Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication

Abstract

The genetic changes underlying the initial steps of animal domestication are still poorly understood. We generated a high-quality reference genome for the rabbit and compared it to resequencing data from populations of wild and domestic rabbits. We identified more than 100 selective sweeps specific to domestic rabbits but only a relatively small number of fixed (or nearly fixed) single-nucleotide polymorphisms (SNPs) for derived alleles. SNPs with marked allele frequency differences between wild and domestic rabbits were enriched for conserved noncoding sites. Enrichment analyses suggest that genes affecting brain and neuronal development have often been targeted during domestication. We propose that because of a truly complex genetic background, tame behavior in rabbits and other domestic animals evolved by shifts in allele frequencies at many loci, rather than by critical changes at only a few domestication loci.

Fig. 1. Experimental design and population data

(A) Images of the six rabbit breeds, sized to reflect differences in body weight, included in the study and of a wild rabbit. (B) Map of the Iberian Peninsula and Southern France with sample locations marked (orange dots). Demographic history of this species is indicated and a logarithmic time scale is indicated to the left. The hybrid zone between the two subspecies is marked with dashes. (C) Nucleotide diversities in domestic and wild populations. The French (FRW1-3) and Iberian (IW1-11) wild rabbit populations are ordered according to a northeast to southwest transection. Sample locations are provided in Table S4.

Fig. 2. Selective sweep and delta allele frequency analyses.

(A) Plot of F_ST values between wild and domestic rabbits. Sweeps detected with the F_ST-H outlier approach, SweepFinder and their overlaps are marked on top. Unassigned scaffolds were not included in the analysis. (B) and (C) Selective sweeps at GRIK2 (B) and SOX2 (C). Heterozygosity plots for wild (red) and domestic (black) rabbits together with plots of F_ST values and SNPs with ΔAF>0.75 (HΔAF). The bottom panel shows putative sweep regions, detected with the F_ST-H outlier approach and SweepFinder, marked with horizontal bars. Gene annotations in sweep regions are indicated; *represents ENSOCUT000000. **SOX2-OT represents the manually annotated SOX2 overlapping transcript (4). (D) Number of SNPs in non-overlapping ΔAF bins (black lines, left y-axis). M-values (log2-fold changes) of the relative frequencies of SNPs at non-coding evolutionary conserved sites, in untranslated regions (UTR), exons and introns according to ΔAF bins (colored lines, right y-axis); M-values were calculated with the average frequency of the corresponding annotation category as reference. (E) Location of SNPs at conserved non-coding sites with ΔAF≥0.8 SNPs (n=1,635) and with ΔAF<0.8 SNPs (n=502,343) in relation to the transcription start site (TSS) of the most closely linked gene; **, P<0.01).

Fig. 3. Bioinformatic and functional analysis of candidate causal mutations.

Three examples of SNPs near SOX2 and PAX2 where the domestic allele differs from other mammals. Fourteen such SNPs assessed with electrophoretic mobility shift assays (EMSA) are indicated by red crosses on top. EMSA with nuclear extracts from ES-cell derived neural stem cells or from mouse P19 embryonic carcinoma cells before (un-diff) or after neuronal differentiation (diff) are shown for three SNPs; exact nucleotide positions of polymorphic sites are indicated. Allele-specific gel shifts are indicated by arrows. WT=wild-type allele; Dom=domestic, the most common allele in domestic rabbits. Cold probes at 100-fold excess were used to verify specific DNA-protein interactions.