Inbreeding has been a common practice among dog breeders for centuries. By mating closely related dogs, breeders aim to fix desirable traits within a lineage. However, this intentional inbreeding can have detrimental effects on the health and fitness of the offspring. In this article, we will explore the concept of inbreeding in dogs, the potential problems it can cause, and the methods used to measure the coefficient of inbreeding (COI).
Inbreeding and Genetic Similarity
Like humans, dogs share a high degree of genetic similarity with other members of their species. Approximately 99.8-99.9% of their genome is identical to that of other dogs. However, the 0.1-0.2% variation in their genetic makeup is responsible for the diverse range of traits seen in different dog breeds. Some of these traits, such as coat color and body shape, have been intentionally perpetuated by breeders. However, there are also harmful genetic variations that can negatively impact the health, lifespan, and reproductive success of dogs.
Harmful genetic mutations in dogs can be classified as recessive, dominant, or additive. Dominant and additive mutations are typically weeded out in large outbred populations due to reduced fitness. However, recessive mutations, which often “break” a gene, can go unnoticed in outbred individuals who possess a working copy of the gene from one parent. The real problems arise when inbred individuals inherit two broken copies of the gene, leading to severe consequences.
Risks of Inbreeding
Every dog population, including purebred dog breeds, contains an abundance of rare recessive mutations. These mutations may have been present in a founder individual or have arisen spontaneously in the population. In outbred individuals, these mutations are usually harmless because they almost always inherit at least one working copy of the gene. However, inbred individuals, offspring of closely related parents, face a higher risk of inheriting two copies of harmful recessive mutations.
To illustrate the risks of inbreeding, let’s consider a mother-son mating. A mother passes along 50% of her genome to each pup, including rare recessive mutations with a frequency of less than 1%. Each of these recessive mutations carried by the mother has a 50% chance of being transmitted to a son. Consequently, there is a 25% chance that the son will inherit two copies of the harmful mutation, which is more than a 100-fold risk compared to an outbred dog.
Research conducted by the Boyko Lab has shown that a 10% increase in inbreeding can lead to a 6% reduction in adult size, poor growth, and a six- to ten-month decrease in lifespan. Inbreeding can also result in reduced litter size and fertility. These risks apply to both classical inbreeding and situations where every individual in a small population is a not-so-distant relative. Assessing these risks requires accurately quantifying the likelihood of mutations being inherited from the same ancestor.
Quantifying the Coefficient of Inbreeding (COI)
The coefficient of inbreeding (COI) is a measure of the level of inbreeding within a dog. It quantifies the probability that two alleles at a particular locus are identical by descent, meaning they have been inherited from the same ancestor. There are three methods commonly used to calculate the COI: pedigree-based, marker-based, and genome-wide.
Pedigree-based COI
Pedigree-based COI estimates are based on the relatedness of individuals in a pedigree. The COI values vary depending on the type of mating. For example, a mother-son or full-sibling mating results in a COI of 25%, while a grandparent-grandchild or half-sibling mating leads to a COI of 12.5%. These values accumulate, and the COI of an individual can range from 0% (completely outbred) to 100% (completely inbred).
Ideally, a complete pedigree from the founding of the breed would be available to calculate the COI accurately. However, in reality, pedigrees often only go back 5 to 10 generations. Most COI calculators assume that the original ancestors in the pedigree are unrelated, which can result in a lower COI calculation compared to a pedigree with a complete lineage. Therefore, the completeness of the pedigree affects what is considered a “good” COI. Additionally, the principle of segregation means that individuals with similar expected COIs based on the pedigree can have different levels of inbreeding, depending on which chromosomal segments they inherit.
Marker-based Inbreeding
Marker-based COI estimates rely on a set of polymorphic markers spread across the genome. These markers can be heterozygous or homozygous, and the overall locus heterozygosity (HL) of the marker panel correlates with inbreeding. However, the absolute values of HL depend on the specific markers chosen. Rare markers being homozygous provide stronger evidence of inbreeding than common markers being homozygous.
However, most of the genome is not linked to any marker, making marker-based estimators less effective in detecting most inbreeding tracts. As a result, they are not well-suited for differentiating between individuals with similar COIs. Marker-based estimators may have limited accuracy when the difference in COI between individuals is less than 5-10%.
Genome-wide COI
Genome-wide COI estimation is considered the gold standard for measuring inbreeding. To calculate the genome-wide COI, tens of thousands of markers spread across the genome are required. This method allows the observation of inbreeding tracts, which are tracks of homozygous markers indicating identity by descent. Inbreeding tracts can be detected by observing runs of homozygous markers above a certain size, typically at least 1 centimorgan.
Calculating the COI directly using genome-wide data offers several advantages. It does not rely on a pedigree, marker frequencies, or complicated statistical corrections for rare or common markers. It also allows for direct comparison across studies, regardless of the specific markers used or the populations being studied. Genome-wide data provides a more comprehensive view of inbreeding tracts, which may be missed by pedigree-based or marker-based estimators.
The Importance of Determining Inbreeding Tracts
Accurately determining inbreeding tracts is crucial for identifying recessive disease mutations through a process called homozygosity mapping. By identifying regions of the genome where an individual is homozygous, breeders and researchers can pinpoint potential disease-causing mutations. Additionally, understanding the risks associated with inbreeding within and across breeds can help breeders make informed decisions when selecting mates. While some level of inbreeding is inevitable in most purebred dog breeds, reducing the inbreeding load in a population is a valuable goal to maintain the long-term health and genetic diversity of the breed.
In the next installment of this blog series, we will discuss how Embark, a leading provider of dog DNA tests, helps breeders evaluate potential breeding pairs and contribute to the long-term health of the breeding population. Embark’s comprehensive DNA test provides valuable information about a dog’s breed, health, and COI, allowing breeders to make informed decisions and minimize the risk of inbreeding-related issues.
To find out your dog’s COI and gain important breed and health insights, consider taking Embark’s dog DNA test. Stay tuned for more information on inbreeding and its impact on dog populations in the upcoming articles of this series.
Embark for Breeders dog DNA test kits are available for sale at a discounted price of $129-$159. Take advantage of this opportunity to gain valuable insights into your dog’s genetic makeup and make informed breeding decisions.
Remember, understanding the effects of inbreeding and taking appropriate measures are essential for the long-term health and vitality of our beloved canine companions. Let’s work together to ensure the well-being of future dog generations.