Embark COI vs UC Davis VGL Haplotype vs Laboklin Heterozygosity of a Golden Retriever

Embark COI vs UC Davis VGL Haplotype vs Laboklin Heterozygosity of a Golden Retriever

The following is the data collected and explained for my Golden Retriever, Red-Dawn Resolute Charlton. He was bred, trained and hunting titled while owned by us, and later sold as a stud dog. Charlton’s is a 5.13% COI in a 12 generation pedigree.

Charlton was tested by three companies for his genetic diversity.

Laboklin in the UK

Embark in the USA

UC Davis VGL in California USA

In addition, Better Bred platform was used to show more details of the UC Davis VGL testing

  • COI = Coefficient of Inbreeding.
    The lower the COI score, the less inbred the dog is.
    The higher the COI score, the more inbred the dog is. 
  • Heterozygosity
    Higher Heterozygosity means the dog is more genetically diverse.
    Lower Heterozygosity means the dog is less genetically diverse. 
  • Haplotype
    The VGL DLA Haplotype test identifies immune system gene patterns, helping breeders pair dogs to maintain genetic diversity. By choosing mates with different haplotypes, breeders can increase  diversity in the puppies. If dogs share haplotypes, diversity decreases.
 

The following is the documentation of each test and details on our findings.

Laboklin Heterozygosity

Laboklin tests the heterozygosity of an individual dog and where he falls in the grouping of his breed. It is not the COI of the dog. Laboklin is not a tool to decide if Dog A & Dog B are a good match or not. For example, Dog A & Dog B could be siblings and both have high heterozygosity themselves… yet their offspring will be highly inbred, and in turn less heterozygous offspring. This tool only helps one to know if the dog tested is either more or less inbred, compared to dogs as a whole and to dogs of his breed. As of July 2025 there are 800 Golden Retrievers & 300 Cavalier King Charles dogs in the Laboklin Heterozygosity testing. That means only a small fraction of dogs for each breed have been evaluated. Also, Laboklin is a European company.

Learn more about Laboklin’s Heterozygosity Testing

Embark Genetic COI

COI = Coefficient of Inbreeding.
The lower the COI score, the less inbred the dog is
The higher the COI score, the more inbred the dog is 

Charlton’s DNA tested genetic COI is 21%
Charlton’s is a 5.13% COI in a 12 generation pedigree

Many hunting line Goldens are 10-25% genetic COI
Many American Show line Goldens are 20-40% genetic COI
Most European Show line Goldens are 25-40% genetic COI

  ** Read more about COI testing vs Pedigree of Goldens in our overview of the data

An outcross of American to European genetics Goldens can reduce the offspring’s COI by half of more of the parent’s high COI. Meaning a 35% COI European dad paired with a 35% COI American mom= 15% COI Puppies
See how we reduce inbreeding on our Red-Dawn Golden Retrievers

Charlton’s DNA tested genetic COI is 21%. His 10 generation pedigree COI is 4.78%

As of July 2025 on Embarks public display there are over 8000 breeding candidate Goldens Retrievers opted in. Embark does not give data on how many total Golden Retrievers are in their full database. 

How Embark Measures COI from DNA

Instead of relying on pedigree records, Embark uses genomic data to directly assess inbreeding. Here’s how:

  1. Genotyping:

    • Embark formerly analyzes over 200,000 genetic markers (SNPs) across each dog’s genome. They changed that to 88,000 markers in 2025.

  2. Runs of Homozygosity (ROH):

    • They look for long stretches of identical DNA inherited from both parents. These are called Runs of Homozygosity (ROH).

    • The longer and more frequent these stretches are, the more inbreeding has occurred.

  3. Calculating COI:

    • COI is calculated as the percentage of the genome that is within these ROH.

    • For example, a COI of 25% means that 25% of the dog’s genome is identical on both the maternal and paternal chromosomes, typically seen in parent-offspring or full-sibling matings. A COI of 25% is commonly seen from generations of line breeding on founder dogs, or overuse of popular sires.

More: Learn about Embark’s COI testing

UC Davis VGL Haplotype Diversity

More details on each part of  Golden Retriever, UC Davis VGL Haplotype diversity testing

Charlton’s Haplotypes

DLA Haplotypes (Immune System Genes)

Charlton has two identical DLA haplotypes:

  • DLA Class I: 1066
  • DLA Class II: 2046

Because both haplotypes are the same, Charlton is homozygous at the DLA region (no diversity there).

