A Deep Dive into COIs: By JustusReichert

Justus and her Schipperke SOL

​Coefficients of Inbreeding: Genetic vs Pedigree- Which is Better?
 
So, let’s talk about the Coefficient of Inbreeding- COI as we like to call it. COI refers to how genetically similar a dog’s ancestors are. For the last hundred years or so we have had a commonly accepted form of calculating COIs that Sewall Wright helped develop in his paper, “Coefficients of Inbreeding and Relationship”. So how does it work? “If an individual is inbred, his sire and dam are connected in the pedigree by lines of descent from a common ancestor or ancestors. The coefficient of inbreeding is obtained by a summation of coefficients for every line by which the parents are connected, each line tracing back from the sire to a common ancestor and thence forward to the dam, and passing through no individual more than once. The same ancestors may of course be involved in more than one line.” (Wright 1922). The “Wright Method” method starts by looking at a dog’s pedigree for several generations, ten is thought to be the minimum number for an accurate representation, but more is better. After you compile a pedigree for the dog, you must count the number of similar ancestors and trace back how closely they are related to one another. There is a simple formula to do this with but it becomes hard to accomplish by hand after just a couple of generations. “F = (½)(n1+n2+1), where n1 and n2 are the numbers of generations separating the individuals in the consanguineous mating from their common ancestor” (Wright 1922). Thankfully there are several programs out there now to help owners and breeders calculate their dogs’ pedigree COIs without having to pour over these numbers.
Now that we understand pedigree COI and have a little background about how it is used, let’s talk about genetic COI and the differences between the two. Genetic COI evaluates the individual pieces of DNA within a dog to trace which parts lead back to inbreeding. What Embark does is a Genome-wide COI calculation. So what’s the big difference, and why can the numbers be so different? Well, pedigree COI has two big flaws that we all often overlook- the assumption that all offspring get exactly 50/50 from each parent and that the founder dogs in a breed are all completely unrelated. The idea that individuals inherit 50% of their father’s DNA and 50% of their mother’s DNA precisely is great... In theory. However, in practice, it doesn’t quite work out so well. Turns out, DNA is really bad at reading textbooks and recombination causes quite a variation in the true amount of DNA the offspring receives from each parent. This may not seem like a big deal for a couple of generations, but after 10 generations, you’re talking about a possible difference of up to 70%! Now, let’s talk about our founders. It’s impossible to know, with certainty, how related the founding dogs in every breed or pedigree truly are; even the most meticulous pedigrees can have mistakes and missing pieces, and dogs go back further than our pedigree databases do. Your dog’s pedigree may go back to the 1800s with a set of dogs who we have assumed were all unrelated when calculating COI- only for them to all have been cousins for all we know! 
Another bonus of genetic COI calculation is that you don’t need a pedigree to do it. Since you are mapping the individual’s genome, you already know more than you would with just the pedigree. You know exactly what alleles the dog has for each gene and what issues it may be at risk for due to the genes that have been passed down through the generations. These two big mistakes that pedigree COI calculators make are why you can see such a big discrepancy between a dog’s predicted pedigree COI and its genetic COI. 
The truth of the matter is, genetics don’t lie- genetic COI is the most accurate and best method for determining the true coefficient of inbreeding in a dog. And while a pedigree COI is a useful tool, having the capability to test dogs and determine their genetic COIs is invaluable. 
References


Beuchat, C. (2014, June 18). Wright's coefficient of inbreeding. The Institute of Canine Biology. Retrieved October 11, 2022, from https://www.instituteofcaninebiology.org/blog/wrights-coefficient-of-inbreeding
Boyko, A., Boyko, A., Scientist, & Dr. Adam Boyko is the Chief Science Officer at Embark and an associate professor in Biomedical Sciences at the Cornell University College of Veterinary Medicine. Dr. Boyko has coauthored over 60 peer-reviewed scientific papers. He is a member of the Board. (2022, September 8). Dog inbreeding, its consequences, and its quantification: Embark. Embarkvet. Retrieved October 11, 2022, from https://embarkvet.com/resources/oedipus-rex-inbreeding-its-consequences-and-its-quantification/
Harrison, J. (n.d.). A Beginner's Guide to COI. Dog breed health. Retrieved October 11, 2022, from https://www.dogbreedhealth.com/a-beginners-guide-to-coi/
Wright, S. (1922). Coefficients of inbreeding and relationship. The American Naturalist, 56(645), 330–338. https://doi.org/10.1086/279872