Brain transcriptomics of wild and domestic rabbits suggests that changes in dopamine signalling and ciliary function contributed to evolution of tameness
Domestication has resulted in immense phenotypic changes in plants and animals despite their relatively short evolutionary history. The European rabbit is one of the most recently domesticated animals but exhibits distinct morphological, physiological and behavioural differences from their wild conspecifics. A previous study revealed that sequence variants with striking allele frequency differences between wild and domestic rabbits were highly enriched in conserved non-coding regions, located in the vicinity of genes involved in nervous system development. This suggests that a large proportion of genetic changes during domestication affects gene regulation. Here, we generated RNA-sequencing data for four brain regions (amygdala, hypothalamus, hippocampus and parietal/temporal cortex) sampled at birth and revealed hundreds of differentially expressed genes (DEGs) between wild and domestic rabbits. DEGs in amygdala were significantly enriched for genes associated with dopaminergic function and all 12 DEGs in this category were upregulated in domestic rabbits, whereas DEGs in hippocampus were highly enriched for genes associated with ciliary function and all 21 genes in this category showed lower expression in domestic rabbits. The results are consistent with an important role of dopamine signalling and ciliary function in the evolution of tameness during rabbit domestication. However, DEGs showed no overall enrichment among genes and genomic regions associated with signals of selection in domestic rabbits, but some were located upstream in interaction networks that showed signatures of selection and may be functionally important. Our study shows that gene expression of specific pathways has been profoundly altered during domestication, but that the majority of genes showing differential expression have not been the direct targets of selection.