This is not dangerous but indicates less immune gene diversity. If breeding, it’s recommended to pair with a dog carrying different DLA haplotypes to increase litter-level immune diversity.

Charlton’s Outlier Index (OI)

  • Charlton has fewer rare alleles and more common ones compared to the average Golden Retriever in the BetterBred database.
  • His OI of 0.20 is slightly lower than the breed average of 0.25, meaning he’s somewhat genetically typical.
  • This does not mean he’s bad genetically—it just means his genetics are more common, which is typical in popular breed lines or those shaped by bottlenecks (like show lines or popular sires).

Best strategy to breed Charlton:

  • Try to pair with a mate who has a higher OI, more rare alleles, or more diversity in their DLA region.
  • This can help increase genetic variety in the litter, which is a goal in sustainable breeding.

OI = 0.20 :  Charlton is slightly below average in genetic uniqueness

Fewer rare alleles: Suggests more typical lineage or common ancestors

More common alleles:  Aligns with well-represented lines in the database

 

Charlton’s AGR = Average Genetic Relatedness to other Golden Retrievers

What is Genetic Relatedness (AGR)?

  • AGR tells you how genetically similar a dog is to others in the breed.
  • It helps identify how many potential mates are genetically different (unrelated)—important for preserving diversity and avoiding inbreeding.
  • Charlton’s AGR score of -0.01 is just above average, meaning he is fairly typical for the breed’s gene pool.
  • 55.5% of Golden Retrievers in the database are genetically unrelated to him, so more than half of the breed could be suitable mates if you’re aiming to preserve diversity.
  • The ideal for breeding is to have a dog with a lower AGR (more unusual genetics), which gives you a larger pool of unrelated mates.

If you’re looking to breed with diversity in mind:

  • Choose a mate who is genetically unrelated to Charlton (from the 55.5% group).
  • Look for dogs with lower AGR and a higher Outlier Index (OI) to maximize genetic spread in the breed.

Charlton’s Internal Relatedness (IR)

This UC Davis Canine Genetic Diversity Analysis for this Golden Retriever, Red-Dawn Resolute Charlton, gives an overview of his genetic diversity and immune system genes (DLA haplotypes).
Here is a breakdown in simple terms: Internal Relatedness (IR): 0.11

  • Shown in the colored bell curve chart (green to red shading)
  • IR measures how genetically similar the dog’s parents were.
  • IR = 0.11 → moderate inbreeding, not extreme but above average.

Charlton’s IR is not alarming, but also not highly diverse. He falls within the average-to-moderate inbreeding range for Golden Retrievers.

The Internal Relatedness (IR) score measures how genetically similar a dog’s parents were. It helps breeders understand the level of inbreeding or outbreeding based on DNA—not just pedigree.

 

Charlton’s Common Genes = Homozygosity by Loci

This table shows the ancestry breakdown of a Golden Retriever based on the UC Davis (BetterBred) diversity testing, comparing it to breed averages. It tells you how “typical” or “unusual” a dog’s genetic background is for the breed. As of July 2025 there are just under 1000 Golden Retrievers in their database. https://vgl.ucdavis.edu/canine-genetic-diversity/golden-retriever/stats

This Golden Retriever “Charlton” has:

  • More typical breed DNA than most Goldens.
  • Less outcrossed/admixture, which could mean a more closed genetic lineage.
  • Slightly below-average diversity in rare/unusual ancestry.
  • Low unusual and admixed ancestry might mean less genetic diversity, which could be important in breeding decisions.
  • High typical ancestry means the dog is genetically representative of the breed—good for preserving breed type, but a concern if everyone is too genetically similar.

 

More details on Haplotype testing on Golden Retrievers

Haplotype limitations

The UC Davis Canine Genetic Diversity Test is a powerful tool, but it does have limitations—especially when applied to a breed like the Golden Retriever. Here’s a breakdown of its key limitations, specific to Goldens:

Limited Scope of the Genome

  • The test analyzes 33 STR markers and DLA haplotypes.
  • These markers cover a very small fraction of the dog’s genome—primarily microsatellites and the immune system region (DLA).
  • It does not give a full picture of overall genetic health or diversity across the entire genome.

