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Breeding for health in pedigreed dogs Wageningen University in the Netherlands has completed an interesting project ‘Breeding for health in pedigreed dogs’. An excerpt from the project page: The “Science shop” of Wageningen University has set up this project in response to questions from three breeding organisations, with the aim to provide knowledge on how to better breed for healthy dogs and use the latest insights from scientific developments. Next to dealing with health problems, genetic management to preserve genetic diversity and prevent high inbreeding rates is essential. A high inbreeding rate caused by using too few and too related dogs in breeding will harm the health of the dogs. Consequently, excluding too many dogs for health reasons will restrict the genetic pool and may cause a too high rate of inbreeding with subsequent health problems. A balance between breeding for health and restricting inbreeding must be found. This has led to the central question of this research: How to set up breeding for healthy pedigreed dogs? A healthy dog is the aim both of dog owners, breeding organisations and society in general. In this report 4 questions are treated: How to deal with a multitude of hereditary health problems in a breed? Can breeding value estimation help to reduce health problems in dogs and how to design it? What is the value of DNA genotyping for estimation of kinships and inbreeding and thereby improving the health of dogs? When and how to set up an outcross, and what does it contribute to the health of the dogs? Tackling health problems is not easy, because the problems are complex and knowledge of genetics is often scarce. Although the task ahead is considerable, there are clear starting points. To manage inbreeding rates the use of mean kinships is most effective and recommended. Additional to that, this report provides specific recommendations on how to deal with the four subjects mentioned above. The project has produced four publications: a full report on the project (in Dutch) by Rita Hoving and Jack Windig, downloadable from the project page (link below) an e-book ‘Het fokken van rashonden - Omgaan met verwantschap en inteelt’ (Breeding of pedigree dogs: dealing with kinship and inbreeding) by Kor Oldenbroek and Jack Windig. The book was developed as part of the Kinship Project, which is an initiative of the IPFD partner Raad van Beheer, together with the Dutch Ministry of Economic Affairs, Agriculture and Innovation. The Kinship Project is part of the Raad van Beheer's sustainable breeding policy: Towards the healthy purebred dog. a paper in the proceedings of the 12th World Congress on Genetics Applied to Livestock Production (WCGALP) 2023 by Windig, Margarita and Doekes: Inbreeding and litter size in Dutch pedigreed dogs a poster at the 7th International Conference of Quantitative Genetics (2024) by Jack Windig and Rita Hoving: 'How to genetically manage inbred populations with a multitude of genetic diseases?’ A pdf of the poster can be downloaded from the project page at the link below. Read more about the project here >> Breeding wisely - Infographics on inbreeding To facilitate all levels of the animal breeding sector, the Centre for Genetic resources, the Netherlands (CGN) at the Wageningen University & Research has developed three infographics to explain the concept of inbreeding, its consequences and how to deal with it. The infographics are aimed specifically at owners and breeding organisations. The infographics have been translated into English in cooperation with the European Regional Focal Point for Animal Genetic Resources (ERFP) network. In 2024, in collaboration with the European Reference Centre for Endangered Animal Breeds (EURC-EAB), the infographics have been translated into French. Futher translations into other languages will follow. You can read more and download the infographics here >>
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The Downside of Inbreeding - It’s Time For a New Approach by C.A. Sharp First published in Double Helix Network News, Winter 1999 I am pulling together a presentation for the Embrark Canine Health Summit and came across an article I have cited before... an oldie but a goldie! This article is by the very knowledgeable C.A. Sharp, expert and person behind ASGHI (Australian Shepherd Genetics and Health Institute) and one of our collaborating partners. Good news - she gives a great coverage of this important topic. Of concern - this was written in 1999 and it is still a hot topic today. READ it here: https://www.ashgi.org/home-page/genetics-info/breeding/breeding-genetic-diversity/the-downside-of-inbreeding Embark has been regularly publishing Coeffiecients of Inbreeding (COI's) on genetic samples from various breeds on its Embark for Breeders facebook page. These are genomic NOT pedigree based COIs (learn about the difference here) and understandably but unfortunately we do not know how many dogs were included in the calculations. Presumably it is an international sample. Notwithstanding this limitation, these are useful to consider. Firstly, remember that a brother-sister mating results in a COI of 25%. That is inbreeding. Look at these values from Embark, as examples. Both the German Shepherd Dog and the Bulldog have average COIs above that level... meaning that many of the dogs have values that are higher still. On average, dogs with a COI >25% share more genetic material from common ancestors than would arise from a brother-sister mating. Results for the Cattle Dog and the Husky below show lower values for COIs. Not surprisingly, perhaps, given a focus on performance in these breeds? Protecting the future of your breed depends on Genetic Diversity. Make sure you understand how breeding practices like line-breeding result in reduced diversity and over time may create health problems like poor reproductive capacity, lowered longevity and more. Other reading: Linebreeding vs. Inbreeding – Let’s be perfectly clear.
