3) How should you think about traits?
Your focus in a crossbreeding program should be on genetic diversity, not specific traits.

Why? Because trait selection requires genetic diversity. You can’t select for particular traits if the necessary alleles aren’t present. By introducing new diversity, you are building the genetic foundation needed to re-establish breed traits later.

Also, keep in mind that genetic health is more than just managing disease mutations. Many traits, including immune system function and adaptability, rely on complex genetic interactions. Focusing too soon on specific physical traits can limit genetic progress and reduce the overall health benefits of crossbreeding.

Remember that for polygenic traits, F1 puppies will get a random collection of only half the alleles of the parent used in the cross. It’s unlikely that a puppy will inherit all of the variants involved in a complex trait. Again, focus on capturing maximum genetic diversity, then you can use focused selective breeding to shape traits with the most diverse genetic pantry possible.  

4) What about genetic disorders?
Every animal carries recessive mutations, but these typically do not cause disease as long as the locus remains heterozygous (i.e., one normal allele is present). Recessive mutations become a problem as a result of inbreeding, which produces homozygosity. The key to good physical health is low inbreeding is supported by high genetic diversity. 

Trying to reduce genetic health disorders by eliminating recessive mutations from the gene pool is difficult (you need to find every last recessive mutation) as well as genetically destructive, because selection against mutations will work against your goal of protecting genetic diversity.

A more effective approach is to:

✔ Focus on maximizing genetic diversity and avoiding inbreeding to reduce the risk of harmful mutations becoming homozygous
✔ Recognize that many disorders are complex or polygenic, meaning we don’t always know which genes are involved
✔ Avoid extreme selection pressure that could narrow the gene pool further

The safest way to minimize risk from inherited disorders is to restore a healthy genetic foundation first.

5) How should backcrossing be handled?
Restoring breed type after a crossbreed introduction often involves backcrossing, but this must be done carefully to avoid losing the diversity you worked to gain.

Let’s look at what happens genetically with each backcross:
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• First-generation (F1) cross: 50% breed A / 50% breed B
• First backcross (A x F1): 75% A / 25% B
• Second backcross (A x 75/25): 87% A / 13% B
• Third backcross (A x 87/13): 93% A / 7% B

As you can see, each backcross reduces the genetic contribution of breed B by half. If you do serial backcrosses, you will eventually lose most of the new diversity, putting the population right back where it started.

Instead, to retain diversity while restoring breed type, use a structured breeding plan that:

✔ Uses multiple unrelated outcross dogs
✔ Balances careful selection with genetic management tools like DNA testing
✔ Prioritizes diversity early on, before selecting too heavily for traits

This is where expert guidance and genetic testing tools can make a critical difference in the long-term success of a crossbreeding program.

Crossbreeding is a Tool, Not a Threat
At some point, every purebred breed will need to take steps to manage inbreeding and restore lost genetic diversity through cross breeding. This is because animal populations in closed gene pools become more and more inbred over time and eventually go extinct due to inbreeding depression that reduces fertility and lifespan  and a high burden of health problem.

As shown above, returning to breed type can be fast and easy, taking as few as three generaetions. But the real challenge is restoring type while keeping genetic diversity intact. Livestock breeders have been successfully using structured crossbreeding strategies for decades, often without access to the molecular tools now available to dog breeders.

For those concerned about potential changes to the breed and its gene pool from crossbreeding, note that the gene pool of your breed is not static now. It changs as a result of inbreeding because:

• Every generation of inbreeding increases homozygosity, changing the composition of the gene pool
• Every generation, alleles are lost through genetic drift, also changing the composition of the gene pool

Crossbreeding does not threaten breed preservation. In fact, crossbreeding is one of the most powerful tools available to protect a breed’s genetic health and long-term viability. Skilled breeders should use crossbreeding strategically with other breeding strategies like outcrossing and inbreeding to maintain breed quality while ensuring genetic health. 

