TALK ABOUT BLIND FAITH. TWENTY YEARS

ago, Gustavo Aguirre and his colleague Gre-

gory Acland were struggling to understand a

common cause of inherited blindness in dogs. They had bred affected and unaffected individuals and traced the inheritance pat- terns in the offspring, but "there was no hope of finding the gene," recalls Aguirre, a vet- erinarian at the University of Pennsylvania's School of Veterinary Medicine ill Philadel- phia. At the time, researchers hadn't even

assigned numbers to the canine chromo-

somes, let alone begun to map the locations of genes. Nonetheless, "I decided that in the future, someone somewhere would come up with [a way] to come up with the gene," he

says. So they banked blood from their dogs and waited.

Their patience paid off. A decade later, their freezers provided the raw material for a

linkage map of the dog genome and, eventu- ally, the discovery of the long-sought gene for pro•'ess.ive r•xt-cone degeneration. With that map as a starting point, l'eseea'chers have built a community that has proven the value

o f dog genetics not just for veterinarians and dog breeders but also for human geneticists.

Dogs are a geneticist's ttream. Pure breeds, as th.e name implies, are often highly inbred tbr specific traits. They have large families and well-documented genealogies, all of which greatly simplifies the task of tracking down mutations that

cause disease or genes that underlie traits such as size, coat color, or even behavior. And the link to humans can be direct: The top 10 diseases in dogs include cancer, epilepsy, allergy, and heart disease--disorders that affect many millions of people. Also, because dogs live in the same environment

as people, they share some of the same envi- ronmental risk factors. As a result, more and

more researchers, including a consortium

Dogged pursuit. E•aine Ostrander helped jump- start canine genomics.

about to be announced in Europe (see p. 1670), are turning to the dog for clues to human genetics. "All of a sudden, people from a wide range of disciplines can see the value, power, and practicality of genetic studies in dogs to shed light on issues of concern 1o them," says Acland, a geneticist now at Corncll University.

Pooch politics It wasn't always that way. In fact, it took years of work by a small but dedicated band of researchers •br tile dog's scientific value to be appreciated. Jasper Rine got the ball rolling almost 20 years ago. A yeast geneticist at the University of California, Berkeley, he recog- nized that dogs were bred for specific behav- iors and that those behaviors probably had a

very strong, and perhaps easily identifiable, genetic basis. Rine crossed Border collies with Newfoundlands to see ifhe could pin- point the genes underlying the former's predilection for herding and the latter's love

o fswimming. But he lacked a key tool: a map of genetic markers--known stretches of DNA prone to variation--that he could track fi-oln parents to offspring to determine which

were passed along with the best swimmers and which were associated with herding. The markers associated with a particular behavior should lie near genes that contribute to that behavior. To develop such a tool, Rine con-

ceived tile idea of a dog genome project. For Elaine Ostrmlder, fl•e timing was Ibr-

tuitous. She had just come to Berkeley in 1990 as a postdoc to study plant genetics, and to tide her over until her new fellowship kicked in, she took a temporary job with. Rine. Her assignment: to begin building the dog map. She never made it to the plant lab. she left in 1993 for the Fred Hutchinson Can- cer Research Center in Seattle, Washin•on,

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she was a complete convert, as comfortable soliciting blood samples from breeders at dog shows as she was poring over gels. Her

puppy, a Border collie named Tess, became her lab's mascot, providing Ostrander and her students with welcome distractions and, once, posing for the cover photo on

Mammalian Genotne. Ostrander's home became a meeting place for colleagues inter- ested in promoting dog genetics. "She drove this whole canine genome initiative," says Matthew Breen, a cytogeneticist at North Carolina State University's College of Veteri-

nat'3., Medicine in Raleigh. Eventually, Rine closed down his dog-

behavior studies for lack of funding and to avoid being hassled by animal-rights actMsts. Ostrander persisted on the map, but

progress was slow until 1996, when she, Acland, and Aguirrejoined forces. "We fig- ured out we needed to check our egos at the door and poot our efforts;' Ostrander recalls. Because Aguirre and Acland had samples from a large number of dogs with known genealogies spanning several generations, Ostrander and colleagues were able to deter- mine the relative order of scores of markers by following which ones were inherited together in these dog families. A year after they began working together, they produced the first map showing the positions of 150 of these markers on the dog genome. With this tool, they quickly narrowed down the loca- tion of the gene for progressive rod-cone degeneration to a region of chromosome 9, although it would take several more years to

get to fl•e gene itself. Very quickly, that map was superseded by a

much more comprehensive one, a joint effort

by Breen, Ostrander, and Francis Galibert, a human geneticist at the University of Rennes, France. Galibert, who became convinced of the value of dogs for gene hunting after hearing Ostrander give a talk at a Cold Spring Harbor Laboratory meeting, had located markers along the genome in a so-called radiation hybrid map. Ostrander and Breen added their markers to it to create a detailed atlas for track- ing genes. With it, researchers "could pull DNA samples from their pedigrees out of their freezers and begin to do genome scans," Ostrander says.

