Inbreeding coefficient, explained
The inbreeding coefficient, usually written COI, answers one precise question: for a given animal, what is the probability that the two alleles at a randomly chosen spot in the genome are identical by descent, both inherited from the same ancestor through both parents?
Why it matters
Recessive conditions only show up when an animal inherits the risk variant from both sides. The more closely related two parents are, the more likely their offspring carries two copies at any given spot, including the ones that carry recessive disease risk. A higher COI does not guarantee a problem, but it raises the baseline probability across the whole genome at once.
Breeding and conservation programs use COI targets for exactly this reason. It is a single number that captures accumulated relatedness.
Where the number comes from
A COI can be read off the recorded pedigree, by following the shared ancestors that appear on both the sire’s and the dam’s side. With enough genetic data, it can also be estimated directly, which can catch relatedness the written pedigree missed.
A pedigree COI can only count ancestors that are recorded. A shallow or incomplete pedigree can miss older shared ancestry and understate relatedness, so check how many generations are known before relying on a low number.
Either way, the number on its own is not the useful part. In AnimalTrace’s pairing simulator (Client Pro), the shared ancestors behind a COI are shown next to the figure, so you can see why a pairing scores the way it does instead of taking the number on faith.
Reading a COI honestly
A COI is a probability, not a verdict. It belongs alongside recessive-risk screening and the practical goals of a program, not as a single gate. The value is in seeing it before a pairing, with the reasoning attached.
See how AnimalTrace puts COI to work in its breeding checks.
Sources
- Calboli and others, Population structure and inbreeding from pedigree analysis of purebred dogs
- Belanger and others (2025), Measures of homozygosity and relationship to genetic diversity in the Bearded Collie