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Genes R US — A different kind of genomic variation in 10 popular dog breeds

Genes R US — A different kind of genomic variation in 10 popular dog breeds

Posted: Wednesday, May 30, 2012 5:00 pm

Last week while in the vet’s office, a kind reader told me that her favorite Genes-R-Us columns were about “the dogs.” This column is, therefore, dedicated to my readers who have a dog — either by their choice or through some needy stray adopting them, as was our case for our Ebony and Ivory.
Using single point DNA variations, called SNPs, we have some breed information about Ebony and Ivory. Neither dog is more than one-quarter of any single breed. The breed test used for Ebony and Ivory incorporated over 4,600 SNPs. 
The selective breeding of dogs provides scientists an amazing opportunity to understand how variations in genes, plus environment, translate to canine features. These features include things like body type (morphology), immune system function and personality traits.  Genetic scientists call this process translating genotype to phenotype. 
The study of canine genetics advances human medicine, too, as we share many evolutionarily similar genes (homologous genes) with our furry friends.
A 2011 paper connected a human hereditary condition that causes a periodic fever to the gene, HAS2, that is primarily responsible for the skin wrinkling found in Shar-Pei’s. Shar-Pei’s are also predisposed to the periodic fevers. (http://bit.ly/JKNdwA)
University of Washington’s Genomic Lab in Seattle, WA (UW Lab) is a leader in canine genetic research. (Hmmm … UW’s mascot is a husky.) Over the last couple of years, the UW Lab has identified several dog breed phenotypes that could be tracked to specific versions of a single gene.
An excerpt from a 2010 paper (http://bit.ly/JKNdwA) shows some of their results. (You can “google” the gene name to find out more about any genes.)
Breed; Gene; Phenotype   
Greyhound; CDH9; Behavioural   
Greyhound; ZFHX3; Cranial morphology   
Greyhound; LRIG3; Elongated body axis Greyhound; SOX9; Skeletal morphology
Brittany; PIK3C3; Behavioural   
Brittany; SOX9; Skeletal morphology   
Dachshund; SEMA3D; Morphology   
Poodle;    DLG2; Behavioural   
Border Collie; SATB1; Athletic performance
To more fully understand why certain breeds have complex traits or health issues, scientists need more than SNPs. Enter copy number variants (CNVs). We will consider two types of CNVs, gains and losses of genomic sequence. 
A gain occurs when a chunk of DNA is repeated multiple times. Imagine a gain as continuous chunk of DNA that is repeated several times along a chromosome. Gains are also called insertions. Analogously, a loss occurs when a strip of DNA is just flat out missing.  Losses are also called deletions.
When gains result in multiple copies of a gene, that can mean some protein is churned out in larger quantities the normal. Losses can be associated with a missing protein. But depending on where the CNV occurs, either gain or loss can disrupt a translation process whereby some critical protein is not created at all. 
The UW Lab has studied CNVs in several specific regions where canine genes of interest are found. In a recent study they measured CNVs for several popular dog breeds and wolves. They included wolves in their study, since domestic dogs are all descended from the wolf. This was the first time CNVs have been studied in dogs. 
They found 1008 CNVs in 403 different chromosomal regions. This impacted the coding behavior of unique 401 genes. The “control” dog for their study was a female boxer. All the CNV measurements for the other breeds were compared to her. 
They found CNVs where all dogs within one or more breeds carried a gain or loss, but was absent in at least one of the remaining breeds.   In total, 49 such regions exhibiting this pattern were identified. Some of these distinct genetic regions contain genes that likely contribute to the phenotypic differences between breeds: (http://bit.ly/pUPI4s) 
Breed; Total CNVs; Gains; Losses   
Wolf; 136; 79; 57
German Shepherd; 113; 52; 61
Basenji; 109; 45; 64
Standard Poodle; 109; 37; 72
Doberman Pinscher; 107; 57; 50
Pug; 97; 44; 53
Rottweiler; 88; 30; 58
Siberian Husky; 86; 47; 39
Shetland Sheepdog; 86; 35; 51
Labrador Retriever; 77; 33; 44
Wolves have a strong digging behavior that has survived in Ebony and Ivory.
I suspect that the genetic regions, responsible for lovely digging behavior, involve many different genetic regions-not in any CNV “loss” region at least compared to a wolf. 
And then there is the chewing behavior. Ivory is still attempting to chew her way into our affection. We have much evidence: once mature rose bushes now clinging to life as denuded nubs, mutilated porch rocking chairs legs, missing design work from wooden front door, door mats and garden hoses in pieces … Yes, Ivory has human-designated toys, but then there is everything else that, no doubt, her DNA tells her is also a toy! 
Editor’s note: Nancy@ NancyMillerLatimer.com has worked in scientific research and development for 27 years. She blogs at NeuronalBeauty.BlogSpot.com Published in The Messenger 5.30.12

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