Spot's Ridges (& Ridge's Spots?)

Miss Amanda is quite excited about two new papers on the Nature Genetics preprint site, though as we don't have a subscription we're stuck reading just the abstracts and the supplementary material. The papers use genetic mapping for fine-scale mapping of the variations responsible for two visible phenotypes: the distinctive back ridge in ridgeback dogs and a coat spotting phenotype found in many breeds.

A particularly striking claim in the one abstract is that this mapping could be accomplished with approximately 20 individuals. This is quite a small number, and would suggest that many mendelian traits in dogs will be rapidly mapped given the modest (by genomics standards) cost of doing an experiment (arrays are already below the $1K/sample mark) I've promised the little miss we can go halfsies on any papers on floppy ears, curled tails or flat faces.

The ridgeback variant is also interesting because it is a copy number variation, a very hot class of genetic variations lately. The duplicated region contains three FGF family members, growth factors known to play roles in development. Of further interest is that the polymorphism also tracks with a nasal abnormality also seen in these dogs. Many pure breeds suffer from distinct maladies which are often direct results of the physical shape of the canine. For example, short snouts raise the risk of eye injury, which is a trauma M.A. suffered soon after arriving at our abode. However, in this case it would appear that the phenotypes have an underlying biological explanation that is not simply that the shape but a common developmental trigger.

This is the time of year for agricultural fairs & I was recently (as usual, biogeek that I am) strolling through one marveling at the range of breeds of various animals. Chickens are perhaps the showiest at these affairs, but there are also lots of varieties of goats, sheep, cows, horses, ducks, rabbits, cavies, etc. Most of these species have draft genomes in one form or another, and with the cost of sequencing sliding down surely all will have one before long. Sequencing a sample of individuals will enable mapping assays to be developed, which is becoming routine. Before long, many of those phenotypic variants, both showy and practical, will be mapped and identified. Other species with many identified breeds, such as cats, goldfish or Darwin's pigeons, will become straightforward to analyze as well.

Dogs do offer the most spectacular gains. This is not just pure boosterism, but just a reflection that dogs seem to have been selected by humans for such a wide variety of traits: shape, color and particularly behavior. I love cats too, but there just aren't any herding breeds!

Dog genetics is also an early example of direct-to-consumer genetic scanning -- one can check up on the breed heritage of a dog. There is a dog up the street which was marketed as a purebred Shih Tzu, but the face is radically different from my companion's. Nothing wrong with that, and it was probably just a bit of confusion at the breeder, though Amanda thinks it is more of an example a Svejk-style skulduggery (I should never have read that stuff to her!).