The canine genome

Next Section Abstract The dog has emerged as a premier species for the study of morphology, behavior, and disease. The recent availability of a high-quality draft sequence lifts the dog system to a new threshold. We provide a primer to use the dog genome by first focusing on its evolutionary history. We overview the relationship of dogs to wild canids and discuss their origin and domestication. Dogs clearly originated from a substantial number of gray wolves and dog breeds define distinct genetic units that can be divided into at least four hierarchical groupings. We review evidence showing that dogs have high levels of linkage disequilibrium. Consequently, given that dog breeds express specific phenotypic traits and vary in behavior and the incidence of genetic disease, genomic-wide scans for linkage disequilibrium may allow the discovery of genes influencing breed-specific characteristics. Finally, we review studies that have utilized the dog to understand the genetic underpinning of several traits, and we summarize genomic resources that can be used to advance such studies. We suggest that given these resources and the unique characteristics of breeds, that the dog is a uniquely valuable resource for studying the genetic basis of complex traits.

Previous Section Next Section Breed diversity and genetic structure The explosion of dog breeds over the past two centuries represents perhaps one of the greatest genetic experiments ever conducted by humans. Distilled from the genome of the wild wolf are animals that differ by more than 40-fold in size with the ability to herd, guard, hunt, and guide (American Kennel Club 1998). Behavioral variation is surpassed by morphologic variation, with individual breeds represented by dogs of every imaginable size and proportion. Coats alone can be described by color, texture, length, thickness, and curl. Tails can be described as plumed, curled, double curled, gay (upright), sickled (arching), otter (down and flat), whipped, ringed, screwed, or snapped (American Kennel Club 1998). The diversity in skeletal size and proportion of dogs is greater than any mammalian species and even exceeds that of the entire canid family (Wayne 1986a,1986c). Such variation may reflect simple modifications of post-natal development (Wayne 1986a,1986c), but the specific genetic mechanisms are not well known (see below). Much of the morphologic variation in dogs is partitioned into over 350 distinct breeds worldwide as a result of the development of breed standards and controlled breeding. In general, in order to register a dog in the American Kennel Club at least both parents must have been registered in the same breed. Consequently, purebred dogs are members of closed breeding populations, which receive little genetic variation beyond that existing in the original founders (Ostrander and Giniger 1997; Galibert et al. 1998; Ostrander et al. 2000; Sutter and Ostrander 2004). Common to the origin and development of many breeds is a founder event involving only a few dogs and, thereafter, reproductive dominance by popular sires that conform most closely to the breed standard. These restrictive breeding practices reduce effective population size and increase genetic drift, resulting in the loss of genetic diversity within breeds and allele frequency divergence among them. For example, in a genetic study of 85 breeds, Parker et al. (2004) showed that humans and dogs have similar levels of overall nucleotide diversity, 8 × 10-4, which represent the overall number of nucleotide substitutions per base/pair. However, the variation between dog breeds is much greater than the variation between human populations (27.5% versus 5.4%). Conversely, the degree of genetic homogeneity is much greater within individual dog breeds than within distinct human populations (94.6% versus 72.5%). Furthermore, in some breeds, genetic variation has been additionally reduced by bottlenecks associated with catastrophic events such as war and economic depression, making them analogous to human populations of limited genetic variation used for disease-mapping studies such as the Finns, Icelanders, and Bedouins. As a result, the unique pattern of LD in dogs provides an exceptional opportunity to study complex traits that are relevant to human biology using robust approaches that would not be possible in human populations. Because many breeds represent closed gene pools, they may define distinct genetic clusters. Analysis of microsatellie loci have strongly supported this notion (Koskinen 2003). For example, in the Parker et al. (2004) study, 96 microsatellite markers were genotyped that spanned all dog autosomes at approximately a 30-Mb resolution (Parker et al. 2004). Excluding data from the highly related Belgian Sheepdog and Belgian Tervuren breeds, they observed that 99% of 414 dogs were correctly assigned to breed. Consequently, a “breed” can be defined at the molecular level and dogs can be correctly assigned to their breed with small amounts of data. These results strongly imply that breeds are distinct genetic units and even closely related breeds do not represent genetic replicates.

