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Genetical Genomics of Behavior: A Novel Chicken Genomic Model for Anxiety Behavior

Martin Johnsson, Michael J. Williams, Per Jensen and Dominic Wright
Genetics January 1, 2016 vol. 202 no. 1 327-340; https://doi.org/10.1534/genetics.115.179010
Martin Johnsson
AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping 581 83, Sweden
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Michael J. Williams
Institutionen för Neurovetenskap, Uppsala University, Uppsala 751 25, Sweden
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Per Jensen
AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping 581 83, Sweden
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Dominic Wright
AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping 581 83, Sweden
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  • For correspondence: domwright@gmail.com
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  • Figure 1
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    Figure 1

    Flow-chart overview of experimental steps taken, plus the findings from each step.

  • Figure 2
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    Figure 2

    Genomic locations of all detected open field behavioral QTL. Bars indicate 1.8-LOD drop confidence intervals.

  • Figure 3
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    Figure 3

    Part of LOD curves and scatterplots of trait vs. gene expression for selected candidates GABRB2, RABGGTB, STK17A and SFRP4, and LOC770352. Bars indicate 1.8-LOD intervals, extended to the closest marker.

Tables

  • Figures
  • Additional Files
  • Table 1 Candidate gene expression levels predicting behavior
    Mouse HS open field LOD scores (additive model)
    ChrTraitQTL C.I. (Mb)eQTLPhQTL posGene P-valueNEO leo.nb scoreModel P-valueMarkerLatencyTotal activityTime in centerMarker
    2Time in center zone trial 245.5–51.9SFRP42@4260.04NANArs2709114———rs13481716
    2Time in center zone trial 245.5–51.9STK17A2@4260.004NANArs1181601———rs6253368
    3Minimum total movement25.1–27RSPH93@2770.030.8235.48E-06rs37784934.77.8—UT_17_45.56
    3Minimum total movement25.1–27C1orf107/DIEXF3@2770.0030.3680.804rs7549523———rs3684501
    8Total velocity average23.9–26.6RABGGTB8@194.00.05NANArs7555627———rs3656403
    10Total velocity average4.3–6.8ADAM1010@1010.030.440.396rs2242321———rs13480265
    10Total velocity average4.3–6.8APBA210@1010.010.04210.0719rs7680321—7.7—rs3717846
    10Total velocity trial 114.4–17.4LOC77035210@185.00.0020.9430.687rs1480617——4.5rs13476065
    10Total movement average14.4–17.4LOC77035210@185.00.00021.070.956rs1480617——4.5rs13476065
    10Minimum total movement14.4–17.4LOC77035210@182.00.0030.8740.925rs1480617——4.5rs13476065
    10Total movement trial 27.6–15.0LOC77035210@64.00.00120.7470.878rs1480617——4.5rs13476065
    10Maximum total movement14.4–17.4LOC77035210@185.00.00031.130.985rs1480617——4.5rs13476065
    10Total velocity trial 14.3–6.8APBA210@99.00.0040.9770.131rs7680321—7.7—rs3717846
    10Total velocity trial 14.3–6.8ADAM1010@99.00.040.5150.37rs2242321———rs13480265
    10Total movement trial 14.3–6.8LOC77035210@99.00.0080.8150.852rs7680321——4.5rs13476065
    10Total movement average4.3–6.8APBA210@99.00.02−0.9660.0002rs7680321—7.7—rs3717846
    13Total velocity trial 21.5–4.1GABRB213@32.00.0014NANArs43026295.15.1—rs6225242
    17Total velocity average1–2.5SLC31A117@10.004NANArs786978———rs3690581
    17Total velocity trial 11–2.5SLC31A117@10.003NANArs786978———rs3690581
    • Chromosome (Chr) and QTL confidence interval are given for the trait that each eQTL significantly correlated with. The phenotypic QTL position (PhQTL pos) is also given in centimorgans. The P-value of the correlation, after Bonferroni correction, is also provided (Gene P-value). The causality modeling scores are also indicated for each gene, as are the WTCCC P-values for each gene region. The association of each gene with the mouse HS cross is also given, with the LOD scores of the gene location for each of the three different open field tests provided.

