Genomic analyses of modern dog breeds

Abstract

A rose may be a rose by any other name, but when you call a dog a poodle it becomes a very different animal than if you call it a bulldog. Both the poodle and the bulldog are examples of dog breeds of which there are >400 recognized worldwide. Breed creation has played a significant role in shaping the modern dog from the length of his leg to the cadence of his bark. The selection and line-breeding required to maintain a breed has also reshaped the genome of the dog, resulting in a unique genetic pattern for each breed. The breed-based population structure combined with extensive morphologic variation and shared human environments have made the dog a popular model for mapping both simple and complex traits and diseases. In order to obtain the most benefit from the dog as a genetic system, it is necessary to understand the effect structured breeding has had on the genome of the species. That is best achieved by looking at genomic analyses of the breeds, their histories, and their relationships to each other.

Figure 1

Neighbor joining tree from 85 dog breeds showing the Ancient breed cluster. Ninety-six microsatellite markers were used to calculate the genetic distance between 85 breeds of dog. Using the gray wolf to root the tree, the nine breeds nearest the wolf formed statistically significant branches. The other 76 breeds form a single node indicating shared ancestry and hybridization between the branches. Figure originally published in Science (Parker et al. 2004).

Figure 2

Clustering breeds based on SNP markers increases breed relationship definition. A neighbor joining tree build from comparisons of 10-SNP haplotypes groups 80 dog breeds into approximately 10 breed clusters. Comparable clusters from a microsatellite analysis of 130 breeds (Parker et al. 2007) are indicated by the colored bars outside of the tree. The haplotype tree of breeds was originally published in Nature (Vonholdt et al. 2010).

Figure 3

Breed composition of Alaskan Sled dogs. The sled dogs are divided into sprint and distance groups based on their performance level. The dogs that perform as sprinters show a considerable contribution from the Pointer breed that is missing in distance runners. The distance dogs appear to be largely mixtures of classic sled dog breeds. The other group is comprised of 9 breeds with >1% but <2% contribution to at least one group. Data is compiled from Huson et al. (Huson et al. 2010).