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The idea for this post came during the discussions around our virtual International Dog Health Workshop on genetic diversity in May (see Ian Seath's great article about the workshop). We were discussing what kind of population statistics would breeders and breed clubs need, in order to take care of their breed population in a best possible way. I spoke to the group about the tools in the Finnish Kennel Club's breeding database, which elicited enthusiastic reactions. The Finnish Kennel Club (FKC), as well as other Nordic kennel clubs, is well-advanced in analyzing data and making it available to breeders and breed clubs. Let’s make a short tour on the FKC breeding database and see what specific tools there are for breed-level genetic diversity. The FKC advises to: avoid inbreeding especially in the first 5 generations (fast inbreeding) or keep this inbreeding coefficient (COI) below the breed average find individuals with rare alleles for breeding, and use as many dogs for breeding as possible, with as even number of offspring as possible. Regarding the advise No 1. - calculating the COI for planned litters is possible using 4-8 generations data: It gives you the pedigree and this info: Regarding the advise No 2. - no mean kinships etc are available, so there's clear need for either pedigree-based or genetic tools for that. But males which not yet have registered progeny you can indeed find in the database, using different search criteria: Regarding the advise No 3. - you can follow the numbers of litters and offspring per males and also per females: Here the cumulative % is very useful, you can see that 10 males accounted for 29 % of all puppies registered during the chosen time period (now 2017-2022). Gipstern Ifender accounted for 4.46 % of puppies during that period. The columns 'Total' are all puppies, also those born outside the chosen period. You can also rearrange this statistics by clicking on the underlined titles. At that point the cumulative % doesn't make sense anymore. And you can click on the name of the dog, which brings you to the page where you can see the pedigree of the dog and the results of health and temperament tests, trials and shows, as well as Estimated breeding values and the list of siblings and offspring. For monitoring, there are statistics by year and by generation (4 years): breeds' average COI ('Inbreeding' - this is calculated with as deep pedigrees as the data for each dog allows, but usually not reaching to the founders) N of different sires, dams and grandparents ratio of sires/dams a figure describing the use of popular sires. If this is 1, there are no popular sires, as the use of males is as variable as possible. this breed is Hovawart, which is famous for its' good breeding practices, but there are breeds where this figure is as low as 0.30. effective population size (should be calculated per generation, so the per year -figure doesn't tell you the right thing. Hopefully removed from the next version of the database.) % of dogs used for breeding note that Hovawarts are not used at a young age so the percents are low here - they are going to grow in the future for these age classes. And the good news is that most breeders / breed clubs know what to do with all this info. The FKC has a template for breed-specific breeding strategies (first version was developed in the beginning of 2000s) and has updated it a few times since then. The template walks you through on which information to include in the strategy and how to 'translate' it. See the sections 4.1, 6.2 and 6.3: https://www.kennelliitto.fi/en/forms/breeding-strategy-jto-template-breeds-large-populations. Thanks for reading! In case you have questions, or want to share information on your own kennel club or breed club, please feel free to contact us at [email protected]. Read also my other blog post on how the FKC is promoting open studbooks and other important genetic diversity tools:
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"Genetic Rescue of the Highly Inbred Norwegian Lundehund" - New Research
Brenda Bonnett posted a blog entry in New Research
Genetic Rescue of the Highly Inbred Norwegian Lundehund ... is a new paper about attempts to 'save' the Lundehund breed and is a good reference for anyone working with a rare breed. This Lundehund was reduced from a relatively rare one to one with such low genetic diversity that its survival was doubtful. Under these conditions, outcrossing to other breeds offered the one possibility. This paper shows some success, but, not surprisingly, researchers found that crossing the first generation back to the Lundehund reduced the genetic diversity of outcrosses. Outcrossing programs have been utilized for other breeds in Finland, with a carefully planned program, with some success (see links below). Breeders must be willing to make some tough decisions in these cases and have the patience to 'do it right' if they wanted to save these rare and endangered breeds. The conclusions of the Lundehund paper are: "This study clearly documents the beneficial genetic effect of outcrossing a highly inbred dog population. It also documents that backcrossing the F1 generation to the parental population results in a loss of some of the desired heterozygosity achieved in the initial outcross. To preserve the characteristics of the Lundehund, the F2 dogs were made by crossing the F1 with the Lundehund and not with other F2 dogs from different lineages." ... "Thus, stakeholders in the program and in future genetic rescue projects can use this data in combination with health data for the F1 and F2 animals to evaluate the effectiveness of the genetic rescue program so far. Our results indicate that additional crossbreeding would extend and augment the genetic rescue process." ... PAPER: Lundehund genetic rescue.pdf LINKS: Crossbreeding in Finland: Pinscher Kromfohrländer Crossbreeding and Outcrossing: Two terms, many concepts. - https://dogwellnet.com/content/health-and-breeding/breeding/breeding-for-health/cross-breeding/crossbreeding-and-outcrossing-two-terms-many-concepts-r730/ The Norwegian Lundehund Outcross Project - https://dogwellnet.com/content/health-and-breeding/breeding/breeding-for-health/cross-breeding/the-norwegian-lundehund-outcross-project-r419/ Norwegian Lundehund - Pedigree Breeds - DogWellNet - https://dogwellnet.com/breeds/pedigree/norwegian-lundehund-r140/ -
DogWellNet Digest: Issue #43 - 16 December 2021
