University of Rochester, Rochester, New York, USA.

    • Cheryl L Ackert-Bicknell
  9. School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK.

    • Arimantas Lionikas
  10. Department of Genetics, Stanford University, Palo Alto, California, USA.

    • Jonathan K Pritchard
  11. Department of Biology, Stanford University, Palo Alto, California, USA.

    • Jonathan K Pritchard
  12. Howard Hughes Medical Institute, Stanford University, Palo Alto, California, USA.

    • Jonathan K Pritchard
  13. Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, Illinois, USA.

    • Abraham A Palmer
  14. Department of Psychiatry, University of California, San Diego, La Jolla, California, USA.

    • Abraham A Palmer
  15. Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, USA.

    • Abraham A Palmer


A.A.P. conceived the study. C.C.P. and A.A.P. supervised the project. S.G. and P.C. designed and implemented the statistical and bioinformatics analyses with contributions from C.C.P., J.K.P. and A.A.P. N.M.G. designed and executed the RNA-seq and GBS protocols with assistance from E.A. and J.D. C.C.P. performed the behavioral phenotyping with assistance from E.L. and Y.J.P. A.L. performed the muscle and bone phenotyping with input from D.A.B. C.L.A.-B. performed the BMD phenotyping. C.C.P., S.G., P.C. and A.A.P. wrote the manuscript, with input from all co-authors.

Competing financial interests

The authors declare no competing financial interests.

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Supplementary information

PDF files

  1. Supplementary Text and Figures (8,706 KB)

    Supplementary Note and Supplementary Figures 1–29.

Excel files

  1. Supplementary Table 1 (16,353 KB)

    Summary of phenotypes.

  2. Supplementary Table 2 (18,098 KB)

    GWAS results.

  3. Supplementary Table 3 (10,779 KB)

    The number of expression QTLs (eQTLs) found in the three brain tissues assayed.

  4. Supplementary Table 4 (10,512 KB)

    Discordance rates when comparing GBS and MegaMUGA genotypes using 24 subjects genotyped using both platforms.

Additional data