In the December issue of Genome Research--a special issue devoted to dog genomes--TIGR researchers Ewen Kirkness and Wei Wang compared the genome sequences of two dogs, a standard poodle and a boxer. Finding key genetic differences between the two dogs, the researchers went on to compare those telltale genetic variations in the genomes from nine additional dog breeds--beagle, Labrador retriever, German shepherd, Italian greyhound, English shepherd, Bedlington terrier, Portuguese water dog, Alaskan malamute, and rottweiler--and five genomes of wild canids (four types of wolves and a coyote).
"This work demonstrates a significant amount of variation that you can see between individual dogs at the genomic level," says Kirkness, lead investigator of the project, funded by TIGR. "That variation can now be exploited to study the differences between dogs, their diseases, development and behaviors." More broadly, Kirkness adds, the comparisons illustrate evolutionary influences that can shape mammalian genomes.
In the study, the scientists first compared the two most complete canine genomes available. Those genomes belong to Shadow, a standard poodle whose genome was published by TIGR in 2003, and Tasha, a boxer sequenced by the Broad Institute of Cambridge, Massachusetts, in 2004.
To compare Shadow's and Tasha's genomes, the researchers tracked short interspersed elements (SINEs)--stretches of DNA that occur randomly in the genomes of many organisms. SINEs are inserted near or within genes, often turning the expression of those genes up, down or even off. The scientists found that the poodle and boxer differed in their content of SINEs at 10,562 locations in their genomes. Broadening the study to compare SINEs among the additional nine dog breeds and five wild canids, the scientists estimated that the overall dog population contains at least 20,000 SINE differences.
To genomics researchers, variable SINEs can act as signposts for specific genes linked to disease or traits. The dog is a unique genomics model. Through selective breeding of dogs, humans have created the highest degree of physical and behavioral differences seen within a species. Roughly 400 dog breeds exist, with specific breeds predisposed to heart disease, cancer, blindness, deafness and other common disorders. Identifying genes responsible for diseases or physical traits may be easier to do in dogs that have been genetically selected.
In a second study, published in the December 8 issue of Nature, researchers from 15 institutions describe a high-resolution draft of the boxer genome. This work includes a high resolution map of canine single nucleotide polymorphisms (SNPs), based largely on a comparison of the boxer and poodle sequences. Eventually, Kirkness predicts, efforts to document genetic differences between dogs will lead to major health gains for the animals. And perhaps us, too: A dog genome is estimated to include some 19,300 genes--nearly all corresponding to similar human genes.
The Institute for Genomic Research is a not-for-profit center dedicated to deciphering and analyzing genomes. Since 1992, TIGR, based in Rockville, Md., has been a genomics leader, conducting research critical to medicine, agriculture, energy, the environment and biodefense.
Journal
Genome Research