Dave St. Louis posted a article in DogWellNet Digest
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Inbreeding has proven negative effects for health, says a new study in dogs
Ann Milligan posted a blog entry in New Research
Inbreeding has proven negative effects for health, says a new study in dogs by Katariina Mäki A recent study by an international team led by veterinary geneticist Danika Bannasch is a welcome wake-up call for all of us in the world of pedigree dogs. While it has been well established that closed studbooks cause inbreeding to accumulate, the special importance of the study lies in the bond between inbreeding and health: the results in 162 breeds show that inbreeding contributes to an increase in disease and health care costs throughout the dogs’ life. Again, a known biological fact, but very important to once again have been proven also in dogs from an actual data. A wide consensus based on studies in other animal species is that negative effects start to show when inbreeding level exceeds 10%. In the Bannasch et al. study, the accumulated average inbreeding based on genetic analysis across 227 breeds was close to 25 %, which is the level if mating together parent and offspring or full sibs. Inbreeding levels in dog breeds have formerly been calculated mostly using pedigree data. It is however difficult to calculate the true coefficient of inbreeding (COI) from pedigrees unless the data reaches all generations – from the most recent ones to the founders of the breed. That’s what makes genotype-based methods so important. You can read more about the difference between pedigree COI and genomic COI in a DogWellNet Blog 'Ask Aimée' here. Few studies based on complete pedigree information are available, one in Leonbergers by Letko et al. (2020), and another in Nova Scotia Duck Tolling Retrievers and Lancashire Heelers by Mäki (2010). Both studies reported levels of inbreeding similar to Bannasch et al. Even more important than the level of inbreeding itself is the rate at which it has been reached. This rate defines the effective size of the population, which is a good indicator of the future viability of the population regarding inbreeding and genetic diversity. To my knowledge, Bannasch et al. is the largest study showing the negative effects of inbreeding in dogs. The authors mention that demonstration of direct negative effects of inbreeding within breeds has been limited, one reason for this being the challenges of phenotyping for individual animals. They mention the studies by: Leroy et al. (2015): close inbreeding had a negative effect on litter size and neonatal survival in seven French dog breeds Chu et al. (2019): inbreeding was associated with smaller litters in Golden Retrievers and Schrack et al. (2017): inbreeding in dams was associated with fertility in the Entlebucher Mountain dog. Mäki et al. (2001) showed also that inbreeding was associated with dogs’ screening results in hip and elbow dysplasia. The association was found in the German Shepherd Dog and the Labrador Retriever, but it was quite weak, probably since the multifactorial nature of both dysplasias. We know the situation – we have known it for a long time – how should we move forward? In any breed population, care should be taken to maintain genetic diversity. The Bannasch et al. study shows that most canine breeds are highly inbred, but some are still quite diverse, thanks to open studbooks or recent crosses. We have tools to improve the situation in the breeds. These include: Use as many healthy dogs for breeding as possible Don’t overuse any dog the so-called matador breeding creates unnecessary additional genetic bottlenecks and decreases variation. We must remember that every dog, even the best one, carries harmful mutations which spread all around in the population, if the dog is overly used for breeding. To avoid adverse effects of inbreeding in your own breedings, don’t combine close relatives – and remember that also linebreeding is inbreeding (See Brenda’s blog post, Linebreeding vs. Inbreeding – Let’s be perfectly clear.) In breeds where negative effects of inbreeding have started to show, or where it is simply difficult to find healthy dogs for breeding, consider using the old, formerly widely used tool – outcrosses. Planned, well-organized outcrossing is an efficient way to bring new genetic variation into population – a good way forward. Inbreeding and genetic diversity is a challenge the International Partnership For Dogs will address in future work. Stay tuned! References and links Bannasch, D., Famula, T., Donner, J. et al. The effect of inbreeding, body size and morphology on health in dog breeds. Canine Genet Epidemiol 8, 12 (2021). https://doi.org/10.1186/s40575-021-00111-4 Bonnett B. Blog: Linebreeding vs. Inbreeding – Let’s be perfectly clear. Chu ET, Simpson MJ, Diehl K, Page RL, Sams AJ, Boyko AR. Inbreeding depression causes reduced fecundity in Golden retrievers. Mamm Genome. 2019;30(5–6):166–72. Leroy G, Phocas F, Hedan B, Verrier E, Rognon X. Inbreeding impact on litter size and survival in selected canine breeds. Vet J. 2015;203(1):74–8. Letko A, Minor KM, Jagannathan V, Seefried FR, Mickelson JR, Oliehoek P, Drögemüller C. Genomic diversity and population structure of the Leonberger dog breed. Genet Sel Evol. 2020 Oct 14;52(1):61. doi: 10.1186/s12711-020-00581-3. Erratum in: Genet Sel Evol. 2020 Nov 18;52(1):70. Llewellyn-Zaidi A. Blog: Ask Aimee: What's the difference between pedigree COI and genomic COI? Mäki K. Population structure and genetic diversity of worldwide Nova Scotia duck tolling retriever and Lancashire heeler dog populations. J Anim Breed Genet. 2010;127(4):318–26. Mäki K, Groen AF, Liinamo A-E, Ojala M. Population structure, inbreeding trend and their association with hip and elbow dysplasia in dogs. Anim Sci. 2001;73(2):217–228. Schrack J, Dolf G, Reichler IM, Schelling C. Factors influencing litter size and puppy losses in the Entlebucher Mountain dog. Theriogenology. 2017;95:163–70. -
