Dog Breeds Research Project

Materials per student: Handout, internet access

DOG DISEASE MAPPING PROJECT

In 2005, Broad researchers gave the world its first complete look at the genetic sequence, or genome, of Canis familiaris, the domesticated dog. They deciphered the DNA sequence of Tasha, a female purebred boxer. Though an interesting revelation, the real story has been and will continue to be in delving deeper into canine genetics of various purebred breeds to find genes that cause disease. “The larger goal, of course, is to use this information to aid in understanding corresponding human diseases,” says Kerstin Lindblad-Toh, scientific director of vertebrate genome biology at the Broad Institute of MIT and Harvard, and professor in comparative genomics at Uppsala University in Sweden. Dr. Lindblad-Toh leads the Broad and Uppsala teams carrying out the dog disease mapping project, or DogDNA project.

Why Dogs?
Domesticated dogs split from their wolf ancestors approximately 30,000 years ago. Contrast this to the scant 200-year history of most breed creation. In the process of breeding dogs for certain desired traits over successive generations, many genetic mutations have inadvertently come along for the ride with undesirable side effects. This includes a genetic predisposition to many diseases ranging from epilepsy, cancer, diabetes, and hip problems to many more breed-specific conditions.

Since Broad researchers and their colleagues first published thedog genomein 2005 they have found nearly 20 genes known to cause several conditions or traits in various dog breeds. This is cool science, but why all the attention on the domesticated dog?

The answer is that it is much easier to find the gene(s) of disease interest in dogs than in humans. “In human studies, you have to enroll thousands of people and look at millions of SNPs, or markers in the genome, to find areas of disease mutation,” says Elinor Karlsson, a Broad associate researcher who works closely with the DogDNA project. “In some cases in dogs, we can find what we’re looking for in just 20K SNPs for a really simple disease. In a more complex disease like cancer, you only need about 200,000 SNPs and about 200 dogs. It is a much simpler, more powerful platform for finding these genes.”

The plan is that by understanding the genes that cause that disease in dogs, we will learn a lot about the disease in humans as well.

The team has arrived at the point where they have found many genes in dogs previously unknown to be linked with disease and are translating that into a similar search in humans. “If we can understand the functionality of the DNA mutations of the dog and find similar pathways in humans, that opens the door to developing new treatments for the future,” says Lindblad-Toh.

From Simple to Complex Mutations
Researchers at the Broad are in the process of investigating nearly 40 diseases in a variety of breeds, some of which are discussed in more detailhere. The team started by mapping a series of disorders that were fairly straightforward in terms of trait characteristics – likecoat colorin the boxer, the presence of theridgein Rhodesian ridgeback dogs, andhairlessnessin the Chinese crested dog.

The new gene tally continues to mount with the discovery of mutations resulting incardiomyopathydisorder in boxers,ALS-like diseasein the Pembroke Welsh corgi, brittle bone (osteoimperfecta) and day blindness in dachshunds, and a neurodegenerative disorder called neuronal ceroid-lipofuscinosis (NCL) in Tibetan terriers. For many of these disorders, this has led directly to a quest to find similar gene mutations in people.

Over time, the DogDNA effort led to finding the genetic mutations of more complex traits. The first example includessystemic lupus erythematosus(SLE) in Nova Scotia duck tolling retrievers. “We identified a cascade of overactive reactions in the immune response,” explains Lindblad-Toh. “We found about five different genes involved in regulating an immune pathway.” This breed was devastated by a canine distemper virus outbreak in which the only dogs to survive were those with the strongest immune response. The suggestion is that the dogs’ strong immune response may have been protective during the distemper epidemic but may be the root cause of overactive reactions and SLE in subsequent generations. This serves as an example of how natural selection also plays a role in continuing certain mutations found widely across a breed that originally came from a small group of surviving dogs.

