Cfq5^SM/J
QTL Variant Detail

Summary

• QTL variant: Cfq5^SM/J
• Name: conditioned fear QTL 5; SM/J
• MGI ID: MGI:5888763
• QTL: Cfq5 Location: Chr1:150606337-159307464 bp Genetic Position: Chr1, Syntenic

Variant origin

• Strain of Specimen: SM/J

Variant description

• Allele Type: QTL

Notes

Mapping and Phenotype information for this QTL, its variants and associated markers

J:216981

Anxiety disorders can be characterized by exaggerations of normal and adaptive emotional response to fearful or stressful events. There is substantial behavioral, genetic, and neuroanatomical conservation between humans and mice. To identify quantitative trait loci (QTL) for conditioned fear and open field behavior an F2 intercross and a 34th generation advanced intercross line (AIL) was used in the current study. Simultaneous analysis of the F2 and AIL provided strong support for QTL within much narrower regions.

Four hundred eighty seven F2 mice (249 males and 241 females) were derived from a cross between LG/J and SM/J inbred strains. Six hundred and eighty seven Aap:LG,SM-G34 AIL mice (353 males and 334 females) were derived from F33 breeders. F33 mice were mated such that no mating pairs shared a common grandparent.

Behavioral testing on F2 mice ranged between 53 and 71 days of age; the range for AIL mice was between 50 and 76 days of age. All mice went through an identical testing sequence.

Open field behavior testing was part of a locomotor testing paradigm. After a brief acclimation period mice were placed in the center of the open field chamber, a sound -attenuating environmental chamber with overhead lighting and a fan in the rear providing ventilation. Three phenotypes were measured: (1) distance traveled in the periphery (centimeters), (2) distance traveled in the center (centimeters) and (3) proportion of time spent in the center of the arena.

One week after open field testing conditioned fear testing was done in a conditioned fear chamber - a sound attentuating chamber with dim illumination and fans that provided a low level of masking background noise. Behavior was digitally recorded by computer and subsequently analyzed with FreezeFrame software. Testing consisted of a 5 minute test that occurred three times over three consecutive days. On day 1, baseline freezing (pretraining freezing) was measured; followed by exposure to a conditioned stimulus (CS), a 30 second tone of 85db that coterminated with an unconditioned stimulus (US), a 2 second foot shock delivered through the floor grid. Day 2 testing began 24 hours later in an identical test environment where no tones or shocks were presented. The proportion of time freezing in response to the test chamber (freezing to context) was measured. Testing on day 3 began 24 hours later where the context was altered: different experimenter, wearing different gloves, no bedding, shock grid, door and one wall covered with hard white plastic, dimmer lighting, vent fan partially obstructed. The same tone was presented that was presented on day one but no foot shock. Freezing to cue was measured which was defined as the average percentage of time spent freezing during the tone presentations.

DNA was extracted from F2 mice; genotypes were called at 162 evenly spaced markers on autosomal and X chromosomes. AIL genotypes at 4601 SNPs on autosomal and X chromosomes were ascertained using an Illumina Infinium Platform custom genotyping array. All SNP identifiers were based on release 37 (July 2007) of the NCBI Mouse Genome Assembly.

To analyze the combined data, the probability of missing genotypes and the genotypes of SNPs that were called in the F34 mice and not called in the F2 mice were estimated. Genotype probabilities were calculated separately in F2 and F34 crosses as they exhibited different patterns of recombination. The Haley-Knott approximation was used to account for uncertainty in missing genotypes. Interval mapping was not performed to assess support for QTL between markers. QTLRel mixed-model framework was used which was developed for QTL mapping in AILS. It included a polygenic effect that captures how correlations in the phenotype are explained by genome wide genetic sharing. QTLRel uses the parameter estimates to compute the log-likelihood ratio test statistic. For each SNP, support for the genotype-phenotype association was reported using the LOD score. Derived estimates of identity coefficients were done using the pedigree and the marker data. All analyses included four covariates in the regression model of the phenotype: age, sex, albino and agouti.

Genome wide association analysis for the six traits, distance traveled in the periphery, distance traveled in the center, and percentage of time in the center of the arena, pretraining freezing, freezing to context, and freezing to cue revealed 24 QTL in the combined analysis. Twelve QTL were identified for the open field phenotypes and 12 for the conditioned fear phenotypes, Table 1:

Open field activity QTL: distance traveled in the periphery (cm):

QTL Opfaq1 (open field activity QTL 1) mapped to Chromosome 2 with a LOD score of 6.20 at peak marker rs27100797. Opfaq1 mapped between SNPs rs33088454 and rs13476394 with a 1.5 LOD interval between 9.5 and 26.9 Mb. Heterozygotes displayed the highest mean phenotypic value (2843.57) at the peak SNP.