Ostrander and Aguirre had long suspected that dog studies could lead to the discovery of genes hnportant to humans. "But at the time, we were fighting the perception that dogs couldn't tell you anything," recalls Aguirre. That changed in 1998, when Emmanuel Mignot of Stanford University in Palo Alto, California, and his colleagues tracked do,aqa a

gene that causes narcolepsy in dogs. After a

decade of work, they found causative muta- tions in the Hcrtr2 gene in narcoleptic dachs- hunds, Labrador retrievers, and Doberman pinschers, a discovery that clued researchers in to a new molecular pathway involved in sleep. With these results, "it was crystal clear that. by studying dog genetics, we were going to learn things we couldn't learn in mice," says OsW, mder.

That realization helped Ostrander achieve her ultirrmte goal: a complete genome sequence of the dog. She and her colleagues had

Community outreach. •HrRI's Heidi P•rker 9ets 0NA from dog-sho• competitor.

their appetites whet- ted when J. Craig Venter, then president ofCelera Genomics ha Rockville, Maryland, turned his sequencing machines on his pet poodle, churning out a

very rough sketch of its genome in 2001. An analysis •.• published 2 years later (Science, 26 September 2003, p. 1898). About the same tirne, the National Human Genome Research Institute (NHGRI) at the Natiot•l Institutes of Health ha Bethesda, Maryland, •began supporting the deciphering of other vertebrate genornes, and Ostrander and her collaborators wasted no time writing up a

white paper arguing that the dog be given high priority. She convinced the Broad Institute of the Massachusetls Institute of Technoiogy and larvard University ha Cambridge, Massachu- setts•a leader in high-thronghput genome seqnencing mad analysis--to sign on. In 2002, the dog beat out the cat and the cow for a spot in the sequencing pipeline.

Ostrander put out a call to dog breeders for a highly inbred candidate. (The more

inbred the individual, the more similar the animal's two sets of chromosomes and the easier it would be to piece the genome together.) After studying hundreds of sam- ples of dog DNA submitted by owners, Ostrander and her colleagues chose a boxer named Tasha as the first canine to have its

genome deciphered. As part of that sequencing effort,

researchers at the Broad Institute compared Tasha's genome with the rough draft of the poodIe genome and DNA sequences from nine other dog breeds and five wild canids and came up with 2.5 million single- nucleotide polymorphisms (SNPs): points on

the genome where a change in a single nucleotide frequently occurs. The analysis, published in the 8 December 2005 issue of Nature, "is a masterpiece," says geneticist Greg Barsh of Stanford University. Broad's Kerstin Lindblad-Toh, who led the dog genome sequencing project, has since worked with Affymetfix in Santa Clara, Cali- fornia, to develop a SNP chip, a microarn•y that. allows researchers to screen samples rap- idly for these variations across the genome. Dog genetics studies were primed for takeoff. These tools, says Aguirre, "put us into the 21 st century."

The power of inbreeding The dog's power in tracking genes comes

largely from inbreeding. "Each [breed] is a

mini Iceland or Finland," explains Ostrander,

O

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now at NHGRI. Many breeds stem from a few individuals whose progeny were haterbred, not because of geographic isolation but to select for specific features and behaviors. As a

result, members of a given breed have extremely long stretches of identical DNA in common--millions of bases long compared to the typical tens of thousands of bases in humans. In humans, "there's a lot of back- ground cackling, but when you look at the dog genome, the message is loud and clear, with- out a lot of background noise," Breen explains. That means researchers can track down recessive genes involved in disease using many fewer animals. They also need an

order of magnitude fewer SNPs than are

needed for human studies. The inbreeding in dogs is especially valu-

able in studies of genetic risks in complex dis-

eases. In people, different mutations, even di f- ferent genes, may be at fatdt ha the same dis- ease. Dozens ofgenes contribute to the risk of

common cancers, for example, with no single one jumping out as key. But because each dog breed is an isolated, inbred population that typically dates back just a few hundred years, not a lot of time has passed for the dogs in any one breed to develop multiple mutations for the same disorder, or for several mutations to have been introduced from outbreeding. "In dogs of one breed,_ you will have exactly the

same mutation in the same gene;' geneticist

Mark Neff of the University of California, Davis, explains. Breeds derived from a com-

tnon ancestral breed might share a mutation, bu• distantly related breeds will not, offering the potential of revealing other genes, perhaps in the same pathway involved h• a disease.