A very recent example of finding a gene mutation for complex disease involves theShar-Peidog from Asia, bred for its characteristic thickly wrinkled skin. Unfortunately this breed is also predisposed to Familial Shar-Pei Fever (FSF), a periodic fever disease linked with chronic inflammation and kidney failure. The DogDNA effort recently published findings showing that the same genetic mutation causes both wrinkled skin and FSF. The team is now investigating a similar link with human periodic fever disorders, like Familial Mediterranean Fever.

Clues to Cancer
A large area of focus of the team’s work is on understanding cancer genetics in purebred dogs. To date, this has involved studying breast cancer in the English springer spaniel — a breed in which more than 35% of the dogs have mammary tumors — and osteosarcoma in racing greyhounds, rottweilers, great Dane, and Irish wolfhounds.

One of the biggest DogDNA efforts is the golden retriever cancer study. Nearly 60% of these purebred dogs develop bone marrow cancers, including mast cell tumors, hemangioma, and lymphoma. Researchers at the Broad have been collecting dog samples from golden retrievers, both dogs with these cancers and old, healthy golden retrievers to find the gene(s) responsible for these cancers.

We have found several gene regions that look exciting and are now resequencing the DNA from these dogs to find the specific mutations involved,” says Noriko Tonomura. DVM, PhD, a research associate in the Broad’s vertebrate genome sequencing and analysis group, and research assistant professor at Cummings School of Veterinary Medicine at Tufts University. Going forward, the team hopes to learn how common these mutations are in various breeds. “This will hopefully help breeders choose what dogs to breed to avoid passing on harmful cancer genes,” says Tonomura. It may even help identify if there are any genetic mutations that interact with each other or with specific environmental factors that lead to the development of cancers.

In concert with the colleagues at Mayo Clinic and Dana-Farber Cancer Institute, the DogDNA researchers are now starting to analyze blood and urine samples from human lymphoma patients to find a possible link with human genetic mutations in the same genome regions.

Psychiatric Illness
Along with studying the dog genome for causes of physiological conditions, the DogDNA team is searching for clues underlying psychiatric disease. After studying just 140 Doberman pinschers, they recently discovered a gene forcanine compulsive disorder(CCD), the dog version of obsessive-compulsive disorder, or OCD. “It is similar to genes for things like autism in humans,” explains Karlsson. They are now expanding this study to include other breeds known to develop CCD, like bull terriers. These dogs are treated with the same drugs used to treat OCD in humans and have almost the same response rate of about 50-60%. The Broad team is now sequencing genes linked to that gene — about 500-600 genes that are in similar pathways — in hundreds of human patients.

Samples, Please
The Broad DogDNA team is very much in need of blood samples from purebred dogs, including older, healthy dogs. “We have found the tip of the genetic iceberg and we know there will be more genetic risk factors,” explains Lindblad-Toh. “We can guess that if we had twice as many samples we would find twice as many risk factors and that would help us build a more complete picture of how these genes interact with each other.” Plus, the team is now moving more into a phase of research where it wants to study specific tumors and see what the consequences of mutations are. “For this work, we need tumor and blood samples paired together from the same dog, along with samples from healthy control dogs, so we can look at follow-up effects,” she adds.

To learn more about donating samples, visit the team’sdonation websiteto find specific directions and contact information.
“These discoveries will identify risk factors for certain diseases, which will help us to understand overall health risks for your dog,” adds Lindblad-Toh. The Broad team gets additional support from other academic research centers, including Uppsala University in Sweden, the European LUPA Project, and major animal health and research organizations including the Canine Health Foundation, the Morris Animal Foundation, the American Kennel Club, and the Golden Retriever Club of America.

Genetics of Dog Breeding

Citation:Adams,J.(2008)Genetics of Dog Breeding.Nature Education1(1):144

How did your friendly Fido become so different from his closest living relative, the wolf? See what scientists believe about humans' artificial selection pressures on the dog genome.