Crossbreeding, when done correctly, should be viewed not as a last resort, but as a valuable strategy for breed preservation and health.

Pedigrees: Your Breeding Program's Foundation

A pedigree is a family tree showing the ancestry of an individual animal. While pedigrees may seem old-fashioned in the age of DNA testing, they remain incredibly valuable for breeders. There is a wealth of genetic and demographic information hidden in a basic pedigree that can provide invaluable insight into a breed's history and development. For a good example, have a look at this analysis of the genetic history of the Afghan hound that I put together for their World Congress a few years ago. This is wonderful information and should be available for every dog breed!

Why should you use pedigrees for genetic information?

First, pedigrees are cost-effective and accessible. All you need is a system to record parentage and keep track of generations, and there is inexpensive software available to do this. Second, pedigrees give you a long-term view of your breeding stock's history. Pedigrees allow you to chart the changes in population size and breeding practices over the history of the breed, they can reveal how and why inbreeding and genetic diversity has changed over time, identify important bloodlines at risk of extinction, and explore the patterns in genetic traits and disorders across generations. 

​Perhaps most importantly, pedigrees let you calculate key genetic information like the inbreeding coefficient of a dog or the predicted level of inbreeding for a litter produced by any pair of dogs. This guides smart breeding decisions to avoid inbreeding and maintain genetic diversity. The pedigree data can also establish the original and current size of the gene pool, the contributions of founder dogs and other ancestors to the gene pool, and how the level of inbreeding has been changing over the generations. The pedigree information can also be used to model the consequences of particular breeding strategies (e.g., how would breeding two versus only one puppy from a litter change the genetics of the breed), and how the number of males used in a breeding program would change the rate of inbreeding.

Note that a five generation pedigree can only tell you about inbreeding that occurred over those five generations, and a 10 generation pedigree documents only the inbreeding that occurred over those generations (and the assumption that the first generation animals are unrelated and not inbred). Short pedigrees will underestimate the true level of inbreeding but the information can nevertheless be useful if you are interested specifically in recent inbreeding.

What about missing data or errors in pedigree databases? Most pedigree problems will result in an underestimate of actual COI, so if your calculated COI is 27%, you can assume that it is at least that high, which is usually all you need to know (i.e., yes, the COI is too high). More generations of data (complete, error-free) in the pedigree will produce better the estimates of true COI. Because pedigree errors are relatively common, techniques have been developed that can verify pedigree relationships using data, even for errors deep in the pedigree, and statistical estimates of relationship can be used when parents are missing. Of course, the best option is to keep good pedigree records (and remember, every registered dog has a pedigree filed with the kennel club of registration), but pedigrees can still be extremely useful if not essential even with limitations from less than perfect data.

A caveat: Pedigrees can provide a wealth of information that you cannot get any other way. But you must understand the data to use it properly. The coefficient of inbreeding (COI) is probably the most frequently used statistic computed from pedigree data, but too many breeders do not understand how it is computed or what it means. Most fundamentally, COI estimates the inbreeding that would occur when a particular dog occurs on both sides of the pedigree. Obviously, it cannot do this correctly if your pedigree does not include the generations where that ancestor occurs. Most dogs were founded on a small number of animals. Because inbreeding likely occurred in the early generations, it is critical that the pedigree is deep enough to include those matings. The calculations assume that the dogs in the first generation of the pedigree are unrelated and not inbred, which is probably not true in many cases. Therefore, the calculated COI estimates the amount of inbreeding that occurred from the first documented generation (which has unknown parents) to the present. 

You can learn more about COI in ICB's FREE online course, "COI Bootcamp". 

DNA Testing: A Powerful Complement to Pedigrees

While pedigrees are the foundation of a genetic management program, DNA testing offers some unique benefits.

