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A DNA Primer for Dog Breeders (You have your dog's DNA data. Now what?)

Discussion in 'General Dog Discussions' started by Institute of Canine Biology, Jun 21, 2018.

  1. By Carol Beuchat PhD
    The world of the dog breeder is undergoing a sea change. We have had DNA tests for individual mutations for a few years, but now (finally!) breeders can get a genotype that documents the DNA of all 38 autosomal chromosomes, the two sex chromosomes, and even the mitochondrial DNA. This is a massive amount of data - the file for a single dog has one row and more than 200,000 columns.
    These DNA tests are using what is now the gold standard for plant and animal genotyping. This technology uses markers called single nucleotide polymorphisms (SNPs), which are just what the name says - a locus on the chromosome at which the nucleotide present can be an A, C, T, or G. These nucleotides are the "alphabet" of DNA, a code that contains the instructions for making a protein that has some function in the body. The SNPs used as markers tend to be variable, or polymorphic, and this variation allows us to use them to estimate genetic diversity, determine the relatedness of animals, and even visualize the distribution of homozygosity (inbreeding) on the chromosomes. The massive amount of information contained in a SNP genotype, together with the reduction in cost over the last few years, have made this technology the method of choice for most genetic studies in both plants and animals.
    SNP genotyping of dogs is now commercially available at a reasonable price ($100-200), and breeders are jumping at the chance to take advantage of this new tool. But in many cases the breeder with raw data file in hand doesn't know what to do with it. The thousands of columns of nucleotide data reveal no information that a breeder can translate. So how can we make it useful?
    With the right software and some expertise in population genetics, we can extract a tremendous amount of information from the file for an individual dogs, and even more if we have data for a modest sample of dogs in the breed. The technology is too new for books or online resources designed for use by the layperson or dog breeder. But I am summarizing in a series of posts the basic information breeders need to understand what their data mean and how they can use it.

    First, I will review the basic tools that can be used by breeders to assess the genetic status of their breed. These evaluate genetic diversity, genetic relationships, and population structure. Then I will show how to use the data for individual dogs when evaluating the suitability of potential mating pairs. Finally, I will provide examples of some resources that breeders can use to develop breeding strategies for sound genetic management and to reduce the incidence of genetic disorders in a breed, including the use of cross-breeding programs when necessary to restore genetic health.


    A DNA Primer for Dog Breeders

    1) Genetic Diversity

    2) Relationships
    • Kinship Coefficient
    • Mean Kinship (genetic value)
    • Dendrograms
    • Kinship Matrix

    3) Population Structure
    • Principal Components Analysis





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