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Genetic Testing in Dogs: Sep 15

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Genetic Testing in Dogs: Principles and Applications

Introduction to Canine Genetic Testing

Genetic testing in dogs, exemplified by the Embark test, utilizes molecular genetics to analyze inherited traits, health conditions, and breed ancestry. These tests are analogous to human genetic tests like 23andMe, but tailored for canine genetics.

  • Embark tests for over 270 health-related conditions and 55 physical traits.

  • Predicts breed mix and identifies DNA relatives.

  • Uses analysis of Single Nucleotide Polymorphisms (SNPs) to detect genetic variation.

Single Nucleotide Polymorphisms (SNPs)

SNPs are the most common type of genetic variation among individuals. They represent a difference in a single nucleotide at a specific position in the genome.

  • Definition: SNPs are single base-pair changes in the DNA sequence.

  • Used to identify unique alleles of genes and track inheritance of traits.

  • Example: SNPs in the T-box transcription factor gene affect tail length in Australian Shepherds.

Genotype and Phenotype Example: Tail Length in Australian Shepherds

  • Possible alleles: C and G

  • Genotypes and associated phenotypes:

    • CC: Normal length tail

    • CG: Bobtail

    • GG: Lethal, not observed

Genome Duplication and Trait Expression

Genome duplication can lead to increased gene expression, affecting physical traits.

  • Example: Blue eyes in Huskies are associated with duplication and increased expression of the ALX4 gene.

Genetic Testing Workflow

Genetic testing involves several steps, from sample collection to DNA analysis.

  1. Sample Collection: Cheek swab from the dog.

  2. DNA Extraction and Purification: Genomic DNA is isolated (dogs have 39 pairs of chromosomes).

  3. PCR Amplification: Specific genomic regions containing SNPs are amplified using Polymerase Chain Reaction (PCR).

  4. Genotyping: Analysis of >200,000 SNPs using the Illumina canine HD array.

Illumina Genotyping Chip Technology

The Illumina genotyping chip is a high-throughput platform for SNP analysis.

  • Single-stranded DNA oligos (probes) are attached to silica beads on a microarray.

  • Each probe binds to a complementary sequence in the dog's DNA.

  • Allele specificity is determined by single base extension with a fluorescent label.

  • Laser excitation causes fluorescent labels to emit signals, which are detected by the scanner.

  • Genotypes are distinguished by color: e.g., TT (clear), CT (carrier), CC (at risk).

Color Coding for Nucleotides

  • Thymine (ddTTP): red

  • Adenine (ddATP): red

  • Cytosine (ddCTP): green

  • Guanine (ddGTP): green

Genetic Health Conditions Identified

Genetic testing can identify predispositions to a wide range of health conditions.

Health Area

Examples

Eyes

Progressive retinal atrophy

Blood

Pyruvate kinase deficiency

Hormones

Thyroid disorders

Muscular

Muscular dystrophy

Kidney and Bladder

Renal dysplasia

Brain and Spinal Cord

Degenerative myelopathy

Heart

Mitral valve disease

Skin & Connective Tissue

Collagen disorders

Metabolic

Diabetes

Gastrointestinal

Malabsorption syndromes

Neuromuscular

Myasthenia gravis

Immune

Autoimmune diseases

Case Study: Degenerative Myelopathy (DM)

DM is a progressive degenerative disorder of the spinal cord, primarily affecting mature dogs.

  • Caused by mutations in the SOD1 gene.

  • Inheritance: Recessive; dogs with AA genotype are at risk.

  • Incomplete penetrance: Not all dogs with the AA genotype develop DM; environmental and genetic factors influence disease manifestation.

  • Pathology: Degeneration of white matter leads to demyelination and axonal loss, impairing communication between brain and limbs.

Progression and Treatment

  • Initial symptoms: Loss of coordination in hind limbs.

  • Progression: Paralysis within 6 months to 1 year; loss of urinary and fecal continence.

  • Treatment: No effective cure; hydrotherapy may slow onset; wheel carts improve quality of life.

Molecular Basis

  • SOD1 gene: Encodes superoxide dismutase, a detoxifying enzyme maintaining reactive oxygen species (ROS) homeostasis.

  • Subcellular location: Cytosol, mitochondria, nucleus, endoplasmic reticulum.

  • Mutation: Missense mutation (E40K) disrupts salt bridge between glutamic acid and lysine, destabilizing protein structure.

  • Mutant SOD1 forms amyloid-like aggregates, suggesting a gain-of-toxic function.

Gene Silencing Therapy

  • Experimental therapy involves RNA silencing targeting mutant SOD1.

  • Goal: Degrade mutant SOD1 RNA and increase ambulatory time for affected dogs.

Genetic Traits and Breed Identification

Genetic testing can predict physical traits and breed ancestry.

  • Trait Example: Muzzle length variation is due to genetic differences in the BMP3 gene.

  • Breed identification: DNA samples compared to 350+ reference breeds; long segments of identical chromosomal DNA indicate breed relationships.

Trait Classification Table

Muzzle Length

Breed Examples

Medium (ancestral)

Gray wolves, Leonbergers

Shortened

Pugs, Bulldogs, Boxers

Elongated

Afghan hounds, Greyhounds, Salukis

Genetic Testing: Pros and Cons

  • Pros: Enables lifestyle changes, informed breeding decisions, and early detection of health risks.

  • Cons: Unexpected results may cause stress; ethical considerations in breeding and disease management.

Assigned Readings and Applications

  • Health problems in purebred dogs: e.g., mitral valve disease, canine syringomyelia.

  • Dalmatian/Pointer backcross project: Unlinking Dalmatian spots from high uric acid production; implications for breed classification and health.

Key Terms and Concepts

  • SNP (Single Nucleotide Polymorphism): A single base change in the DNA sequence.

  • Genotype: The genetic constitution of an organism at a specific locus.

  • Phenotype: Observable traits resulting from genotype and environment.

  • Penetrance: The proportion of individuals with a genotype who express the associated phenotype.

  • Missense Mutation: A point mutation resulting in a single amino acid change in a protein.

  • Gene Silencing: Techniques to reduce or eliminate expression of a specific gene.

Relevant Equations

  • Hardy-Weinberg Equation: Used to calculate genotype frequencies in a population.

  • Superoxide Dismutase Reaction:

Additional info:

  • Genetic testing in dogs provides a practical application of core genetics concepts, including Mendelian inheritance, molecular genetics, and population genetics.

  • Technologies like Illumina arrays are widely used in both human and animal genomics for high-throughput SNP genotyping.

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