Previous Section Next Section Genetics of morphology The genetic basis for differences in size and proportion among dogs has yet to be revealed. However, both candidate gene and association studies are beginning to provide insight into the complexity underlying morphological differentiation. For example, two potential candidate genes, MSX2 and TCOF1, which are expressed during cranial facial development, were sequenced in 10 different dog breeds that varied in cranial and face shape (Haworth et al. 2001a,b). However, only a single amino acid change in the TCOF1 protein showed an association with short and broad skulls. Nonetheless, greatly expanded surveys of candidate genes may prove more fruitful; for example, variation in the production of insulin-like growth factor 1 (IGF-1) was shown to correlate with differences in the body size of poodles, suggesting it may be a candidate gene for size variation in dogs (Eigenmann et al. 1984). More definitive associations have been demonstrated through quantitative analysis of morphologic measurements combined with genome marker scans. For example, Chase et al. (2002) analyzed data from nearly 700 Portuguese Water Dogs genotyped with ∼500 markers and http://www.georgieproject.com/. For 460 dogs, they recorded 91 measurements from a set of five x-rays taken on each dog. The data were analyzed using principal component analysis, which defines independent component axes based on linear combinations of variables. Each axis is ordered by a decreasing fraction of the total variation in the data set. The first four axes explained 61% of the variation in the data set and represented different components of size and shape. For example, the first principal component axis reflected overall size variation of the skeleton, whereas the second reflected the relationship between the pelvis, head, and neck, such that the size and strength of the pelvis and head–neck musculoskeletal systems are inversely related. Quantitative Trait Loci (QTLs) have been localized that are related to variation on each of the above four principal components. Moreover, using a data set of 286 phenotyped dogs, Chase et al. (2004) defined two loci on chromosome one spaced 95 Mb apart that appear to account for a modest percentage of hip dysplasia, as defined by Norberg angle in the Portuguese Water Dog. Nonclassical genetic variation may also be an important source of phenotypic variation in dogs. Fondon III and Garner (2004) suggested that highly mutable simple tandem repeats imbedded in genes may be the source of new variation in recent developed lines and may explain their high rate of morphologic change. To test this hypothesis, these investigators analyzed three-dimensional models of dog skulls from 20 breeds and seven mongrels. In representatives of 92 different breeds, they also sequenced 37 repeat-containing regions from 17 genes known or thought to be involved in craniofacial development. In general, they found that dogs had more perfect repeats than humans and may be changing faster in length. Additionally, they found that the size and the ratio of lengths of two tandem repeats in the Runx-2 gene correlated with the degree of dorsoventral nose bend (clinorhynchy) and mid-face length in a variety of breeds. Although this evidence is suggestive, clearly more detailed studies are needed associating repeat change with specific phenotypic traits (Pennisi 2000). If such genetic mechanisms are unique to the dog, they may explain, in part, the apparent phenotypic plasticity of dogs. However, dogs also have a unique skeletal development whose alterations may more readily result in novel phenotypes (Wayne 1986a,b,c; Morey 1992, 1994). One area of morphology we do not discuss in detail is that of canine coat color, which has been written about extensively in the past. More recently, progress on dissecting coat color genetics in the dog has been done by two groups (Kerns et al. 2003; Berryere et al. 2005). Particular progress has been made in understanding the interactions between the Agouti protein and the Melanocortin 1 receptor, which control the type of pigment synthesized in mammalian hair (Berryere et al. 2005). Additional recent work has focused on black color in dogs, which appears to be independent of the above interactions (Schmutz et al. 2002; Kerns et al. 2003). Very interesting work that is just beginning focuses on the role of polymorphisms in coat color affecting genes, such as the melanophilin gene (Philipp et al. 2005). With the availability of the canine genome sequence, this is an area that will surely expand in the coming years.

Previous Section Next Section Genetics of behavior Dog breeds have distinct behaviors, and dogs as a whole have unique behaviors not found in gray wolves (Hare et al. 2002). However, the genetic basis of behavior is less well understood than morphology. In general, the greatest need remains the development of assays to reproducibly score specific behaviors. However, some understanding is likely to come from the study of pedigrees of dogs displaying aberrant behaviors. For example, Moon-Fanelli et al. (1998) have characterized pedigrees of Bull Terriers displaying obsessive compulsive disease (OCD) phenotypes, such as tail chasing, which in other respects is similar to human OCD. As genome scans of affected pedigrees are completed, they may shed light on both the human and canine disease conditions. Expression patterns may also provide clues to the genetic basis of behavior. Saetre et al. (2004) surveyed the expression pattern of 7762 genes in three different regions in the brains of domestic dogs and in gray wolves and coyotes. They found that the pattern of gene expression in the hypothalamus of domestic dogs was different from that in gray wolves and coyotes, whereas patterns of gene expression in the amygdala and frontal cortex were less differentiated. The hypothalamus controls specific emotional, endocrinological, and autonomic responses of dogs and is highly conserved throughout mammals. The results of Saetre et al. (2004) suggest that behavioral selection in dogs may have affected this central part of the brain, initiating a cascade of effects that result in some of the unique behaviors found in dogs.

Previous Section Next Section Conclusions The domestic dog has long fascinated evolutionary biologists and geneticists because of the extreme phenotypic diversity exhibited by the species and the short time frame over which this diversity has evolved. Molecular genetic evidence suggests that dogs are indeed the oldest domesticated species and their origin may have even well preceded their first appearance in the archeological record about 15,000 yr ago. The dog has a diverse genetic origin that likely involved multiple gray wolf populations and subsequently was enriched by backcrossing with wolves throughout their history. This substantial input of variation from wild ancestors has provided the raw material for phenotypic change, but unique development and genetic mechanisms may also have assisted the course of artificial selection. Dogs clearly have behaviors, phenotypes, and diseases that are not evident in their wild progenitors. Finally, in the more recent evolution of dog breeds, limited interbreeding has imposed a remarkable genetic structure such that nearly all breeds represent distinct genetic pools that can be divided into at least four distinct genetic groupings. Understanding the genetic mechanisms that have given rise to the unique attributes of domestic dogs may finally be within reach. A complete and a partial genome sequence are available from a boxer and a poodle, respectively, and mapping resources are well developed and increasing in sophistication. The dog genome in general has high levels of LD, such that whole-genome association studies will be facilitated and genomic scans of specific breeds segregating traits of interest may readily be found through patterns of LD or reductions in heterozygosity due to selective sweeps (Weiss and Clark 2002; Bamshad and Wooding 2003; Luikart et al. 2003; Pollinger et al. 2005). In this review, we have provided the evolutionary and empirical framework for understanding the molecular diversity of dogs with the aim of taking the first step toward answering the questions posed in the introduction. The primary intent of this article was to help generate the enthusiasm that will lead to realizing the promise of the dog genome for solving significant problems in evolution, genetics, and human health.

Previous Section Next Section Acknowledgments We thank two anonymous reviewers, Kerstin Lindblad-Toh, Heidi Parker, Nate Sutter, Ed Giniger, and Francis Galibert for thoughtful comments and helpful suggestions on this manuscript. We also thank Kerstin Lindblad-Toh for sharing data in advance of publication. Finally, we thank the many colleagues, dog owners, and breeders who have generously shared samples and made much of the work reviewed here possible.