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The Relatedness of Breeds - A fun, interactive resource with some cautions ...see references below... The Guardian has come out with an interactive tool for looking a the relatedness between breeds. Based on 'clades' (genetic groupings) research and genomic work by by Heidi Parker and Elaine Ostrander's team, it is an interesting resource. Click on your breed - see what others breeds it is related to. Fun! But there are a couple of cautions that apply: This is great work - but the relatedness has changed to some extent with each new edition of the research, with the advancement of techniques, so this is not written in stone. Using gene patterns to determine relatedness is just that - it does not say that another breed was part of the development of your breed - or whether your breed has been used to develop the other one. They are simply 'related'. Difference in relatedness may be seen depending on how 'old' your breed is. Relationships that have occurred more recently may show up as stronger. This should not be confused with commercial tests that tell you the breed composition of your mixed breed dog. This is different technology and looks primarily at 'pedigree' dogs. To learn more about mixed breed testing see recent blogs: Ask Aimee: Can my dog's ancestry test tell me who its parents are? and HGTD This week: Guess my dog! Are breed/type genetic tests right for you? This is, however, a good reminder that what some people call 'purebred' dogs - what we generally call pedigree dogs (listed in an official registry as a specific breed) are not really 'pure'. Which is likely a good thing! A breed can approach 'pure' only through heavy inbreeding that leads to all sorts of other problems. On the other hand, the work to assign dogs to related clades and to determine relationships among breeds is beneficial in terms of: It is simply interesting and informative. It may provide food for thought when selecting breeds for out-crosses when trying to improve the genetic diversity within a breed. This can go both ways, i.e. it is nice to find already related breeds, but using a breed closely related may not increase the diversity that much. And, as seen in our outtakes - the number of related breeds varies quite a lot. Expanding on comments by Dr. Ostrander... This type of research could have a lot of value to dog breeds (and other species) by having a deeper understanding of the genetic differences between breeds/varieties of dogs. Identifying these genetic differences may be fundamental to furthering research into many aspects of canine health and welfare - from better investigations of complex disease, to improving longevity and genetic diversity. Anyway, check it out! References: Interactive: see how your favourite dog breeds are related to each other in The Guardian. Genomic Analyses Reveal the Influence of Geographic Origin, Migration, and Hybridization on Modern Dog Breed Development authors Heidi G. Parker, Dayna L. Dreger, Elaine A. Ostrander, the National Human Genome Research Institute. 2017.
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Summary of Kennel Club Breed Records: Pug 2020 A new research report, Summary of Kennel Club Breed Records: Pug 2020, has been produced by Cassandra Smith. The report utilises publicly available data offered by The Kennel Club to describe health and breeding-related statistics and information. The author’s previous reports on similar and other breeds have been well-accepted, with appropriate methodology and presentation. This analysis includes KC-registered dogs with statistics presented separately for Pugs of Standard colour and Non-Standard (NBS) colours. Included is information on litter statistics, inbreeding values, caesareans and AI, breeding stock used, health schemes and genetic testing. The report is clear and speaks for itself. (see PDF of the full report attached); it was originally posted [CRUFFA]. Below are a few comments on/highlights from the material. For those who wonder why the separation by colour: the designation of colour variations differ from breed to breed and across registries. Generally speaking, within the Pug breed, puppies (or litters of puppies) are registered by colour as either Standard (as described in the Pug Breed Standard) or Non-Standard (and other colour). Not unique to the Pug, colour classification is often based simply on historical choices in acceptable coat colours and markings, and are not automatically indications of a dog’s “purity” or lack thereof. However, the breeding community may be quite sensitive on this issue and feel there are differences across breeders and dogs beyond the colours. Relatively rarely, genetic mutations may produce certain colours or ‘dilutions’, generally randomly, however, there are instances where deleterious colours have been selected for. Of course, it can also happen that the occasional non-standard colour puppy might simply not be registered. Interestingly, but perhaps unrelatedly, the median number of puppies per litter was slightly higher in the NBS litters. One area of particular interest in wider discussions on breed-health strategies, is the limited extent to which existing health programs have been embraced by breeders. Although the creation of such programs has been acclaimed (see https://www.pughealth.org.uk/pug-5-star-health-scheme/), the fact that they are clearly not being embraced in a way to impact the health of the breed is very disappointing. There is a caution, however, that this might have been impacted by the Covid-19 pandemic, so future reports will be needed. Although Standard Colour Pugs have access to both health schemes, for 88% of litters neither parent had health scheme results recorded. As for Respiratory Function Grading, “Table 12 shows the RFG testing results of each parent [Standard Colour litters] prior to the birth of the litter. 12.6% of litters had at least one tested parent, with sixteen litters (2.5%) meeting the current criteria for lowest risk of BOAS, as documented in the Breeding Advice on the Kennel Club website. Testing was less frequent for NBS litters. Summary of Findings See paper for further discussion and descriptions of calculations, e.g. for coefficients of inbreeding COIs: Pugs UK 2020: summary statistics (C. Smith, 2020) Parameter Standard Colour 638 litters/2576 puppies Non-Breed Standard Colour 733 litters/3429 puppies Litter size (median) 4 5 COI % (mean/median/highest) 5.4/ 4.4/ 30.9 3.7/ 2.7/ 21.4 Litters with COI>25% 4 0 Sire age at birth of pups (mean/ median/ minimum) 3.9/ 2.2/ 0.65 3.1/ 2.7/ 0.54 Of note: some high coefficients of inbreeding. Perhaps a better picture of the challenges of inbreeding in the pug, or any breed, would be to utilize the rapidly improving "genetic COI" DNA tests available. A robust genetic COI test drastically improves precision compared to pedigree-based COI. Regardless, a COI (pedigree based or not) of more than 12, 25, 30% is a cause for concern. There is also a high proportion of young sires being used. It is generally recommended to wait until sires are at least 2 or 3 years of age, health tested, and so-far free from inherited conditions. Similarly, a considerable number of litters indicate that the dam was bred at a young age. In addition, the number of litters per sire indicates that there is overuse of certain popular sires, relative to general recommendations. Final Thoughts There are causes for concern here and much to inform evaluation of breeding within Pugs in the UK. The information should also be used by Pug clubs and breeders outside of the UK. These types of statistics – not simply the recording of the data – are crucial to monitor the breeding and breed population and to provide metrics for the uptake and possible impact of health testing programs. Ms. Smith is to be commended and thanked for her efforts. As we have written in other blogs and our recent article on the Norwegian Lawsuit on Dog Breeds and Breeding against some breeds with extreme conformation (see additional resources) it is not enough to say health and longevity is important. Breeding practices, attitudes and specific decisions must be made with those goals prioritized. Further resources: Summary of Kennel Club Breed Records: Pug 2020 – Cassie Smith. (links: to discussion on facebook and link to file and pdf - attached below) Blog: Is it "tough talk" or "open dialogue" - and why is it a challenge in the dog world? Blog: Linebreeding vs. Inbreeding – Let’s be perfectly clear Blog: The Big Picture - in the Dog World as a Whole and for your next Breeding Decision Norwegian Lawsuit on Dog Breeds and Breeding - The "First" But Not the Last? PugBreedRecordsSummary2020.pdf
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Ask Aimee: What's the difference between pedigree COI and genomic COI?
Aimee Llewellyn-Zaidi posted a blog entry in Ask Aimee
Recently we have had questions from dog breeder health advisors about using inbreeding tools, particularly pedigree-based tools such as estimating Coefficients of Inbreeding (COI). This blog discussion describes COIs, some advantages and disadvantages, and provides thoughts on usage. There are several resources available to both individual breeders and breed organizations (clubs and kennel clubs) that can help to monitor and track genetic diversity, and estimate an individual dog's diversity relevant to a breed population. Each have advantages and disadvantages but can play a role in improving genetic diversity, including: Pedigree-based COI estimations (Coefficient of Inbreeding) Genomic COI calculations Often associated with COI: Popular sire tracking. Access to breed-wide data will vary by country, breed/kennel club. Some clubs restrict numbers of litters born to sires/dams to reduce the impact of popular sires. Breed diversity reports/research. Some kennel clubs, breed clubs, researchers and commercial genetic test providers have undertaken breed reports on population differences, including genetic diversity and inbreeding, popular sires/dams, etc. There are also other genetic tools used to estimate genetic diversity, such as MHC/DLA testing, but for the purposes of this article, we are focusing on COI-based concepts. We hope to follow up with more information on all types of genetic testing-type diversity tests in another article. Pedigree-based COI This tool uses pedigree information to estimate how closely related a dog's parents are. The more ancestors a dog's parents share, the more likely that duplicate genes will have been passed down, accumulating over generations (called identity by decent, or IBD) and thus reducing genetic diversity. Pedigree COI probability calculations are based on the dog's relatedness, not specific genes or regions of the genome. It does not attempt (nor claim) to be able to tell you which parts of the genome a dog has randomly inherited from the dam or sire, but instead focuses on how many relatives are held in common throughout the dog's known ancestry. All dogs in the same litter will have the same COI probability. Pedigree-based COI probabilities can not account for any influence of recombination or specific genes/sections of genetic code. Advantages: There are some advantages to pedigree-based COI. There are a number of kennel and breed clubs who have invested in providing pedigree COIs to members, allowing free or low-cost access. There are also many free tools available for breeders to use, particularly when they have a breed or type that is not registered with a kennel club. If the COI is based on a large number of generations, ideally as many generations as known, and good-quality pedigrees, it can be informative and helpful in selecting dogs for breeding that are less closely related. It can also be used to look at changes over time in a fairly simple way that doesn't require special technology or access to the dogs. It may also have the advantage of being based on something familiar to breeders - pedigrees - and therefore may overcome some of the education challenges other genetic diversity tools may face. Pedigree-based COI calculations have been used effectively to impact genetic diversity across a wide range of animal breeding practices. Disadvantages: The big challenge is confidence in the accuracy and quantity of the pedigree data used. If based on a small number of generations, or on inaccurate pedigree information, the COI can be wildly inaccurate in measuring relatedness in a meaningful way. There have been numerous studies that have shown that restricting the number of generations included in the calculations can be very misleading. Examples have shown a COI based on 5-generations, vs 10+ generations can give a false impression that the COI is much lower, and not reflect the accumulation of inbreeding/relatives in common over time. There can also be the temptation to have generational calculation cut-offs to either reduce the time required for COI calculations or to compare different breeds to each other. This leaves COI vulnerable to being used to support practices and strategies that may agree with biased agendas, but do not improve dog health. To provide good-quality COIs requires large amounts of pedigree data, time to analyze this data, and some expertise. Without this, there is a very high risk that decisions could be made on poor information. Can we calculate better? Genomic COI: