The Institute of Canine Biology
  • HOME
  • Blog
  • Courses
    • COI BootCamp (FREE!)
    • Basic Population Genetics (FREE)
    • The Science of Canine Husbandry
    • Managing Genetics For the Future >
      • Syllabus - Managing Genetics for the Future
    • The Biology of Dogs (Open Reg )
    • DNA For Dog Breeders >
      • Syllabus - DNA for Dog Breeders
      • Open Reg - DNA For Dog Breeders
    • Understanding Hip & Elbow Dysplasia >
      • Open Reg - Understanding Hip & Elbow Dysplasia
    • Genetics of Behavior & Performance >
      • Syllabus - Genetics Behavior & Performance
      • Open Reg - Genetics of Behavior & Performance (Open Reg)
    • Strategies for Preservation Breeding >
      • Open Reg - Strategies for Preservation Breeding
    • Group Discounts
    • MORE FREE COURSES >
      • Quickie Genetics (Free!)
      • Heredity & Genetics (Free!)
      • Useful Genetics (Free!)
      • Basic Genetics Videos
  • Breed Preservation
    • Breed Status
    • Breeding for the future >
      • BFF Breed Groups
    • The "Elevator Pitch"
    • What's in the Gene Pool?
    • The Pox of Popular Sires
    • What population genetics can tell us about a breed
    • What population genetics can tell you...Tollers & Heelers
    • How to use kinship data
    • Using EBVs to breed better dogs >
      • How population size affects inbreeding
      • EBV Examples
    • How to read a dendrogram
    • Global Pedigree Project >
      • The Database
    • Finding the genes without DNA
    • How to read a heat map
  • Health Data
    • Bloat (Purdue Study)
    • Body Condition Score >
      • % Dysplastic vs BCS
    • Breed Comparions
    • Cancer
    • Cardiac
    • Cataracts
    • Caesareans
    • Deafness
    • Degenerative Myelopathy
    • Elbow Dysplasia
    • Epilepsy
    • Genetic Diversity
    • Genetic Diversity (MyDogDNA)
    • Hip Dysplasia >
      • Hip Dysplasia (Hou et al 2013)
    • Inbreeding Effects
    • Inbreeding (Gubbels)
    • Inbreeding (Dreger)
    • Lifespan
    • Litter size
    • Metabolic
    • mtDNA
    • Orthopedic
    • Mode of Inheritance
    • Patella Luxation
    • Thyroid
    • Portosystemic shunt
    • Purebred vs Mixed (UC Davis)
    • Purebred vs Mixed Breed (Bonnett)
    • Spay & Neuter Effects
    • Calboli et al 2008
    • Hodgman (1963)
    • Scott & Fuller (1965)
    • Stockard: Purebred crosses
    • Summers (2011)
  • Projects
    • How To Interpret Breed Analyses
    • Afghan Hound
    • More details about the Toller study
    • Belgian Tervuren >
      • Belgian Terv p2
      • Belgians- why population size matters
    • Bernese Mountain Dog
    • Boxer
    • Brussels Griffon
    • Bullmastiff
    • Canaan Dog >
      • Canaan analyses
    • Cesky Terrier >
      • Cesky genetic history
    • Chinook
    • Curly-coated Retriever
    • Doberman
    • Entelbucher Mountain Dog
    • Flatcoat Retriever
    • French Bulldog
    • German Shorthair
    • Golden Retriever >
      • Golden Retriever Pedigree Charts
    • Irish Water Spaniel >
      • IWS (6 Nov 17)
    • Labrador Retriever
    • Manchester Terrier
    • Mongolian Bankhar >
      • Research Updates
      • Bankhar 1
    • Norwegian Lundehund
    • Plummer Terrier
    • Otterhound
    • Portuguese Water Dog >
      • Portuguese Water Dog (pt 2)
    • Ridgeback
    • Schipperke
    • Standard Poodle >
      • The Problem With Poodles
      • 3poodle pedigree charts
      • 3Poodle Wycliff dogs
      • Poodle Genetics
    • Tibetan Spaniel
    • Tibetan Mastiff
    • West Highland White Terrier
    • Whippet
    • Wirehaired Pointing Griffons
    • UK KC Graphs >
      • UK KC Breed Status
      • UK Groups
      • KC Gundogs
      • KC Hounds
      • KC Terriers >
        • Terriers (select breeds)
      • KC Pastoral
      • KC Toys
      • KC Working
      • KC Utility
      • Australian KC
    • Breed outcrossing programs
  • Resources
    • Genetics Databases
    • Stud Books >
      • American Kennel Club stud books
      • Field Dog stud books
      • The Kennel Club (UK)
    • Learn
    • Videos about dog genetics
    • The Amazing Things Dogs Do! (videos) >
      • Livestock Management
      • Livestock guarding
      • Transportation, exploration, racing
      • Conservation & wildlife management
      • Detection Dogs
      • Medicine & Research
      • Entertainment
      • AKC/CHF Podcasts
    • Read & Watch
    • Bookshelf
  • Preventing Uterine Inertia

No pedigree? No problem!

6/17/2018

 
By Carol Beuchat PhD
The most basic tool of the dog breeder is the pedigree. In essence, it is the documentation of the genetic and demographic  history of an animal, and it can hold a treasure trove of useful information.

