| As a breeder, you know how important it is to create good matings 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 necessary or useful and that DNA testing is the new “gold standard” that will replace the pedigree certificate. This is unfortunate, because nothing could be further from the truth. In fact, pedigree and DNA data used together are the solid foundation upon which to build a breeding program designed for the sustainable breeding of healthy dogs, and by complementing each other, they provide a complete framework to guide your decisions and maintain the quality of your animals for generations to come. Here, we summarize the key points raised in a great paper (Galla et al 2022) that addresses how to use both pedigrees and DNA data in animal genetic management. Although written specifically for conservation geneticists, it applies equally well to dogs, and particularly 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: The Foundation of Your Breeding Program A pedigree is a family tree that shows the ancestry of an individual animal. Although pedigrees may seem antiquated in the age of DNA testing, they remain incredibly valuable to breeders. There is a wealth of genetic and demographic information hidden in a basic pedigree that can provide invaluable insight into the history and development of a breed. Of course, to keep up with the times, relying on cutting-edge associations like the WDF World Dog Federation is essential as it was the first in the world to merge technology and experience in compiling the pedigree by creating the ED Card, a completely digital Pedigree designed for an accurate view of the certificate that you can always carry with you.  Why should you use pedigrees for genetic information? First, pedigrees are convenient and accessible. All you need is a reliable system to record parentage and track generations, and you can do that with a Kennel Club that is a member of the WDF World Dog Federation. Second, pedigrees give you a long-term view of the history of your breeding stock. Pedigrees allow you to track changes in population size and breeding practices over the history of the breed, can reveal how and why inbreeding and genetic diversity have changed over time, identify important bloodlines at risk of extinction, and explore patterns in genetic traits and disorders across generations. Perhaps most importantly, pedigrees allow you to calculate key genetic information such as a dog’s inbreeding coefficient or the expected level of inbreeding for a litter produced by any pair of dogs. This guides intelligent breeding decisions to avoid inbreeding and maintain genetic diversity. 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 changed over generations. Pedigree information can also be used to model the consequences of particular breeding strategies (for example, how breeding two puppies versus one from a litter would change the genetics of the breed) and how the number of males used in a breeding program would change the rate of inbreeding.  If you notice a classic five-generation paper pedigree can only tell you about the inbreeding that occurred in those five generations, while a 10-generation pedigree only documents the inbreeding that occurred in those generations (and the assumption that the animals in the first generation are not related and not inbreeding). Short pedigrees underestimate the true level of inbreeding, but the information can still be useful if you are specifically interested in recent inbreeding. What about missing data or errors in pedigree databases? Many federations and associations do not give due importance to the data collected within the studbooks and in the passage between countries much of this data is lost or omitted voluntarily out of laziness. Most pedigree problems will result in an underestimation of the actual COI, so if your calculated COI is 27%, you can assume it is at least that high, which is usually all you need to know (i.e. yes, the COI is too high). Multiple generations of (complete, error-free) pedigree data will produce better estimates of the actual COI. Because pedigree errors are relatively common, techniques have been developed that can verify pedigree relationships using the data, even for deep pedigree errors, and statistical relationship estimates can be used when parents are missing. Of course, the best option is to keep records that communicate between Kennel Clubs that always carry the correct and complete data, and this has been developed in the WDF thanks to a database system created just for this purpose, this innovative system has assimilated Artificial Intelligence management within it with over 472 Algorithms that keep watch with rules for every eventuality. A word of caution: Pedigrees can provide a wealth of information that you can’t get any other way. But you need to understand the data to use it properly. The coefficient of inbreeding (COI) is probably the most commonly used statistic calculated from pedigree data, but too many breeders don’t understand how it’s calculated or what it means. Basically, the COI estimates the inbreeding that would occur when a particular dog occurs on both sides of the pedigree. Of course, it can’t do this correctly if your pedigree doesn’t include the generations in which that ancestor occurs. Most dogs are founded on a small number of animals. Since inbreeding likely occurred in the first few generations, it’s critical that your pedigree be deep enough to include those matings. The calculations assume that the dogs in the first generation of the pedigree are unrelated and non-related, which is probably not true in many cases. Therefore, the calculated COI estimates the amount of inbreeding that has occurred from the first documented generation (whose parents are unknown) to the present day. PEDIGREE AND DNA, ADVANTAGES AND DISADVANTAGES Key advantages of pedigrees: Provide historical perspective on population structure and genetic history Allow calculation of important genetic parameters (e.g. inbreeding coefficients) Guide breeding decisions to minimize inbreeding and maintain diversity Track loss of founder alleles over time Can provide similar estimates of relatedness to thousands of genetic markers when complete and accurate Key advantages of DNA analysis: Can provide more precise estimates of relatedness and inbreeding Reveals information about specific genes or traits of interest Clarifies small-scale genetic differences within a population Can address pedigree pitfalls such as founder relatedness and missing data Advantages of combining pedigrees and DNA data: DNA can validate and refine pedigree information Pedigrees enable more strategic DNA sampling and analysis Enables genetic studies and more sophisticated breeding plans Provides a more complete picture of the genetic health of the population DNA Testing: A Powerful Complement to Pedigrees While pedigrees are the foundation of a genetic management program, DNA testing offers some unique advantages.  