Genomic COI works off the same concept of IDB as pedigree COI, but does this by comparing tens of thousands of markers across the dog's genome (or, in theory, could use a dog's whole genome). It aims to capture specific swathes of homozygous markers of the genome inherited over generations, rather than estimate the probability that duplicate parts of the genome have been inherited. In this way, it should be more reflective of what precisely has been inherited in common, or what is IDB, over all of the generations of a breed's development, and not be restricted to a specific number of generations. Advantages: Genomic COI is more precise, and if based on a large volume of genomic data, has a high standard of accuracy. It can also be more precise in reflecting an individual dog's level of inbreeding compared to a defined breed population. There is also the potential for much more precise estimations of inbreeding risk or improving diversity in matings. This could be especially helpful in choosing between two potential dogs who are otherwise equal in breeding qualities. Disadvantages: There are costs for testing (usually around the $100-200 range, but often with other genetic tests included), and you need to have access to the dogs to provide genetic samples. There may be challenges (e.g. costs, compatibility) for integration into kennel club databases or other resources trying to collate health, pedigree, and genetic diversity information. Like all genetic diversity genetic tests, identifying presence or absence of areas of homozygous genetic markers does not mean identifying what those markers may be coding for. The assumption with genetic diversity is that the more diversity that is in place, the less likely that undesirable traits will be passed down. However, there could be rare or less common markers for a reason, such as an association with a disease or other undesirable traits. What about other genetic diversity tests? We hope to follow up this blog with more articles exploring different kinds of genetic diversity genetic testing tools. How could COI be useful? There are many ways a COI % can be used. For the individual breeder, the COI can be one way to add in genetic diversity as a consideration in breeding plans for individual matings, or as a way to track breeding plans over time. For breed clubs, or kennel clubs, it can be particularly useful in observing breed-wide trends and changes. Many clubs have recommendations based on the current breed-average - usually that a breeder should aim to breed at or below the current breed average COI. This is not necessarily to breed the lowest COI possible, and certainly not to prioritize COI over the health or health risks of an individual dog. For example, the Finnish Breed Club encourages breeders to integrate COI information into breeding plans based on the first 5 generations to avoid high COI% matings in the near-generations, as a way to reduce the likelihood of passing on deleterious genes that could impact the individual dog's health. The Swedish Kennel Club monitors 5-gen COI over time, to look at near-generation trends and changes. And, the Kennel Club (UK) provides the COI for the individual dog, and the breed average, based on all available generations included in the calculation. They also include the number of generations included in the calculation as this can impact how informative the COI may be (e.g. 3 gen is more dynamic and changeable than 22 gen). The recommendation for the Kennel Club is therefore to breed at or below the breed average. These examples illustrate the differences between focusing on the near-generations which could reflect "fast" inbreeding and also intentional inbreeding vs. COIs calculated with 10-20 generations more suitable for describing the situation and trends for the whole breed. There is also the consideration of COI changes over time. It is usually more concerning if a breed sees a rapid, drastic increase in inbreeding, leading to a rapid loss of genetic diversity, which, in a closed breeding system, cannot be regained without outcrossing to a new breed or "unrelated" breed population. Rule of thumb: aim to breed for type, not relatedness... Even without specific tools, breeders can start by considering their own practices when selecting mates. Options could include: avoiding popular sires and their close relatives who have been used extensively for breeding, exploring lines that have not used for breeding previously, seeking dogs from populations that are “new” to them (e.g. field/working vs show), aiming to seek dogs that have desirable traits but are not as likely to be closely related: Use available tools to help make breeding plans - including genomic COI or genetic diversity tests, pedigree COI if that's the best you can access, with as many generations as possible. Use genetic trait/disease tests and clinical screening schemes, as well as knowledge of familial longevity, behaviour, etc. to help select the healthiest representatives of the breed Use MORE dogs of both sexes. Most breeds use less than 10% of the available dogs for breeding... you're losing 90% of the possible genetic diversity! Genetic diversity is an important factor of breeding for the Big Picture. It should be one consideration in breeding. There is much more to explore in genetic diversity tools and applications both for individual breeders' plans, and breed-wide strategies than can be discussed in this short blog. Look for more information to come! More resources and reference publications: Get a GRIHP! on several breeds offers a variety of international information on a breed, including genetic diversity reports. Find them here. Relatedness of Breeds Genetic Diversity webinar excerpt Genetic Diversity and the Big Picture Janes M, Lewis TW, Ilska JJ, Woolliams JA. The usage of Mate Select, a web-based selection tool for pedigree dogs for promoting sustainable breeding. Canine Med Genet. 2020 Oct 19;7(1):14. doi: 10.1186/s40575-020-00094-8. PMID: 33372639; PMCID: PMC7574414. Photo by Blue Bird from Pexels -
What are the Consequences of Inbreeding Dogs? Dr. Aaron J. Sams, Embark Senior Scientist The following lecture was given in February 2021 at Embark's Inaugural Canine Health Summit. More information on the Summit is available on DogWellNet. See: IPFD and the Canine Health Summit Feb 2021 by Embark Veterinary
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Linebreeding vs. Inbreeding – Let’s be perfectly clear.
