Pedigree vs. Genetic COI in Flatcoats
The Coefficient of Inbreeding (COI) measures an animal’s homozygosity. For most practical purposes, you can think of COI as a measurement of genetic “sameyness” or lack of diversity. We can calculate predicted COIs of prospective matings and we can also aggregate the COI of several individuals to ascertain an average COI for a population. COI is important because it is one indicator of population health, and it is directly correlated with health outcomes - higher COIs / greater homozygosity leads to poorer health outcomes.
Historically, breeders utilized pedigrees to determine COI, along with a formula that considers the number of common ancestors in a pedigree, the number of generations between the common ancestor and the subject dog, and the COI of the common ancestor if known.
The limitations of pedigree COI are immediately apparent - you’re limited to the data in the pedigree and even 10-generation pedigrees fail to incorporate significant events that have an obvious impact on inbreeding rates. In Flatcoats, for example, the breed started with a small number of breed founders then suffered a near extinction when the breed was reduced to ~41 dogs during WWII, both of which pre-date a contemporary 10-generation pedigree. Consequently, dogs can present on paper as being entirely unrelated despite descending from the same handful of ancestors.
Calculating COI with pedigree tracing back to founders is much more accurate, but is prohibitively processor-intensive and will likely contain gaps that impede accuracy and require that assumptions be made. At it’s most accurate, pedigree COI will still fail to differentiate among siblings, whose actual COIs can vary significantly. It is also important to note that, despite the problems inherent in pedigree-based COIs, pedigree databases can still incorporate powerful tools to optimize diversity outcomes in breeding decisions.
Genetic COIs use an individual dog’s genome to determine COI. DNA from a saliva sample is run through a microarray where thousands of individual probes examine different locations on the dog’s genome. This technology has demonstrated reliability and is used extensively for human genetic testing, DNA evidence, and advanced research. If you want to learn more about how this works, here is a video summarizing the process.
Determining genetic COI is a simple genomic analysis whereby the number of matching alleles are tallied and compared against the total number of loci surveyed. This project uses Embark, which examines 230K+ markers and provides COI figures for the breed very similar to those offered by whole genome sequence (WGS) analysis. Any high-resolution SNP profile tool will offer similarly accurate and reliable COIs.
The discrepancy between a Flatcoat’s pedigree and genomic COI is stark and reveals the extraordinary impact of historic bottlenecks on the breed’s population structure. Here are the COI results of a handful of Flatcoats from varied lineages:
Pedigree COI calcuated by FlatcoatData. Genetic COI determined by Embark.
Embark’s average Flatcoat COI is currently 33% and is increasing as more dogs are tested over time. To lend a bit of context, here are some COI benchmarks:
First cousin mating - 6.25%
Grandparent - grandkid mating - 12.5%
Parent-child or full sibling mating - 25%
Full sibling mating over 3 generations - 50%
Target ceiling COI of healthy managed populations - 10%
Three consecutive generations of sibling matings - 50%
As you can see, the homozygosity in Flatcoats has aggregated over time to exceed that of even the closest possible inbreedings, and regardless of how diverse a dog appears on paper.
To learn more about the accuracy and relevance of pedigree, SNP, and WGS COIs in pedigree dogs, this 2016 article by Dreger, et al. provides some illustrative comparative data, while also demonstrating how pedigree COIs can prove beneficial to understanding population architecture precisely because of their inaccuracy.