To help sort out how different breeds are

related to each other, Ostrandet•, Heidi Parker in her lab, and •heir colleagues have looked for genetic variants that are shared across breeds: The more shared variants, the more closely the breeds are related. They initially studied 85 breeds, and the results helped them home in on a gene for short stature (Science, 6 April, p. 112). They have now expanded the work---called the PhyDo Project•to 130 of the 155 breeds recognized by the American Kennel Club. In work in press at Genome Research, they report that breeds cluster into

five geneticall.y defined groups, with some subdivisions within each group.

As these researchers will report, they have. used these relationships to track down a gene causing collie eye anomaly, which is the canine equivalent of a human birth defect in which part of the eye does not fonaa properly. In 2003, they had narrowed the gene's loca- tion down to a 1.7-million-base stretch of dog chromosome 37. Then they went further: "By comparing different herding breeds with the same disease, we whittled down [the possibil- ities] to four genes;' Ostrander explains.

A close look revealed the likely culprit: a

gene calledNHEJ1 missing 7800 bases. They found the same mutation in two more dis- tantly related breeds, Nova Scotia duck tolling retrievers and Ionghaired whippets, which likely had farm collies in their family trees. But urn'elated soft-coated wheaten ter- riers, which also get this disease, don't have the mutalion. "We think we will be able to play that trick [of looking for mutations in closely related breeds] agaha and a.gaha," says Nathan Sutter, who recently left Ostrander's lab for Cornell Universi•.

PhyDo is also helping Ostrander's group make sense of bladder cancers. Five breeds tend to develop this cancer. The most suscep- tible, with a 30-Ibld increase in risk, is the Scottish terrier. Three other at-risk breeds are terriers, which likely share the same

Europe Going to the Dogs While U.S. researchers were beginning to piece together the first genetic maps for dogs in the 1990s, University of Copenhagen pig researcher Merete Fredholm was wdnging her hands in frustration at the tack of funds to support a European consortium with the same goat. But now, she and collaborators from more than 20 institutions are poised to make a champion showing in this field, thanks to a pending European Union award for about S$6 million.

Named after the legendary wolf who nourished the founders of Rome, the LUPA consortium plans to get DNA samples and health histories from 8000 dogs and hunt down genes for 18 diseases, including four cancers, four inflammatory disorders, and three heart diseases. "We have decided to focus on certain areas and to standardize the cfinical characterization of these diseases," explains Leif Andersson, geneticist at Uppsala University in Sweden. In this way, they use the DNA from animals across different coun- tries, as welt as across different breeds, to find genes. Once they have found the gene, they plan to see what role it plays in humans, says LUPA coordina- tor Michel Georges of the University of Liege in Belgium.

Georges is a recent convert, having never studied dogs before. But ioin- ing him are key players in canine genomics. Kerstin Lindblad-Toh, who headed the dog sequencing proiect at the Broad Institute of •assachusetts Institute of Technology and Harvard University in Cambridge, Massachu- setts, is now spending three-quarters of her time at Uppsala University. "Her recognition, competence, and working capacity wit[ change [European dog genomics]," says collaborator •ke Hedhammar, a long-term dog researcher at the Swedish University of Agricultural Sciences in Uppsala, who has used kennel club records and records from companies that provide heatth insur-

Best of Show. Olle K•mpe, 66ran Andersson, Kerstin Lindblad-Toh,/],ke Hedhammar, and Leif Andersson ([eft to right) have teamed up to tackle human diseases through dog studies.

ance for pets to sort out which individual dogs and breeds are best suited for particular gene searches.

The European effort promises to push the field to warp speed. "We're going to learn a lot more about a tot of diseases," says Elaine Ostrander, a geneticist at the National Human Genome Research Institute in Bethesda, t•aryland. Until recently, much of the high-profile work on dog genetics came from Ostrander and her collaborators, but already Europe is churning out a stew of key papers. With LUPA, "there will be a lot of competition," says Fredholm. -E.P.

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mutation. But PhyDo data verify that the fifth susceptible breed, the beagle, is not at all related, so its bladder tumor risk probably stems from a difi'erent genetic abnormalib,.

Dog fanders Ostrander's group is working with Carlos Bustarnante of Con•ell University to make SNP profiles of individual breeds available in a public database called "CANMAP." It should provide researchers and breeders with powerful tools to track down the traits in which they are most interested. Already, researchers are intrigued by the possibilities.

The data set includes wolves, the common ancestor of all dogs, which should give evolu- tionary biologists a "wonderful perspective on the evolution of the dog;' says collaborator Robert Wayne, an evolutionary biologist at the University of California, Los Angeles. Since the 1980s, he's wanted to find the genes underlying the evolution of dogs and dog breeds. Back then, "it was clear we didn't have the tectmology to address the basic ques- tions," he recalls. Now, says Sutter, by com- paring SNP profiles of dogs and wolves, "we ,adll haow what changes occurred in the dog during domestication."