  • Table 2 Candidate genes trait correlations and ranking vs. all eQTL
    GeneTraitOverall rank (of 535 eQTL)Trait–gene correlation P-value
    ADAM10Average velocity520.027
    ADAM10Velocity trial 1350.018
    APBA2Average total movement340.024
    APBA2Average velocity270.010
    APBA2Velocity trial 1110.002
    C1orf107/DIEXFMinimum total movement70.003
    GABRB2Velocity trial 270.006
    LOC770352Total movement trial 1110.004
    LOC770352Total movement trial 220.001
    LOC770352Maximum total movement1<0.001
    LOC770352Minimum total movement40.001
    LOC770352Average total movement2<0.001
    LOC770352Velocity trial 1130.002
    RABGGTBAverage velocity230.008
    RSPH9Minimum total movement390.033
    SFRP4Time in center trial 2240.018
    SLC31A1Average velocity170.004
    SLC31A1Velocity trial 1150.003
    STK17ATime in center trial 210.002
  • Table 3 Association of the nine genes tested in the GWASs
    Bipolar:Schizophrenia:Major depressive disorder:
    PGCBD 2011 studySWGPCCa 2014PGCMDD
    GeneP-valueMarkerP-valueMarkerP-valueMarker
    SFRP40.0001*rs7807315NS—NS—
    STK17ANS—NS—NS—
    RSPH9NS—0.00009#rs72859036NS—
    DIEXFNS—NS—NS—
    RABGGTBNS—NS—NS—
    ADAM10NS—0.00001*rs6494035NS—
    APBA2NS—NS—NS—
    GABRB2NS—NS—NS—
    SLC31A1NS—NS—NS—
    • Significant (*) and suggestive (#) P-values are given for each gene, along with the marker showing the highest association in the gene interval. In the case of RSPH9 and ADAM10 the distance of the marker from the gene is also given.

    • ↵a Schizophrenia Working Group of the Psychiatric Genomics Consortium.

Additional Files

  • Figures
  • Tables
  • Supporting Information for Johnsson et al., 2015

    Supporting Information

    • Figure S1 - Scatter plots of behavioural phenotypes between the first and second trials. (.pdf, 389 KB)
    • Figure S2 - Scatter plots of the remaining candidate genes. (.pdf, 467 KB)
    • Figure S3 - LOD graphs of overlapping candidate eQTL and QTL. (.pdf, 283 KB)
    • Table S1 - Pearson Correlations between open-field measurements from trial 1(A) and trial 2 (B) measurements. (.pdf, 302 KB)
    • Table S2 - Behavioural QTL for open field behaviour. Chromosome, position (in cM), Lod score, r-squared (in %), additive and dominance values are given, as well as the confidence intervals (C.I.) as defined by a 1.8 LOD drop. (.pdf, 1,010 KB)
    • Table S3 - cis and trans eQTL. (.pdf, 411 KB)
    • Table S4 - Number of eQTL correlated with traits for which candidate genes identified. (.pdf, 301 KB)
    • File S1 - Supplemental methods. (.pdf, 312 KB)
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Volume 202 Issue 1, January 2016

Genetics: 202 (1)

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Genetics of complex traits
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Genetical Genomics of Behavior: A Novel Chicken Genomic Model for Anxiety Behavior

Martin Johnsson, Michael J. Williams, Per Jensen and Dominic Wright
Genetics January 1, 2016 vol. 202 no. 1 327-340; https://doi.org/10.1534/genetics.115.179010
Martin Johnsson
AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping 581 83, Sweden
  • Find this author on Google Scholar
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Michael J. Williams
Institutionen för Neurovetenskap, Uppsala University, Uppsala 751 25, Sweden
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Per Jensen
AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping 581 83, Sweden
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Dominic Wright
AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping 581 83, Sweden
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  • For correspondence: domwright@gmail.com
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Citation

Genetical Genomics of Behavior: A Novel Chicken Genomic Model for Anxiety Behavior

Martin Johnsson, Michael J. Williams, Per Jensen and Dominic Wright
Genetics January 1, 2016 vol. 202 no. 1 327-340; https://doi.org/10.1534/genetics.115.179010
Martin Johnsson
AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping 581 83, Sweden
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Michael J. Williams
Institutionen för Neurovetenskap, Uppsala University, Uppsala 751 25, Sweden
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Per Jensen
AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping 581 83, Sweden
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Dominic Wright
AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping 581 83, Sweden
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: domwright@gmail.com

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