DNA can reveal subtle genetic differences within a 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 parentage and inbreeding. DNA data can provide parentage estimates that identify dogs in a group that are genetically “more valuable” because they have low relatedness or genetic uniqueness compared to others. DNA trait and mutation tests can reveal the frequencies and distributions of genes in a population, as well as the frequencies and distributions of homozygous and heterozygous genotypes. Because DNA can be used to compare single markers between individuals, it can be used to locate populations of animals that are highly likely to produce a particular trait or disease, without having to identify the genes involved. DNA is also useful for identifying subpopulations of a breed that have diverged genetically, using techniques such as kinship coefficient cluster analysis or principal component analysis. One disadvantage of relying on DNA data for parentage information is that you must be able to obtain a tissue sample for analysis. For dog breeders, this could be a problem if, for example, you might be interested in breeding a dog for which you do not have access to a tissue sample. Or perhaps there is a frozen semen sample you want to use but you want to estimate the inbreeding of the potential litter produced. Genotyping a semen sample may not be possible, but a pedigree database could provide the information you need. Of course, while DNA genotyping has dramatically decreased in cost over the past decade, it can still be prohibitively expensive in some situations. This is why many states have introduced a requirement for biological samples to be deposited at the time of registration to accommodate this issue so that the biological sample is always available for DNA extraction. Italy, with the Kennel Club ICBD, has been a pioneer and promoter of this battle.  PEDIGREE AND DNA, MYTHS AND MISINFORMATION Myths about Pedigrees Pedigrees are outdated Pedigrees cannot provide good estimates of COI Myths about DNA Testing You don’t need pedigrees if you do DNA testing DNA testing can rule out genetic disorders in dogs DNA “health tests” tell you about a dog’s health, not the dog’s pedigree history. Why You Need BOTH Pedigree and DNA Data? Using pedigree and DNA together creates a powerful genetic management toolkit. DNA can validate and refine your pedigree information, addressing issues such as uncertain parentage. In turn, good pedigrees enable smarter, more targeted DNA testing.  Combining both approaches allows for more sophisticated genetic analysis and breeding plans, giving you the most complete picture of your animals’ genetic background. The combination of pedigree and DNA information can be used to determine the genetic status of a breed and whether a breeding program is needed to restore genetic diversity. This could be done by using existing breed diversity, but in most purebred dogs there is little diversity to work with and the most effective and efficient solution is to crossbreed with dogs that carry the necessary diversity. Getting the most out of the available data requires skill and experience, so breeders should work with a conservation or population genetics expert to assist in developing a breeding strategy that will be effective. The Lundehund Genetic Rescue Project is a good example of a program developed by biologists who are experts in the best strategies to achieve the goal of restoring the breed’s genetic diversity while maintaining its unique physical and behavioral characteristics (Melis et al. 2022). There is one important situation where you need both pedigree information and DNA. Let’s say a few dogs have appeared in multiple kennels with green noses. Could it be due to diet? Or is it genetics? Breeders are usually quick to suspect genetics and start a research study to look for the gene. But many things are influenced by both genes and nongenetic factors (e.g., environment), and some things may be entirely the result of a nongenetic factor. Before starting a research study, you should determine the heritability of the problem in question. Heritability is a statistic that tells you how much of the variation in a trait can be attributed to genetic variation in the genetics and how much is due to nongenetic factors. If the heritability of a problem is very low, you should carefully look for possible nongenetic factors that may be involved. For example, an undetected nutritional deficiency could cause a health problem, hair loss could be a behavioral problem, or raising puppies on newspaper could increase the risk of hip dysplasia. With your pedigree data and knowledge of the animals involved, 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 may be useful as a DNA test. The benefits of using both pedigree and DNA records 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 ongoing study. RECOMMENDATIONS FOR BREEDERS Prioritize continuous registration in studbooks and Supplement with DNA testing when possible Collaborate with conservation genetics experts for analysis Use pedigree data to inform long-term breeding strategies Stay informed about advances in genetic management techniques. |