Why this matters for Goldens: A Golden Retriever could appear diverse in STR markers but still be highly inbred in other parts of the genome (Embark might show a high COI despite good UC Davis score

DLA focus breeding is limited

  • The DLA (Dog Leukocyte Antigen) system is just one part of immune genetics.
  • Having “diverse” or “rare” DLA haplotypes doesn’t mean a dog is more disease-resistant overall.
  • Conversely, common DLA haplotypes are not necessarily bad.

Many Golden Retrievers share the same DLA haplotypes, so this portion of the test may have limited discriminatory power within the breed.

  • The test’s value depends on the size and diversity of the reference database for Golden Retrievers.
  • If certain lines (field vs. show) are underrepresented, the results may skew toward what is in the database.
  • As of July 2025 just under 1000 Golden Retrievers have been profiled by UC Davis VGL

For Goldens, most DLA haplotypes are already common, so a dog having a “rare” one might just mean less represented, not necessarily better or healthier.

  • The test doesn’t show pedigree-level relationships or actual family history.
  • It can’t identify linebreeding, popular sire effect, or bottlenecks specific to your dog’s line unless you combine it with pedigree analysis or COI DNA testing.

Especially in Golden Retrievers, where many dogs trace back to a few popular sires, this is an important limitation.

Does Not Replace Genetic COI Testing

  • The VGL test does not show genome-wide inbreeding estimate using SNP data across the whole genome relationships or actual family inbreeding.
  • It can’t identify linebreeding, popular sire effect, or bottlenecks specific to your dog’s line unless you combine it with genetic COI analysis.

 6. STR Marker Inheritance Can Be Noisy

  • STR markers mutate more frequently than SNPs.
  • Two dogs might look diverse at STR level but still be closely related.
  • STR-based diversity is less precise than SNP-based genetic testing for estimating COI.

 When It’s Most Useful

  • When combined with SNP-based tests (like Embark) for a full picture.
  • For breeding decisions aimed at improving immune diversity (via DLA haplotypes).
  • For identifying outliers or rare immune lineages within the breed.

Image 7-25-25 at 2.36 PM.jpeg

More details on Embark’s Genome wide SNP testing of inbreeding vs UC Davis Haplotype Diversity Test

For Golden Retriever breeders, using both tests together is ideal:

  • UC Davis haplotype testing tells you how diverse your dog is within the breed, especially for maintaining immune diversity.
  • Embark’s COI helps you avoid pairings that will result in highly inbred litters.

Together, they give a complete picture of genetic diversity and risk, helping you breed for long-term health and sustainability in the breed.

 Haplotype Testing (UC Davis)

What it is:

  • Haplotype testing looks at specific blocks of DNA that are inherited together — called haplotypes.
  • UC Davis, through the Canine Genetic Diversity Project, measures genetic diversity across specific markers (typically 33 STR loci) in the DLA (dog leukocyte antigen) region and elsewhere in the genome.

What it tells you:

  • How genetically diverse a dog is within the breed.
  • Whether two dogs have similar or different immune system haplotypes (especially in the DLA region, important for immune function).
  • Whether a dog’s genetics are underrepresented or overrepresented in the breed.

Why it’s useful:

  • Helps breeders avoid bottlenecks by choosing mates that increase genetic diversity.
  • Highlights unique or rare haplotypes worth preserving.
  • It’s breed-specific, and tailored to Golden Retrievers at UC Davis.

Golden Retriever diversity testing at UC Davis

COI (Embark)

What it is:

  • COI stands for Coefficient of Inbreeding.
  • Embark calculates COI using runs of homozygosity (ROH) across the dog’s entire genome — this is called a genomic COI.

What it tells you:

  • The percentage of the genome that is identical on both the maternal and paternal sides — basically how inbred the dog is.
  • A higher COI means more inbreeding, which can increase the risk of genetic diseases or reduced fertility.
  • Embark gives a  genome-wide COI percentage and compares it to breed averages.

Why it’s useful:

  • Helps breeders choose mates that lower COI in offspring.
  • Tracks how inbred individual dogs are, even beyond pedigree-based estimates.
  • Useful for spotting genetic health risks tied to inbreeding.

Learn about COI testing at Embark