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Materials and Methods (How the testing was done)

The Optimal Selection Genetic Breeding Analysis is a process that analyzes a dog's DNA on many key chromosomes.  The objective is to compare the chromosomes of potential breeding pairs, giving the breeder an opportunity to diversify the genetic makeup of their puppies and reduce the risk of recessive medical conditions while still selecting for the physical and behavioral traits that are important to them.  With this process, breeders can select a breeding pair that will maximize the potential genetic heterozygosity (aligning different haplotypes on each chromosome).  Studies have shown that limiting heterozygosity (or increasing homozygosity) can cause decreased litter size and lead to greater health risks, thus increasing individual heterozygosity  can help with these issues.
 
The homozygosity is determined for each dog and is the percentage of markers tested in the dog with the same allele (e.g. AA so the dog inherited an A from the dam and an A from the sire).  Heterozygosity is the opposite of homozygosity and is when the dog inherits different alleles from each parent (e.g. AG).  For the average homozygosity in a breed, the level of homozygosity in each dog is averaged across all of the dogs we have in our database for that breed (and the curve in the homozygosity graph shows the range of homozygosities observed in the breed).

Two key aspects were involved in homozygosity determinations:

1.  SNP Testing:  Wisdom Panel Insights only uses what are called autosomal DNA markers, chromosomes that contain most of the genetic instructions for every canine's body make up (height, weight, size etc.). There are no markers from either the so-called sex chromosomes (the canine X or Y chromosomes). Mitochondrial DNA, or Y-chromosome DNA testing, is rather different as these parts of the genome are passed on intact from mother to daughter and father to son respectively, but are therefore only representative of either the female or the male lineage. Autosomal DNA is inherited both from the maternal and paternal lineages equally and constantly shuffled by a process called recombination at each successive generation, and therefore is able to give useful information on the breeds found on both sides of a dog's lineage.

To find the genetic markers that performed best at distinguishing between breeds, Mars Veterinary tested over 4,600 SNPs (single nucleotide polymorphisms or genetic markers, where genetic variation has been found between different dogs), from positions across the whole canine Autosomal genome from over 3,200 dogs. To further refine the search, Mars Veterinary determined the best 1,536 genetic variations and ran them against an additional 4,400 dogs from a wide range of breeds. This stage of testing resulted in the selection of the final panel of DNA markers that performed best at distinguishing between breeds, ultimately creating the Wisdom Panel genetic database.

References using SNP analysis:  Francisco De La Vega et. al, Nature Genetics (2008), 40 (5), 491-492; Victor Enciso-Mora et. al., European Journal of Human Genetics (2010) 18, 909-914. 

2.  Principle Component Analysis 

Principle component analysis (PCA) allows us to look at the genetic relatedness between dogs or how similar they are. Closely related samples would be expected to cluster closer together than more distantly related samples. Therefore, dogs from the same breed tend to create a cluster of points. However, you may notice some separation between sub-clusters indicating different family lines due to geography (e.g. US vs. UK), variety (e.g. size or coat type), or use (e.g. working vs. show lines).  For an example of what PCA results can look like, the PCA below shows two Airedales currently in the breed database.

webassets/PCAexample.JPG 

 

Optimal Selection/Wisdom Panel FAQs 

 

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