DNA methylation in canine brains is related to domestication and dog-breed formation

Epigenetic factors such as DNA methylation act as mediators in the interaction between genome and environment. Variation in the epigenome can both affect phenotype and be inherited, and epigenetics has been suggested to be an important factor in the evolutionary process. Dogs are not only our oldest domesticated species but also extremely diverse in physical as well as behavioral attributes. This is thus a good model for studies of epigenetic involvement in diversification. In the present study, we explore DNA methylation changes between wolf and dog breeds. For this, we optimized a combined method of genotype-by-sequencing (GBS) and methylated DNA immunoprecipitation (MeDIP) for its application in canines, to obtain a reduced representation of the canine genome. Genomic DNA from the frontal cortex of 38 dogs of 8 breeds and of three wolves were extracted. Two libraries (GBS and GBS-MeDIP) were prepared and sequenced on Illuma HiSeq2500 platform. The reduced sample represented 1.18 ± 0.4 % of the total dog genome (2,4 billion BP), while the GBS-MeDIP covered 11,250,788 ± 4,042,106 unique base pairs which represents 0.47 ± 0.17 % of the total genome. We show that our reduced sample is representative of the dog genome as wolf and dog breeds cluster according to breed in a neighbor-joining tree based on single nucleotide polymorphisms. We find substantial DNA methylation differences between wolf and dog and between the dog breeds. The methylation profiles of the different groups imply that epigenetic factors have been important in the speciation from dog to wolf, but also in the divergence of different dog breeds. Specifically, we highlight methylation differences in genes related to behavior and morphology, that may alter gene expression and phenotype. We hypothesize that these differences are involved in the phenotypic variation found among dogs, whereas future studies will have to find the specific mechanisms. Our results not only add an intriguing new dimension to dog breeding, but are also useful to further understanding of epigenetic involvement in evolution.