Often, however, the quality of the pedigree information available for a dog is not what you would like it to be. Most often, dog pedigrees are incomplete, either not including generations back to the founding of the breed, or missing animals in the subsequent generations. Of course, there are also errors, both deliberate and inadvertent, that can change the historical picture. Finally, a pedigree database might exist for a breed but is not accessible, perhaps for technical reasons such as a computer platform that does not communicate well with the rest of the world (e.g., self-designed pedigree software), an out-of-date computer (yes, there are still data being kept on old Commodore computers...), or not computerized at all (think folders of paper). Perhaps the most distressing reason for lack of accessibility is the unwillingness of people who have custody of the information to allow public access. (This means you too, AKC.) It's hard for me to imagine how anyone could argue that this is in the best interests of the breed; it can only be selfish or ego-driven in someone who fails to see that data that can't be used might just as well not exist. These databases die with their creators, with the records being tossed out by relatives or even strangers who see no value in them. Such as waste.
In any case, when the pedigree database is less than ideal for a breed, all is not lost. The high-density SNP (single nucleotide polymorphism) arrays used now for DNA analysis can provide very high quality information with a fine resolution. Up until just a few years ago, the most common method of DNA analysis to determine relatedness among animals used "microsatellites" (referred to by several different acronyms, among them  STRs, or single tandem repeats).
In the last 5-10 years, however, the cost of genotyping using SNPs has dropped substantially, and SNPs are replacing microsatellites as the tool of choice in the types of analyses that would be most useful for animal breeders, such as determining genetic diversity and relatedness. 
Picture
SNP panels have the further advantage that single mutation and trait tests can be incorporated into the test panel and run at the same time as the genotyping for the same cost. The most commonly used SNP tests today have 170,000 to more than 200,000 markers, which means that the entire genome (i.e., all of the chromosomes) can be assessed with a very high density of loci. A decade ago, a test like this would cost about $1,000; today's commercially available tests are $100-200.
For breeds without an adequate pedigree database for whatever reason, the data produced by SNP testing can be used to reconstruct the genetic relationships among all of the individuals you can get samples for. Software compares the similarity of the genotypes based on SNPs among the tested individuals. From this information, a tree can be constructed that displays the organization and degree of relatedness among the members of the population. This is based on the same information as used to create a kinship matrix.

In the chart below, I have used the SNP genotyping information for a group of dogs to reconstruct their pedigree relationships based on genetic similarity. The tree structure outside the square is the "family tree" illustrated as a dendrogram. (Learn how to read a dendrogram HERE.) The square in the middle is a "heat map" of the kinship values that depicts at just a glance the degree of relatedness of groups of animals in the breed as reflected in the dendrogram. (Learn how to read heat maps HERE.) The same animals are on both axes in this heat map, so it is symmetrical across the diagonal. (You can match up the clusters across the top with those along the left axis.)
Picture

In the absence of pedigree information, I have been able to reconstruct the genetic relationships among this group of dogs using a very large number of SNP markers that are distributed across all of the chromosomes. Where pedigree information is not available or is incomplete, this tree of relationships can be used to establish the genetics of an existing population of animals. If good pedigree records are kept going forward, they can be an excellent tool for assessing relationships among individuals and making predictions of litter inbreeding coefficients without the cost and logistic hassles of DNA analysis. The pedigree relationships can also inform the strategic choice of animals to be genotyped in the situations where that information is needed (e.g., trait or mutation testing).

​For breeders trying to breed more strategically to reduce the incidence of genetic disorders in their dogs, but might not have the best pedigree information, DNA analysis using high density SNP markers can provide research quality genetic information for a modest cost. We can convert the data for thousands of SNPs into a chart that displays the true genetic relationships among a group of dogs. 

To learn more about the genetics of dogs, check out
ICB's online courses

***************************************

Visit our Facebook Groups

ICB Institute of Canine Biology
...the latest canine news and research

ICB Breeding for the Future
...the science of animal breeding


Comments are closed.

    Archives

    January 2025
    November 2022
    July 2022
    May 2022
    April 2022
    March 2022
    February 2022
    November 2021
    October 2021
    December 2020
    January 2020
    August 2019
    July 2019
    June 2019
    May 2019
    April 2019
    March 2019
    February 2019
    January 2019
    December 2018
    November 2018
    September 2018
    August 2018
    July 2018
    June 2018
    May 2018
    October 2017
    August 2017
    May 2017
    April 2017
    March 2017
    February 2017
    January 2017
    December 2016
    November 2016
    September 2016
    August 2016
    July 2016
    June 2016
    April 2016
    March 2016
    February 2016
    January 2016
    December 2015
    November 2015
    October 2015
    September 2015
    August 2015
    July 2015
    June 2015
    May 2015
    April 2015
    March 2015
    January 2015
    December 2014
    November 2014
    October 2014
    September 2014
    August 2014
    July 2014
    June 2014
    May 2014
    February 2014
    December 2013
    October 2013
    September 2013
    July 2013
    March 2013
    July 2012
    April 2012

    Categories

    All
    Behavior
    Border-collie
    Herding

Blog

News


About Us

Contact Us








Copyright © 2012-2017 Institute of Canine Biology
Picture
Picture