Genomic Selection

The dramatic fall in DNA sequencing costs has lead to the use of DNA sequencing by breeders of agricultural plants and animals to improve their breeding stock. For examples of this being done in various cases, see ([1] dairy, [2] cattle, and [3] crops, forestry, fish)

What about dog breeding?

Genomic selection has already been used in dog breeding in two cases of which I am aware (see [4] and [5]) - both US government programs for producing working dogs for military and homeland security purposes. However with the continued fall in the price of DNA sequencing, genomic selection is now at a price where it can be used by hobby breeders of dogs.

Breeders currently make breeding decisions based upon particular traits that they want to improve. They do this by breeding to dogs with phenotypical expression of a trait or traits of interest. The only thing new that is being proposed here is to use genomic selection as an additional tool along with phenotypical selection.

How is genomic selection done?

Full sequencing of DNA is still price-prohibitive for the hobby breeder. (As of 2015, it costs approximately $1,000 to fully sequence a person's genome.) Thus genomic selection is most commonly done by marker-assisted selection - making use of of single-nucleotide polymorphisms (SNPs) as "markers" for (unknown) genes that lead to traits of interest. A large number of SNPs (approximately 170,000) are chosen that are uniformly spread out through out the canine genome. Sequencing these SNPs costs less than $200 per dog. Two populations of canines are sequenced for their SNPs - one population that has the trait of interest, and a second which does not. There is a strong likelihood that SNPs will be in close proximity (in other words, act as a "marker") to the genes that produce the particular trait of interest. Most SNPs of course will be identical for dogs of the same breed. However in principal, the SNPs that are different can be divided into two sets - one from the population with the trait of interest, and the others from the population that does not have the trait of interest. Practice is of course different from principal, and mathematics and statistics are often needed to identify SNPs of interest.

Once "marker-SNPs" have been identified, progeny can be tested to see if they carry the marker-SNPs. If it is believed that the marker-SNPs identify ("mark") the genes that produce a trait of interest, progeny with the trait of interest can be identified at a very young age - even before they leave the whelping box.

One big unknown is the number of dogs needed to be initially sequenced. Most likely this will depend on the particular trait of interest - some traits will be easier to identify genomically with markers than others.

What I propose to do ...

I propose to research marker-assisted selection for a particular trait of interest. I do this as a personal learning project to educate myself more about DNA technology and the necessary mathematics and statistics. (It is just more fun working on data in which one has a personal interest.) All sequencing data will be made publically available (see privacy considerations), and any results will be shared.

While this exact same technology is used to narrow down the search space for disease-causing genes, I will not be using it for that purpose. Such research is better performed by researchers who have access to larger DNA sample sets and better sequencing technology. I am interested in traits that are unlikely to be of interest to scientists (who are more interested in how canine disease can help human disease research). However where markers for diseases have been published (see "hip dysplasia and SNP markers) I will be interested if such markers also appear in the samples that I sequence.

Blair Kelly
Shaksper Norwich
AKC Breeder of Merit


[1] Genomic selection in dariy cattle: Integration of DNA testing into breeding programs, J.M. Schefers and K.A. Weigel, Animal Frontiers, Jan 2012.

[2] Various articles by Dr. Alison L Van Eenennaam of UC Davis on marker-assisted selection in the beef industry.

[3] Marker-assisted Selection: Current status and future perspectives in crops, livestock, forestry and fish, Food And Agriculture Organization Of The United Nations Rome, 2007.

[4] Genome-Wide Association Mapping for Intelligence in Military Working Dogs National Technical Information Service, Sep 2011.

[5] The Role of Genetic Improvement in the Production of Explosives Detector Dogs for National Security, Liz Hare