QTL Opfaq2 (open field activity QTL 2) mapped to Chromosome 4 with a LOD score of 6.75 at peak marker rs32242095. Opfaq2 mapped between SNPs rs27817374 and rs27790884 with a 1.5 LOD interval between 30.2 and 33.9 Mb. SM/J homozygotes displayed the highest mean phenotypic value (2039.04) at the peak SNP.

QTL Opfaq3 (open field activity QTL 3) mapped to Chromosome 11 with a LOD score of 6.54 at peak marker rs29391262. Opfaq3 mapped between SNPs rs29435763 and rs29431896 with a 1.5 LOD interval between 73.6 and 81.9 Mb. LG/J homozygotes displayed the highest mean phenotypic value (2908.44) at the peak SNP.

QTL Opfaq4 (open field activity QTL 4) mapped to Chromosome 14 with a LOD score of 4.51 at peak marker rs6289260. Opfaq4 mapped between SNPs rs3670736 and rs30259301 with a 1.5 LOD interval between 111.3 and 118.8 Mb. Heterozygotes displayed the highest mean phenotypic value (2836.09) at the peak SNP.

QTL Opfaq5 (open field activity QTL 5) mapped to Chromosome 17 with a LOD score of 5.01 at peak marker rs29501002. Opfaq5 mapped between SNPs rs6303335 and rs49110321 with a 1.5 LOD interval between 25.8 and 29.2 Mb. SM/J homozygotes displayed the highest mean phenotypic value (3002.24) at the peak SNP.

Open field activity QTL: distance traveled in the center (cm):

QTL Opfaq6 (open field activity QTL 6) mapped to Chromosome 4 with a LOD score of 5.11 at peak marker rs32263942. Opfaq6 mapped between SNPs rs32320402 and rs31878303 with a 1.5 LOD interval between 118.8 and 121.1 Mb. LG/J homozygotes displayed the highest mean phenotypic value (596.55) at the peak SNP.

QTL Opfaq7 (open field activity QTL 7) mapped to Chromosome 10 with a LOD score of 4.44 at peak marker rs6236374. Opfaq7 mapped between SNPs rs6157058 and rs6236374 with a 1.5 LOD interval between 127.3 and 129.0 Mb. LG/J homozygotes displayed the highest mean phenotypic value (585.54) at the peak SNP.

QTL Opfaq8 (open field activity QTL 8) mapped to Chromosome 12 with a LOD score of 5.12 at peak marker rs6176279. Opfaq8 mapped between SNPs rs29212678 and rs29221863 with a 1.5 LOD interval between 55.9 and 58.9 Mb. SM/J homozygotes displayed the highest mean phenotypic value (618.88) at the peak SNP.

Open field activity QTL: percentage of time spent in the center

QTL Opfaq9 (open field activity QTL 9) mapped to Chromosome 4 with a LOD score of 5.06 at peak marker rs6318014. Opfaq9 mapped with a 1.5 LOD interval between 104.5 and 114.0 Mb. LG/J homozygotes displayed the highest mean phenotypic value (11.93) at the peak SNP.

QTL Opfaq10 (open field activity QTL 10) mapped to Chromosome 10 with a LOD score of 4.42 at peak marker rs29369956. Opfaq10 mapped between SNPs rs29334025 and rs6236374 with a 1.5 LOD interval between 125.2 and 129.0 Mb. SM/J homozygotes displayed the highest mean phenotypic value (12.15) at the peak SNP.

QTL Opfaq11 (open field activity QTL 11) mapped to Chromosome 12 with a LOD score of 5.12 at peak marker rs6176279. Opfaq11 mapped between SNPs rs29174777 and rs29134430 with a 1.5 LOD interval between 54.2 and 58.3 Mb. SM/J homozygotes displayed the highest mean phenotypic value (12.40) at the peak SNP.

QTL Opfaq12 (open field activity QTL 12) mapped to Chromosome 15 with a LOD score of 5.46 at peak marker rs32422569. Opfaq12 mapped between SNPs rs32100330 and rs32514574 with a 1.5 LOD interval between 34.2 and 38.3 Mb. SM/J homozygotes displayed the highest mean phenotypic value (11.96) at the peak SNP.

Conditioned fear QTL: pretraining freezing day 1:

QTL Cfq1 (conditioned fear QTL 1) mapped to Chromosome 4 with a LOD score of 4.83 at peak marker rs27528211. Cfq1 mapped between SNPs rs27498062 and rs28308541 with a 1.5 LOD interval between 116.9 and 119.9 Mb. SM/J homozygotes displayed the highest mean phenotypic value (4.69) at the peak SNP.

Conditioned fear QTL: freezing to context day 2:

QTL Cfq2 (conditioned fear QTL 2) mapped to Chromosome 2 with a LOD score of 5.86 at peak marker rs33188452. Cfq2 mapped between SNPs rs13476394 and rs32872527 with a 1.5 LOD interval between 26.9 and 56.3 Mb. SM/J homozygotes displayed the highest mean phenotypic value (11.89) at the peak SNP.