Stanford's Barsh has a different quarry in his sights. Over the past 15 years, he has worked on the genetics of coat color in mice, but recently he's focused on dogs and is well on his way to under- standing the genetic basis of the stripes in the brindle coat of Great Danes. Like Barsh, Danielle Karyadi in Ost•,n.nder's lab is also a

recent convert to dog genetics. She has spent much of her career chasing down genes that make people more susceptible to prostate cancer. Now, she has turned her attention to squamous cell carcinoma, a cancer found only in solid black dogs, such as poodles. "It will be really exciting when we can identify genes in dog cancers" mad use fi•em to understand human cancers, says Karyadi.

Lindblad-Toh has also been won over to the hounds. She specialized iaa human genet- ics when she came to Cambridge but by chance got roped into running the mouse genome sequencing project and eventually all mammalian sequencing projects at the Broad Institute. Working with European col- laborators, Lindbtad-Toh's group has two

papers in press demonstrating the power of genomewide association studies in dogs to pin do•.xqa genes. In one, they used fewer than two dozen boxers to txack down the gene for white coat color. The gene is the same one

that is mutated in humans with Waardenbu• syndrome, an inherited disease daaracterized by hearing loss and skin and pigmentation abnormalities, and in several mouse pigmen- tation disorders. A second study on Rhode- sian ridgebacks has led the group to a muta- tion possibly involved in neural tube defects; that study required fewer than tnvo dozen ani- mals ,as well. "It sbows how little material you need," says Ake Hedhammar, a geneticist at the Swedish University of Agricultural Sci- ences in Uppsala.

He and Lindblad-Toh expect to make progress understanding more complex dis- eases as well. For example, boxers, bull terri- ers, and West Highland white terriers are

Common ills. Dogs and humans suffer from many of the same diseases, such as atopic dermatitis (left).

prone to atopic dermatitis, a skin disease that in both dogs and humans has environ- mental and genetic components. Genetic studies are under way in these breeds to find the genes that influence this risk.

A window on behavior The rapid progress in dog genetics is prompt- ing some researchers to get back to studies that motivated a canine genome project in the first place: tracking down genes associated with behavioral traits. Neff has teamed up with [llumina Inc. in San Diego, California, to

use a microarray to look for SNPs associated with "pointing." About 40 breeds point-- fr•zing and lifting a paw in the direction of a

rabbit or other quan-y. "I finally feel we have a

chance Io understand the behavior;' says Ne• who worked with Rine in the 1990s.

Even x.xdth the best genetic resources, how- eve•, the work is still challenging. "The prob-

lem is identifying the phenotype and separat- ing what is learned versus what they are born with," says Parker. Adds Barsh: "We kaaow whether [a dog] is yellow or black, but some- times it's not .so easy to tell how good a dog is at herding versus retrieving.'" In Ostrander's lab, Tyrone Spady--who used to study visual behax4or in fish---depends on DNA from dogs that live in different places, with different upbringings and lifestyles. So Spady asks owners to fill out questionnaires: how fre- quently does the dog chase other animals, what quarry gets it ru•ming, and so on. By pooling surveys from many people, he corrects for bias in the owners' resporLses mad uses the data in genomewide association studies.

At the Nora,egian School of Veterinary Sci- ence in Oslo, Frode Lh•gaas is taking a shnilar tack in looking into "cocker rage." In this syn- drome, generally amiable pets turn on their owners, exhibiting frighteningly aggressive behavior. He and his European colleagues assess the dogs' personalities through inter- views with the owners and questionnaires. Several hundred seaaaples will come fi'om Eng- lish cocker spaniels, but a few will come from English springer spaniels, which are also prone to this mental disorder. These dogs should get the researchers close to the gene, and a com-

parison with golden rela'ievers, which c• also be four-legged Jeckylls and Hydes, should get them within strildng distance. Because rage is often a symptom in schizopba-enia, bipolar dis- ease, obsessive-compulsive disorder, and other mental problems, finding this gene could help researchers understand why it develops in patients with mental illness.

Swedish researchers have a leg up on Spady and Lingaas. In Sweden, breeders often evaluate their yotmg dogs using a stma- dardized personality test. By looking at aggression, boldness, shyness, and sociabil- ity, they are able to bett.er assess which ones should be trained as working dogs and for what jobs. So they have a large data set to •vork with and are moving tbrward with those studies, says Hedhammar. And in Russia, a

long-term breeding program in foxes has yielded docile, doglike animals whose genes might yield insights into what makes dogs so affectionate and loyal.

Although Ostrander is curious about the genetic basis of why dogs get sick, grow tall, or excel at hunting, the intimacy she and oth- ers share, with their canine pets is not some- thing she cares to be intellectual about. Just the thought of the death of her lab's •nascot a

year ago still brings tears to her eyes. "There's some genetics buried in that," she says, "'but am going to leave that to someone else."'

-ELIZABETH PENNISI

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