DNA can reveal subtle genetic differences within your population that may not be apparent from pedigrees alone. Genotypes obtained from high density panels of SNPs (single nucleotide polymorphisms) provide very precise estimates of relatedness and inbreeding. DNA data can provide estimates of kinship that identify the dogs in a group that are genetically "most valuable" because they have low relatedness or genetic uniqueness compared to others. 

DNA trait and mutation testing can reveal frequencies and distributions of genes in a population, as well as frequencies and distribution of homozygous and heterozygous genotypes. Because DNA can be used to compare individual markers across individuals, it can be used to localize the populations of animals that are at high probability of producing a particular trait or disease, without needing to identify the genes involved. DNA is also useful to identify subpopulations of a breed that have drifted apart genetically using techniques like cluster analysis of kinship coefficients or principal components analysis.

A disadvantage of relying on DNA data for information about relatedness is that you must be able to get a tissue sample for analysis. For dog breeders, this could be a problem if, for example, you might be interested in breeding to a dog that you don't have access to for a tissue sample. Or perhaps there is a sample of frozen semen that you wish to use but you want to estimate the inbreeding of the potential litter produced. Genotyping a semen sample might not be possible, but a pedigree database could provide the information you need. Of course, while DNA genotyping has dropped dramatically in cost over the last decade, it can still be cost-prohibitive in some situations. Maintaining a pedigree database can be done with readily available software and some time for regular data entry.

The combination of pedigree and DNA information can be used to determine the genetic status of a breed and whether a breeding program to restore genetic diversity is necessary. This could be through making use of existing diversity in the breed, but in most purebred dogs there is little diversity to work with and the most effective and efficient solution is cross breeding to dogs that carry the needed diversity. Getting the most from the available data requires skill and experience, so breeders should connect with an expert in conservation or population genetics to assist in the development of a breeding strategy that will be effective. The Lundehund genetic rescue project is a good example of a program developed by biologists familiar with the best strategies to achieve the goal of restoring the genetic diversity of the breed while retaining its unique physical and behavioral features (Melis et al. 2022).

There is an important situation when you need both pedigree and DNA information. Let's say a few dogs have appeared in multiple kennels with green noses. Could this be due to diet? Or is it genetic? Breeders are usually quick to suspect genetics and launch a research study to look for the gene. But many things are influenced by both genes and non-genetic (i.e., environmental) factors, and some things might be entirely the result of some non-genetic factor.

Before you launch a research study, you should determine the heritability of the issue in question. Heritability is a statistic that tells you how much of the variation in a trait can be attributed to genetic variation in genetics and how much is due to non-genetic factors. If the heritability of an issue is very low, you need to look carefully for possible non-genetic factors that might be involved. For instance, an undetected nutritional deficiency might be causing a health problem, or hair loss could be a behavioral issue, or raising puppies on newspaper could be increasing the risk of hip dysplasia.

And the critical thing here is that you need a pedigree database in order to calculate heritability, because it accounts for the pedigree relatedness of the animals with and without the trait. With the pedigree data and knowledge of the affected animals, you can determine whether you should be looking for genes or an environmental factor. If the heritability estimate is high and you have DNA genotype data, you can look for a causative or predictive gene that might be useful as a DNA test.

The advantages of maintaining records of both pedigree relationships and DNA are significant, and the value of the information they can provide together when used to estimate heritability should justify the time and expense of maintaining both. 

You can learn more about how to use both pedigree and DNA data to assess the genetic status of your breed and plan a breeding program to reduce inbreeding and improve genetic diversity in ICB's new online course, "ICB Genetic Rescue: the Genetics of Cross Breeding".

REFERENCES

Galla SJ et al. 2021. The relevance of pedigrees in the conservation genomics era. Molecular Ecology 31:41-54.
https://onlinelibrary.wiley.com/doi/epdf/10.1111/mec.16192

Melis et al. 2022 ​Genetic Rescue of the Highly Inbred Norwegian Lundehund. Genes 13:163. https://doi.org/10.3390/ genes13010163

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