By Carol Beuchat PhD
As a breeder, you know the importance of making good pairings to produce healthy offspring. But did you know that two powerful tools - pedigree databases and DNA testing - can take your breeding program to the next level?
Since the advent of commercial DNA testing, there has been a growing but unfounded belief among dog breeders that pedigrees are no longer needed or useful, and that DNA testing is the new "gold standard". This is unfortunate, because nothing could be further from the truth. In fact, pedigree and DNA data used together are the solid foundations on which to build a breeding program designed for sustainable breeding of healthy dogs. Complementing each other, they provide a complete picture to guide your decisions and maintain the quality of your animals for generations to come.
Here, I summarize the key points made in a nice article (Galla et al 2022) that addresses how to use of both pedigrees and DNA data in the genetic management of animals. Although it is written specifically for conservation geneticists, it applies just as well to dogs, and especially to purebred dog breeds that often have limited genetic diversity and relatively small population sizes. You can download a copy of the paper at the bottom.
Since the advent of commercial DNA testing, there has been a growing but unfounded belief among dog breeders that pedigrees are no longer needed or useful, and that DNA testing is the new "gold standard". This is unfortunate, because nothing could be further from the truth. In fact, pedigree and DNA data used together are the solid foundations on which to build a breeding program designed for sustainable breeding of healthy dogs. Complementing each other, they provide a complete picture to guide your decisions and maintain the quality of your animals for generations to come.
Here, I summarize the key points made in a nice article (Galla et al 2022) that addresses how to use of both pedigrees and DNA data in the genetic management of animals. Although it is written specifically for conservation geneticists, it applies just as well to dogs, and especially to purebred dog breeds that often have limited genetic diversity and relatively small population sizes. You can download a copy of the paper at the bottom.
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".
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".
PEDIGREES AND DNA:
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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.
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.
PEDIGREES & DNA:
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Why You Need BOTH Pedigree and DNA Data
Using pedigrees and DNA together creates a powerful toolkit for genetic management. DNA can validate and refine your pedigree information, addressing issues like uncertain parentage. In return, good pedigrees allow for smarter, more targeted DNA testing.
Combining both approaches enables more sophisticated genetic analysis and breeding plans, giving you the fullest picture of your animals' genetic background.
Diagram illustrating the mutual benefits between molecular and pedigree data. (Galla et al 2022).
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".
RECOMMENDATIONS FOR BREEDERS
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Putting It Into Practice
How can you harness these tools in your breeding program?
Here are some key tips:
- Prioritize pedigree maintenance. Start by establishing a reliable system to record and maintain pedigrees. This forms the foundation of your genetic management efforts.
- Supplement with DNA when possible. While DNA testing can be pricier, it provides valuable additional information. Consider testing key breeding animals or using it to resolve uncertainties in your pedigrees.
- Collaborate with experts. Don't hesitate to reach out to conservation geneticists or breed organizations for help interpreting complex data or developing breeding strategies.
- Think long-term. Use the historical perspective from pedigrees to inform breeding decisions that will maintain genetic diversity for generations.
- Learn how to use the tools properly. Take advantage of courses that provide an in-depth understanding instead of relying on random Facebook posts or advice from individuals with no actual training.
- Stay educated. Keep up with advances in genetic management by attending workshops, reading breed publications, networking with other breeders, and following publications in scientific journals.
By leveraging both pedigrees and DNA, you can develop more effective, sustainable breeding strategies. Your efforts play a crucial role in maintaining the genetic heritage and health of your breed for years to come. With these powerful tools at your disposal, you're well-equipped to breed not just for today, but for the future.
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
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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