QTL Cfq3 (conditioned fear QTL 3) mapped to Chromosome 3 with a LOD score of 5.99 at peak marker rs31289463. Cfq3 mapped between SNPs rs30843783 and rs46551270 with a 1.5 LOD interval between 122.0 and127.1 Mb. SM/J homozygotes displayed the highest mean phenotypic value (11.93) at the peak SNP.

QTL Cfq4 (conditioned fear QTL 4) mapped to Chromosome 17 with a LOD score of 6.74 at peak marker rs29506726. Cfq4 mapped between SNPs rs33693466 and rs33454963 with a 1.5 LOD interval between 44.8 and 49.1 Mb. SM/J homozygotes displayed the highest mean phenotypic value (10.79) at the peak SNP.

A second suggestive QTL mapped to Chromosome 17 with a LOD score of 6.39 at peak marker rs33425954. The QTL mapped between SNPs rs33664000 and rs33593781 with a 1.5 LOD interval between 23.6 and 31.4 Mb. SM/J homozygotes displayed the highest mean phenotypic value (10.56) at the peak SNP.

Curator Note: The Table 1 legend states that, "support for the other QTL on chromosome 17 falls short of our criteria for significance once we condition on this QTL; our data support at most one QTL on Chromosome 17." MGI curators have selected the Chr 17 with the highest LOD score as the significant QTL (Cfq4) and have included data associated with the second Chr 17 QTL.

Conditioned fear QTL: freezing to cue day 3:

QTL Cfq5 (conditioned fear QTL 5) mapped to Chromosome 1 with a LOD score of 4.75 at peak marker rs31862254. Cfq5 mapped between SNPs rs33860680 and rs30802730 with a 1.5 LOD interval between 152.5 and 161.4 Mb. SM/J homozygotes displayed the highest mean phenotypic value (37.81) at the peak SNP.

QTL Cfq6 (conditioned fear QTL 6) mapped to Chromosome 2 with a LOD score of 5.18 at peak marker rs27143196. Cfq6 mapped between SNPs rs6168198 and rs13476468 with a 1.5 LOD interval between 31.1 and 44.4 Mb. SM/J homozygotes displayed the highest mean phenotypic value (35.73) at the peak SNP.

QTL Cfq7 (conditioned fear QTL 7) mapped to Chromosome 2 with a LOD score of 5.75 at peak marker rs27453770. Cfq7 mapped between SNPs rs3149909 and rs33186999 with a 1.5 LOD interval between 118.3 and 125.0 Mb. LG/J homozygotes displayed the highest mean phenotypic value (42.11) at the peak SNP.

QTL Cfq8 (conditioned fear QTL 8) mapped to Chromosome 3 with a LOD score of 4.57 at peak marker rs29599008. Cfq8 mapped between SNPs rs13477022 and rs31004134 with a 1.5 LOD interval between 24.6 and 31.1 Mb. Heterozygotes displayed the highest mean phenotypic value (35.62) at the peak SNP.

QTL Cfq9 (conditioned fear QTL 9) mapped to Chromosome 4 with a LOD score of 4.76 at peak marker rs27538669. Cfq9 mapped between SNPs rs27517761 and rs27560257 with a 1.5 LOD interval between 129.8 and 133.6 Mb. SM/J homozygotes displayed the highest mean phenotypic value (39.77) at the peak SNP.

QTL Cfq10 (conditioned fear QTL 10) mapped to Chromosome 8 with a LOD score of 5.14 at peak marker rs3710389. Cfq10 mapped between SNPs rs6382412 and rs33287905 with a 1.5 LOD interval between 82.5 and 91.5 Mb. LG/J homozygotes displayed the highest mean phenotypic value (43.58) at the peak SNP.

QTL Cfq11 (conditioned fear QTL 11) mapped to Chromosome 10 with a LOD score of 4.78 at peak marker rs6247407. Cfq11 mapped between SNPs rs6314360 and rs6372589 with a 1.5 LOD interval between 56.3 and 60.5 Mb. LG/J homozygotes displayed the highest mean phenotypic value (37.84) at the peak SNP.

QTL Cfq12 (conditioned fear QTL 12) mapped to Chromosome 17 with a LOD score of 8.49 at peak marker rs33357930. Cfq12 mapped between SNPs rs3679791 and rs13482944 with a 1.5 LOD interval between 26.7 and 30.5 Mb. SM/J homozygotes displayed the highest mean phenotypic value (39.57) at the peak SNP.

The 1.5 LOD support intervals were examined for consequential SNPs that had the potential to directly alter proteins (nonsynonymous coding, stop-gain, stop-lost, frameshift and splice sites. The numbers of genes in each mapped QTL interval and the number of genes with nonsynonymous SNPs within that interval are given in Table 1.

References

• Original: J:216981 Parker CC, et al., High-resolution genetic mapping of complex traits from a combined analysis of F2 and advanced intercross mice. Genetics. 2014 Sep;198(1):103-16
• All: 1 reference(s)