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Evaluating the genetic status of a breed using both pedigrees and DNA

By Carol Beuchat PhD

There's a nice little paper just out about the Bullmastiff that provides a useful discussion of how both pedigree information and DNA analysis can be used to assess the genetic status of a dog breed. They worked on the population of Bullmastiffs in Australia, which descended from dogs imported from the UK. Although the breed was recognized by the British Kennel Club in the 1920's, the pedigree data for the animals in the Australian registry only go back to 1980, so documentation of the ancestry of the population is incomplete. This means that pedigree analysis will underestimate the current inbreeding level because it documents only the inbreeding that has accumulated since 1980. While there is much to be learned even from incomplete pedigree data, DNA analyses can complement pedigree analysis as well as fill in some of the gaps in pedigree data.
A nice thing about this study is that they genotyped nearly 200 of the 16,739 dogs in their pedigree database, so the were able to compare information produced on both platforms. They also compared their estimates of homozygosity (inbreeding) for Bullmastiffs with information for 12 other breeds from previous studies. Finally, they examined the genetic relationship between the Bullmastiff and 30 other dog breeds.
They characterized the Australian Bullmastiff population using standard statistics from population genetics, and they do a nice summary of what these mean in the paper. Those with some basic background in population genetics of dogs will recognize some of these, such as effective population size, effective number of founders, and effective number of ancestors. They also used some techniques specific to DNA analysis such as "runs of homozygosity" (ROH), which reflects the abundance and magnitude of stretches of the DNA that are homozygous. ROH can be used to distinguish between recent and ancient inbreeding (e.g., from the time of breed establishment).
A really cool thing they were able to do with the genotype data is display the relationships among all individuals as a network, with closely related dogs organized as clusters and lines connecting related clusters. This a nice way to convey the complex relationships among animals, especially in populations like dogs where the breeding patterns can be unusual and even involve animals long since deceased.​
Unless you have Bullmastiffs, you probably won't be interested in the details of the results, but this is a great resource for learning about the basics of population genetics and the use of both pedigree and DNA information to reveal the genetic health of a breed. As the authors point out, managing inbreeding and reducing the expression of genetic disorders will require information about the genetics of both the individual and the breed, and you can expect to see more and more of these studies as breeders adopt modern strategies for genetic management. Pedigrees provide a roadmap that documents the genetic history of a breed and the relationships among current animals, while DNA can distinguish between old and recent inbreeding and provide fine scale resolution of genetic differences between closely related animals.

Although many of these tools (and the jargon) will be unfamiliar to some breeders, I think this paper is a great place for the novice to dip their toes into the modern genetics of populations. You will find some basic courses about population genetic on the ICB website, and courses to help breeders understand and use the tools of molecular genetics are coming soon. The next five years or so is likely to see an explosion of breed studies similar to this one as breeders recognize the importance of genetic management at the breed level to the control of genetic disorders.
Mortlock, S-A, MS Khatkar, & P Williamson. 2016. Comparative analysis of genome diversity in Bullmastiff dogs. PLoS ONE 11(1): e0147941. doi:10.1371/journal.pone.0147941 (download the pdf)​
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