Hipmt3^DBA/2J
QTL Variant Detail

Summary

• QTL variant: Hipmt3^DBA/2J
• Name: hippocampal morphometry trait 3; DBA/2J
• MGI ID: MGI:5912096
• QTL: Hipmt3 Location: Chr11:47977325-50277325 bp Genetic Position: Chr11, Syntenic

Variant origin

• Strain of Specimen: DBA/2J

Variant description

• Allele Type: QTL

Notes

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

J:242956

Variation in hippocampal neuroanatomy correlates well with spatial learning ability in mice. The wide individual variation in spatial learning and memory abilities among humans is also linked to differences in hippocampal size and morphology. In the current study both hippocampal neuroanatomy and behavior were studied in 53 isogenic BXD recombinant strains derived from C57BL/6J and DBA/2J parents.

One task to test spatial learning in rodents is the radial maze. Learning capability in the test is heritable and strongly strain-dependent; C57BL/6 mice are fast learners while DBA/2 mice are slow learners. Large variation in the size of hippocampal fields (hilus, suprapyamidal and intra-and infrapyramidal mossy fibers, and the strata pyramidale, oriens, radiatum, and lacunosum-moleculare have been found in mice.

Data were collected on seven hippocampal subregions in CA3 and CA4 after testing spatial memory in an 8-arm radial maze task. For the spatial learning and navigation test, the performances of 914 mice were evaluated for their ability to learn a standard 8 arm radial maze. Data were obtained from 451 female (52 strains) and 463 male mice (53 strains), as well as for 10 males and 10 females for each of the parental strains. For hippocampal morphometry data were obtained from 207 female (51 strains) and 215 male mice (53 strains), as well as for 5 males and 5 females for each of the parental strains.

The QTL mapping module of GeneNetwork was used to identify QTL for hippocampal morphometry and radial maze trait data (NCBI Build 37). The module enables interval mapping, composite interval mapping, and a pairwise scan option to identify epistatic effects. QTL significance was assessed using the likelihood ratio statistic (LRS) obtained after 5000 permutations and 2000 bootstrap tests. QTLs were deemed significant if P<0.05 and suggestive if P<0.63. Male and female data were analyzed separately because of possible interactions between strain and sex.

To identify candidate genes, the areas under the QTL peaks and shoulders that cross the suggestive threshold were screened. The selection criteria used were based on criteria used in similar studies: (1) whether a gene is expressed in the relevant tissue (the hippocampus), (2) presence of SNPs within the candidate genes (3) the occurrence of missense or non-synonymous mutations or other DNA variants, and (4) the presence of cis acting expression QTLs.

Significant QTLs were detected for three of the seven hippocampal morphometry traits:

QTL Hipmt1 (hippocampal morphometry trait 1), a measure of the area of intra- and infrapyramidal mossy fibers (IIPMF), mapped to 48.1 Mb on Chromosome X, p=0.029, LRS=18.241. Hipmt1 accounted for 26% of the trait variance between strains. A single gene met all selection criteria: Gpc4.

QTL Hipmt2 (hippocampal morphometry trait 2), a measure of the area of the stratum radiatum in male mice, mapped between 16.2-17.8 Mb on Chromosome 2, p=0.043, LRS=17.181. Hipmt2 accounted for 24% of trait variance between strains. The initial candidate gene list filtered to 4 candidate genes related to neurological processes and pathologies: Fbxw5, Armc3, Kcnt1 and Ptgds.

QTL Hipmt3 (hippocampal morphometry trait 3), a measure of the area of the stratum pyramidale in female mice, mapped between 47.9-50.2 Mb on Chromosome 11, p=0.035, LRS=23.389. Hipmt3 accounted for 26% of the trait variance between strains. Six candidate genes in the QTL interval were associated with neurological processes and/or pathologies: Hint1, Agxt2l2, Gemin5, Slc22a4, Tenm2 and Gabrg2.

QTL Rmerr1 (radial maze error rate 1), a measure of radial maze error rate in female mice, mapped between 12.6-15.8 Mb on Chromosome 3, p=0.035, L=17.896. Rmerr1 accounted for 24% of trait variance between strains. The initial candidate gene list filtered to 3 candidates: Car2, Ralyl, and 1810022K09Rik.

In general, strains that inherited the B haplotype at these loci had larger IIPMF, stratum radiatum, and stratum pyramidale sizes and made fewer errors. Composite interval mapping controlling for each of the QTLs did not reveal any secondary QTLs. In addition, no significant pairwise epistatic interactions were found between these QTLs.

No significant QTLs were identified for body or brain weight, probably indicating a highly-polygenic mode of inheritance for these characteristics, with each individual gene's contribution below the detection threshold of this study. Although several significant QTLs were localized, none were common between behavior and morphometrical variation.

References

• Original: J:242956 Delprato A, et al., Systems genetic analysis of hippocampal neuroanatomy and spatial learning in mice. Genes Brain Behav. 2015 Nov;14(8):591-606
• All: 1 reference(s)