Genetic Structure and Breed Relationships of the Domestic Rabbit, Oryctolagus cuniculus

The domestication and artificial selection of the rabbit has led to the advent of sub-populations known as breeds. As a matter of breed club policy, members of breeds are reproductively isolated. Breeds differ greatly by coat color and pattern, body size and “arch” body shape along the back line. With the goal of describing rabbit breed phylogenetic relationships, we have genotyped 3,552 SNPs in a sample of 261 rabbits representing 42 breeds. Our sample includes most of the common breeds found in North America, including large-bodied and small-bodied breeds, commercial breeds like the New Zealand, Satin and Californian, and six lop breeds. We did inverse-PCR to generate libraries enriched for CSINE3A retrotransposon flanking sequences. The libraries were sequenced at approximately 90-plex in four Illumina Hi-Seq lanes. Flanking sequences were masked for repeats then aligned for SNP discovery and genotyping using the Genome Analysis Toolkit. Using PLINK, the 7,696 SNPs genotyped in at least 90% of samples were further filtered to 3,552 SNPs in which 1) no SNP pair had LD above r² > 0.2, and 2) each SNP’s minor allele occurred on at least two chromosomes. We investigated rabbit breed relationships via STRUCTURE and principal components analysis of the genotypes. We find three major groups of breeds that share ancestry based on 1) commercial body type, 2) lop heritage, and 3) small body size.