Using progenitor strain information to identify quantitative trait nucleotides in outbred mice

Abstract

We have developed a fast and economical strategy for dissecting the genetic architecture of quantitative trait loci at a molecular level. The method uses two pieces of information: mapping data from crosses that involve more than two inbred strains and sequence variants in the progenitor strains within the interval containing a quantitative trait locus (QTL). By testing whether the strain distribution pattern in the progenitor strains is consistent with the observed genetic effect of the QTL we can assign a probability that any sequence variant is a quantitative trait nucleotide (QTN). It is not necessary to genotype the animals except at a skeleton of markers; the genotypes at all other polymorphisms are estimated by a multipoint analysis. We apply the method to a 4.8-Mb region on mouse chromosome 1 that contains a QTL influencing anxiety segregating in a heterogeneous stock and show that, under the assumption that a single QTN is present and lies in a region conserved between the human and mouse genomes, it is possible to reduce the number of variants likely to be the quantitative trait nucleotide from many thousands to <20.

Figure 1.

Dynamic programming analysis of chromosome 1 QTL. The vertical scale is in log P units and the horizontal scale is in megabases. The position and name of genes are shown above the likelihood curves. Three tests are shown: black, the fit to an additive model; red, the fit to a full model; and purple, the results of a partial F-test comparing additive to full models. A significant difference between full and additive models is shown by the significance of the partial F-test result (purple line) as can be seen at position 1.7 Mb.

Figure 2.

Quantitative trait nucleotide analysis across a 4.8-Mb QTL on mouse chromosome 1. The horizontal axis is the coordinate in megabases. The top half shows the QTN merge analysis. Yellow bars indicate the positions of the exons of genes in the region. Each gene's name is positioned at the leftmost exon of the gene. The vertical black lines are the positions of genotyped markers; each region between adjacent lines defines a marker interval. The positions and log P significance levels of 1720 sequence variants under a merged strain analysis are indicated by black dots. The unmerged value for the marker interval is shown by a horizontal red line, whose placement is identical to that in Figure 1. The vertical position of a black dot relative to the red line measures the evidence that the variant could be a QTN for the trait. Variants with black dot values <log P 2 are unlikely to be QTN, while variants with very high black dot values could be QTN or share the same strain distribution pattern with a nearby QTN. The gray and white horizontal tracks in the bottom half of the figure show the spatial arrangement of the variants' strain distribution patterns. Each track corresponds to the SDP indicated in the left margin by a string of 0's and 1's representing the alleles for the eight founder strains of the HS, in the order A/J, AKR, BALB/c, C3H, C57BL/6, DBA, I, RIII. Repeat-length polymorphisms are combined into a single track, as are rare variants (all SDPs occurring <10 times). Within each SDP track the vertical black lines give the locations of the variants with that SDP.

Figure 3.

Merge analysis of 139 variants surrounding the rgs18 gene. See Figure 2 legend for explanation. The SDP track labeled “repeats” gives the positions of all repeat polymorphisms.

Figure 4.

Conditional merge analysis. Scatter plot of the merge log P is shown for each variant (x-axis) vs. the maximum merge log P (y-axis) for all other variants, conditional on the variant being fitted. Red dots indicate variants with an SDP that distinguishes A/J and C57BL/6 strains, the strain pair used to map the QTL in an F₂ intercross.