Many dog lover knows that Labrador retrievers are friendly, Dalmatians are hyper, and Australian shepherds are smart (Scott & Fuller, 1974). Some dog lovers also know that Labradors are susceptible to hip dysplasia, while deafness and kidney stones run in Dalmatians. But why is this the case?

Breeding dogs for particular characteristics, or phenotypes, has been going on for centuries. Dogs are companions and workers, in service to humans, and they have thus been bred to accentuate desired traits. For instance, Dalmatians have long been coach dogs, in part because of their striking looks and their comfort around horses. Bred for endurance, they can run alongside horse-drawn carriages all day. When kept as a housebound family pet, however, a Dalmatian's excess of energy can make the dog seem wired and can lead to less desirable behaviors, such as gnawing on furniture.

Dogs' closest living relatives are wolves. Analysis of the twospecies' genomes has revealed differences that some scientists believe are a result of dogs being subject to artificialselectionimposed by humans. It appears that with domestication, beginning as long as 14,000 years ago, came a relaxation of selective forces typical of nature (forces that continued in earnest on wolves), as well as an increase in variability in the dog genome compared with the genome of their ancestral stock (Björnerfeldtet al., 2006).

Dogs and Appearance

One question that tugged at Swedish researcher Carles Vilà is how dogs can have such a wide variety of phenotypes—imagine a tiny Chihuahua standing next to a Great Dane, or a Chinese shar-pei peering from under its skin folds at an Old English sheepdog who peers back through its long hair. In fact, the variation among breeds of dogs is far greater than the variation among other completely distinct species in the family Canidae.

If dogs evolved from wolves, which seems to be the case, then wolves must have had the capacity for this diversity somewhere in their genomes. Thus, Vilà and his colleagues decided to compare the mitochondrialDNAof dogs and wolves in an attempt to understand the genetic consequences of these species' different lifestyles: domesticated versus wild. (Remember, both dogs and wolves evolved from a common ancestral wolf species, so wolves are an ideal control with which to study the consequences of dogs' life with humans.) The mitochondrial genome was used because of earlier work by Vilà that showed the nuclear genomes of dogs and wolves to be too similar to study their molecularevolution. On the other hand, this research indicated that mitochondrial lineages are clearly distinguishable for the two species.

Vilà hypothesized that certain mutations—those that might be deleterious, but not strongly so—accumulated faster in populations in whichnatural selectionhad been relaxed, resulting in a decline infitness. In other words, after dogs started to live with humans, less fit individuals were more likely to survive and reproduce than they were in the wild. In addition, it is highly likely that dogs were strongly selected for certain behavioral traits, such as tameness. "It is therefore possible that this process led to an increase in functional genetic diversity throughout the entire doggenome," wrote Vilà, "including bothgenesand elements affectinggene expression." Such a relaxation of selective pressures might have led to the wide phenotypic diversity in dogs, as well as the variety of diseases seen in dogs today (Figure 1).

Tameness

Many researchers have noted that beyond tameness, dogs appear to retain certain traits associated with juvenile wolves, especially behavioral traits such as whining, barking, and submissiveness. Russian geneticist Dmitry Belyaev focused on tamability as a guidingcharacteristic. His idea was not only that early humans would have selected the tamest animals to live with them, but also that selecting for a single trait could give rise to an entire set of changes in form, physiology, and behavior. Belyaev thus launched an experiment that would last longer than his life, seeking to test whether selecting for tameness would indeed produce a set of domesticated traits similar to those seen in dogs (Trut, 1999).

Belyaev chose the silver fox for his experiment; this species is related to the dog, but it is not domesticated. The initial foxes in Belyaev's experiment were not trained in any way, but simply tested for tameness at an early age. Starting at age one month, a human researcher would try to feed and pet the foxes, either alone or in the company of other foxes. The animals' responses varied from aggressive behaviors (such as biting), to indifference, to seekinginteractionwith the person more than with the other foxes. The tamest foxes were then selected for breeding the next generation, although fresh genes were supplied through continual outbreeding.