Targeted resequencing of a genomic region influencing tameness and aggression reveals multiple signals of positive selection

Abstract

The identification of the causative genetic variants in quantitative trait loci (QTL) influencing phenotypic traits is challenging, especially in crosses between outbred strains. We have previously identified several QTL influencing tameness and aggression in a cross between two lines of wild-derived, outbred rats (Rattus norvegicus) selected for their behavior towards humans. Here, we use targeted sequence capture and massively parallel sequencing of all genes in the strongest QTL in the founder animals of the cross. We identify many novel sequence variants, several of which are potentially functionally relevant. The QTL contains several regions where either the tame or the aggressive founders contain no sequence variation, and two regions where alternative haplotypes are fixed between the founders. A re-analysis of the QTL signal showed that the causative site is likely to be fixed among the tame founder animals, but that several causative alleles may segregate among the aggressive founder animals. Using a formal test for the detection of positive selection, we find 10 putative positively selected regions, some of which are close to genes known to influence behavior. Together, these results show that the QTL is probably not caused by a single selected site, but may instead represent the joint effects of several sites that were targets of polygenic selection.

Figure 1

Inverse cumulative coverage plots. For each rat, the fraction of targeted bases that match or exceed a given depth of coverage are plotted. The dashed vertical line indicates the minimum coverage used for calling consensus sequences. Rat IDs are coded as: A, aggressive; T, tame; F, female; M, male.

Figure 2

Examples of sequence variation in the QTL region. (a) A region where tame and aggressive founder rats are fixed for a continuous stretch of sequence. (b) A region where tame, but not aggressive founders have no sequence variation. Allele frequency difference is plotted in black, π in blue (tame rats) and red (aggressive rats). Blue (red) dots indicate SNVs segregating among tame (aggressive) rats; black dots indicate fixed SNVs.

Figure 3

Scan for positive selection. (a) Illustration of the demographic model used in the selection scans. (b, c) Distributions of the width of regions with no observed nucleotide diversity (‘dips') in 1000 simulations of the rat population history without any selection. The dashed lines show the 95% cutoff. (b) Dips in one of the two lines. Blue (red) arrow: most extreme dip in real data from tame (aggressive) rats. (c) Regions with fixed differences. Arrow: most extreme region in real data. (d) Results from the maximized composite likelihood surface-based scan for positive selection. Likelihood ratios between the respective best selection model and the background site frequency spectrum in tame (blue) and aggressive (red) rats are plotted. The dashed line is the Bonferroni-corrected significance threshold.