Brenda Bonnett posted a blog entry in Brenda's Blog
Linebreeding vs. Inbreeding – Let’s be perfectly clear. Note: This topic was prompted partly by IPFD's participation in the Canine Health Summit put on by Embark Veterinary. See our Q&A article on breeding and genetics topics here. Inbreeding is the mating of related individuals – that is those who have one or more relatives in common. Linebreeding is not simply a form of inbreeding – it IS inbreeding. How close that inbreeding is depends on the selection of individuals within that line. Linebreeding/inbreeding - by definition - reduces genetic diversity. By how much depends on the closeness of mating pairs and the time/number of generations over which the process is repeated. It is scientifically proven and widely recognised that inbreeding/linebreeding in dogs has led to: An increase in the prevalence of inherited disorders A decrease in viability/ longevity A decrease in reproductive ability (reduced fecundity, decreased litter sizes, etc.) The loss of genetic diversity (i.e. decrease in genetic variation) Studies in various species have shown that inbreeding can also result in: developmental disruption, higher infant mortality a shorter life span and reduction of immune system function. And it is known that impaired immune function can lead to higher rates of cancer, and a myriad of other issues for skin, digestive, and other systems as well as resistance to infectious agents. Collectively, these effects of inbreeding/linebreeding are called inbreeding depression. Importantly, inbreeding depression increases as the extent of inbreeding/linebreeding increases. For example, see Inbreeding depression reduces litter sizes in golden retrievers. I was asked by a breeder at a lecture series, during a talk on breeding ethics, “What level of inbreeding is okay? Where is the cut-off for ‘too close’?” I asked the breeder, “Why do you want to do inbreeding/linebreeding? Do you think that will improve health and longevity?” Those at the seminar had previously stressed that their goal was to produce healthy, long-lived puppies. I suggested that inbreeding/linebreeding is generally done to fix certain characteristics in a line - ‘desirable’ characteristics. But what is desirable? Generally, linebreeding is on physical, conformational, or structural characteristics. Not necessarily, and perhaps rarely, primarily on characteristics associated with health and longevity. Therefore, the latter are unlikely to be achieved by inbreeding/linebreeding and will be reduced by the associated decrease in diversity. From the AKC article above: ”Want to add new things to improve the quality of your line? Outcross with a line that has those characteristics you want. Want to be sure to keep the great things you have? Breed closely to get a very consistent litter. When you know what you want, then you can plan to attempt to create the result you desire.” Maybe it is time to be transparent and honest. ‘What you see’ in any pedigree breed – appearance, health, length of life – is ‘what you got’ – a reflection of what was selected for – and what was not selected against – by those who bred them. If your primary goal is to produce healthy, long lived puppies – and that includes all the puppies in all litters – then you would first and foremost mate only from dogs that are themselves healthy, who come from a long line of relatives that are healthy and long-lived; from a long line of dogs that have not exhibited the deleterious conditions listed above as arising from inbreeding/linebreeding or any other conditions of significance in your breed. And you would want to be sure there was a history of great temperaments and breed-appropriate abilities. You would make sure that all the dogs in your line can see, and breath, and move without impediment, and are able to exhibit natural dog behaviours. This is not only the art and science, but the common sense of dog breeding. Once prioritized on those aspects, eliminate from breeding dogs with genetic or other screening results that indicate that they are likely to pass on detrimental traits. After that, only after that, you might do some selection on specific physical attributes. Is all that easy to achieve? No, but who ever said that manipulating the development and genetics of a species should be easy? And, unfortunately, within the breeding populations for many breeds, there may be rather few individuals who are as acceptable as is described above. If what you want is, however, consistency based on physical characteristics, then linebreeding and inbreeding may well give it to you. But, as history has proven, eventually, at a breed level it will often result in the increase in other characteristics, challenges, and issues - not likely to be primarily health and longevity. There are many questions about how to measure genetic diversity, how to determine it – really what is genetic diversity and how do we achieve it? There are no simple answers to those questions. There are major challenges in some breeds where characteristics associated with health and welfare problems are ‘fixed’ and can not be bred away from within a closed population. Here are some facts about genetic diversity: Genetic diversity cannot be achieved by selecting for conformity and consistency in appearance or specific physical traits – i.e. for a lack of diversity in appearance and physical characteristics. In other words, a lack of diversity in observable characteristics reflects a lack of genetic diversity. Eliminating from breeding dogs with variations in ‘minor’ characteristics that are not associated with poor health or function, e.g. many coat colour varieties that are simply deemed as undesirable, will reduce genetic diversity. (Recognizing that a few coat characteristics reflect deleterious mutations or fads. Interested in challenges around coat colours? See Ian Seaths' blog: Systems Thinking and Non-standard Breed Colours.) Diversity will always be reduced by inbreeding and linebreeding – the closer the mating pairs, the longer the linebreeding/inbreeding is followed, the bigger the effect. The ability to increase genetic diversity by breeding only within a closed population is limited, However, calculated measures of diversity may be inaccurate within a registry if only a small proportion of the available population is bred or included in calculations. Pedigree-based calculations of Coefficients of Inbreeding (COIs) – especially on a limited number of generations – underestimate inbreeding compared to genomic based COIs as they are based on average/ predicted inheritance of genetic material from ancestors, rather than the actual case for an individual dog. Measures of genetic diversity are one more tool to inform breeding for the ‘Big Picture’. (See my blog: The Big Picture - in the Dog World as a Whole and for your next Breeding Decision.) What can be done for your breed? There are increasing numbers of breed-specific research studies on genetic diversity. The whole picture for a breed cannot be understood by one calculation or measure done on a limited group of dogs. For an example of a broad-based, global picture, read, e.g.: Genomic diversity and population structure of the Leonberger dog breed. You do not need to focus on the details of the technology and methodology to get the main messages from this paper. For example: "Conclusions: The increasing size of the Leonberger population has been accompanied by a considerable loss of genetic diversity after the bottleneck that occurred in the 1940s due to the intensive use of popular sires resulting in high levels of inbreeding." and "The breed has predispositions to neurodegenerative disorders and cancer, which is likely due in large part to limited genetic diversity." Aaron Sams, expert in genetic diversity at Embark, was responding to a question on the summit that again, was someone knowing how much inbreeding was okay, what level was okay in a breed. And among other sage advice he said that ultimately the breeders and breed club must determine what they can 'tolerate'. And I would add that goes for all aspects of health and lack of it, and longevity issues. Bottom line – you get that for which you select, not that for which you wish. Let’s all be perfectly clear. Other resources on DogWellNet.com: 1. Genetics Vocabulary - Glossary of Terms 2. Relationships between genetics, breeding practices and health in dogs - Grégoire Leroy (France) -
This article talks about two common terms used in dog breeding, and as part of strategies for impacting genetic diversity. Though sometimes used interchangeably, and used to mean multiple different practices, understanding the differences in the terms and the potential application in breeding programs is one tool dog breeders can use to change and improve genetic diversity.
