In this video from the 2022 Embark Canine Health Summit, Embark Veterinary’s Senior Scientist I Samantha Hauser, PhD explains how Embark can measure and quantify inbreeding as the genetic coefficient of inbreeding (COI), the consequences of inbreeding on dog’s health and lifespan, and how breeders can leverage COI to make the best breeding decisions for your dogs and your breed.
The Embark for Breeders dog DNA test includes a COI score that breeders can consider when planning their next litter.
What is inbreeding? How do we measure inbreeding at Embark?
Inbreeding is the production of offspring from the mating of genetically related individuals. Pedigrees have historically been used to estimate the coefficient of inbreeding. Pedigree COI is based on predicted DNA inheritance, such as a dog sharing on average 50% of DNA from each parent. In contrast, Embark can measure genetic COI with runs of homozygosity (ROH), which are stretches of a chromosome where both copies of an individual’s DNA (maternal and paternal) are identical by descent (IBD).
How do pedigree COI and genetic COI differ? Why is genetic COI valuable?
Pedigree-based COI is a probability and does not account for specific genetic recombination events within a dog’s pedigree or ROH. When you measure pedigree COI, all littermates appear equal and it does not take into account recombination or inbreeding. Pedigrees become more inaccurate as inbreeding increases.
Pedigrees can be incomplete or have errors, which can lead to large under-estimation of COI. Genetic COI becomes more valuable to a breeder when considering breeding pairs because it is a direct measure of realized inbreeding.
How is COI distributed across different breeds?
There is variation both within a breed and across breeds for COI. The Doberman Pinscher, for example, can have a genetic COI anywhere from 25% to 60% in individual dogs with a median of 40% across the breed, whereas Siberian Huskies or Poodles can have a median COI of 20%.
There is also variation when inbreeding occurs within a breed’s history. ROHs are broken up into smaller segments over time or generations due to recombination or the shuffling of DNA. Longer segments of ROH reflect more recent inbreeding in a breed and shorter segments reflect older inbreeding, going back more generations.
The Doberman Pinscher accrued most of its inbreeding in the last century, while the Bulldog’s inbreeding occurred in the 1830s when bull baiting was banned and a dramatic decrease in demand for the dog occurred. As a result, the breed went through a severe bottleneck thus reducing genetic diversity.
What is the link between COI and dog health?
Historical inbreeding via strong artificial selection during breed formation has led to the increased frequency of deleterious or harmful variants in many dog breeds. For example, breeding for a Bulldog’s brachycephalic head or a Poodle’s furnishings may have also created unintended consequences for canine health. This happens when genetic material near a chromosome used to select a trait also contains a deleterious variant for a health condition. Dalmatians and HUU (Urate kidney and bladder stones) are a prime example where selecting the gene for spotting, also selected for HUU inadvertently.
Inbreeding depression is the reduced survival and fertility of the offspring of related individuals. This happens when we have deleterious genes that underlie complex traits. We can correlate COI on expected litter size for example. Embark found, in collaboration with the Golden Retriever lifetime study at the Morris Animal Foundation, for every 10% increase in COI there was one less puppy per litter.
The Embark study also found that higher COIs mean shorter lifespans, up to two years, and that dogs were more likely to be diagnosed with a range of complex diseases. Inbreeding is a significant predictor of longevity, overall health, and likelihood of being diagnosed with a range of complex diseases.
What can breeders do to reduce inbreeding?
A simulation study by Embark found that genetic diversity is only preserved where measured. Microsatellite panels only cover 5% of the genome, so genome-wide genetic panels are necessary to preserve genetic diversity across the entire genome in a breeding program.
Can loss of genetic diversity be slowed by minimizing inbreeding in individual dogs?
Based on conservation genetics theory and practice, there are two rules of thumb breeders can follow: Breed pairs with the lowest expected COI to avoid unnecessary inbreeding, and breed as many different pairs as you can to avoid the popular sire effect.
Embark can assist breeders with the Pair Predictor tool located in the breeder dashboard. A breeder can select two Embark-tested dogs and it will provide the expected COI for that match. It compares potential sires and lets the breeder choose the sire with the lowest expected COI. Pair Predictor also assesses predicted health condition risks.
Breeders are the future of their breeds. They can contribute to a healthy breed population by avoiding unnecessary inbreeding, testing for health conditions, and keeping as many breeding animals of both sexes in the gene pool as possible.
An Embark for Breeders kit contains the most comprehensive DNA test using 230,000 genetic markers to test for 250+ health conditions, 35+ traits, and COI, in addition to breeding tools and services, including free genetic results counseling, to help breeders make the best decisions.
Read more about COI and canine health in Measuring Inbreeding and How Genetic COI Can Help Your Breeding Program and Inbreeding Depression and Reduced Fecundity in Golden Retrievers.