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Abstract - In this chapter, we examine the specificities of dog breeding and selection in order to better understand how these practices impact breed health. Selection within the species is characterised by breeding in closed populations, selection objectives that are generally aimed at conformation, animals that receive substantial veterinary care, selection that is often empirical using a small number of breeding dogs and, more occasionally, the use of practices such as mating between close relatives. These practices can have different direct or indirect consequences on breed health. We address in particular the potential health impacts of selection based on morphology (hypertypes, etc.), as well as genetic drift, linked to a limited basis of selection, resulting in particular in an increase in inherited diseases. Faced with these recurrent problems, it is important that clubs and breeders hoping to improve their breed health adapt their practices and use the appropriate tools, especially in terms of breeding strategies and diagnoses. -
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Whole genome sequence, SNP chips and pedigree structure: Building demographic profiles in domestic dog breeds to optimize genetic trait mapping Authors: Dayna L. Dreger, Maud Rimbault1, Brian W. Davis1, Adrienne Bhatnagar1, Heidi G. Parker, Elaine A. Ostrander Key Words: population, homozygosity, canine, inbreeding SUMMARY STATEMENT "Successful application of whole genome sequencing and genome-wide association studies for identifying both loci and mutations in canines is influenced by breed structure and demography, motivating us to generate breed-specific strategies for canine genetic studies." ABSTRACT "In the decade following publication of the draft genome sequence of the domestic dog, extraordinary advances with application to several fields have been credited to the canine genetic system. Taking advantage of closed breeding populations and the subsequent selection for aesthetic and behavioral characteristics, researchers have leveraged the dog as an effective natural model for the study of complex traits, such as disease susceptibility, behavior, and morphology, generating unique contributions to human health and biology. When designing genetic studies using purebred dogs, it is essential to consider the unique demography of each population, including estimation of effective population size and timing of population bottlenecks. The analytical design approach for genome-wide association studies (GWAS) and analysis of whole genome sequence (WGS) experiments are inextricable from demographic data. We have performed a comprehensive study of genomic homozygosity, using high-depth WGS data for 90 individuals, and Illumina HD SNP data from 800 individuals representing 80 breeds. These data were coupled with extensive pedigree data analyses for 11 breeds that, together, allowed us to compute breed structure, demography, and molecular measures of genome diversity. Our comparative analyses characterize the extent, formation, and implication of breed-specific diversity as it relates to population structure. These data demonstrate the relationship between breed-specific genome dynamics and population architecture, and provide important considerations influencing the technological and cohort design of association and other genomic studies." excerpt... "The work presented here examines variables of inbreeding and homozygosity in a large and comprehensive set of dog breeds through parallel use of pedigree data, genome-wide SNP genotyping, and WGS. Specifically we compare data from extended pedigree analysis, genotyping with a SNP chip of 173,622 potential data points, and WGS with an average depth of 27.79X. We found that each dog breed has a unique profile of genome diversity, varying by amount of total homozygosity as well as number and size of homozygous regions. Likewise, while we observe variation between members of the same breed, multiple individuals from a single breed can be combined to obtain an accurate reflection of breed-specific homozygosity and knowledge regarding fluidity of variation within breed confines. This allows us to define metrics that inform the design of canine genetic studies while also allowing us to develop an understanding of the intricate complexity of the diversity of dog breeds. Individual diversity metrics are provided for over 100 breeds as a resource for investigators in the field." -
What is a breed, a purebred, a pedigree dog?
Brenda Bonnett posted a article in Definitions and Background
These terms are often confused or used inappropriately. Here we provide some information and links to help clarify the situation. See related content from the 4th IDHW 4th IDHW Theme #1: The Concept of ‘Breed’ The Concept of Breed Theme Presentations DEFINITION OF 'BREED' ACROSS SPECIES AND COUNTRIES: CROSSCUTTING CONCEPTS - Gregoire Leroy The Concept of Breed: Past, present - and future? - Helena Skarp New Expanded Content - February 2021 Crossbreeding and Outcrossing: Two terms, many concepts. Linebreeding vs. Inbreeding – Let’s be perfectly clear.