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Genetic Selection of Horses. Introduction. Genetics are not as utilized in the horse industry as in livestock species who select for size, length, weight, efficiency of or maximal production of livestock Horse breeders look more at pedigree, eye catching traits, and subjective criteria.

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  • Genetics are not as utilized in the horse industry as in livestock species who select for size, length, weight, efficiency of or maximal production of livestock
  • Horse breeders look more at pedigree, eye catching traits, and subjective criteria
what traits do horse breeders select for



Athletic ability


Style (Hunter etc.)

Color pattern



What traits do horse breeders select for?
difficult to measure traits
Difficult to Measure Traits
  • Conformation
  • Disposition
  • Athletic ability
  • Intelligence
breeding systems
Breeding Systems
  • Crossbreeding - breeding different breeds together
    • major heterosis - variable results
    • breed registry book:
      • closed - AHR and Half-Arabian
      • open - ApHC and APHA to QH
        • AQHA, ApHC, APHA to TB
breeding systems7
Breeding Systems
  • Outbreeding - mating crosses of horses less related than the average within a breed
    • variability large
    • heterozygosity increases
    • increases genetic “pool”
breeding systems9
Breeding Systems
  • Inbreeding -
    • breeding horses more related than the breed average
      • increases homozygosity
      • increases the predominance of recessive diseases
      • uniformity of offspring increases
  • Linebreeding - increases the relationship to some admired ancestor
    • relationships within a pedigree are additive

Three Bars

Zippo Pat Bars

Leo Pat

I Inspire

Big Step

Teeny Step

Teeny Brown

CK Zippos Bar Bee

Zippo Pat Bars

Zippo Bar Pine

Dollie Pine

Zip Bar Bee

Double Bar Leo

Money Bee Honey

Chetterette Bar

effect of inbreeding
Effect of inbreeding
  • Uncover undesirable recessive genes
  • Reduced vigor
  • Reduction in growth rate
  • Increased mortality in offspring
  • Reduced immune response of foals
performance trait selection
Performance Trait Selection
  • How do we measure performance traits
    • # of wins/placings in shows
    • dollars earned
    • points earned/horses beaten
    • race placings - speed
performance testing
Performance Testing
  • 100 day test in warmbloods at stallion testing center
  • Train and compete horses before breeding
progeny testing
Progeny testing
  • Train and compete offspring
  • Only breed those animals with superior performance offspring
sib or family selection
Sib or family selection
  • Relies on performance of collateral relatives
  • Performance data in the pedigree
  • Often seen in sales catalog pages and reference stallions
  • Look for black type

1st dam

BRAVE RAJ, by Rajab. 6 wins in 9 starts at 2, $933,650, champion 2-year-old filly in U.S., Breeders' Cup Juvenile Fillies S. [G1], Del Mar Debutante S. [G2], Sorrento S. [G3], Florida Stallion/My Dear Girl S. [LR] (CRC, $240,000), Florida Stallion/Susan's Girl S. [LR] (CRC, $45,000), 2nd Junior Miss S. [L] (DMR, $10,000). Dam of 14 foals, 11 to race, 10 winners--

BRAVO BULL (c. by Holy Bull). Black type winner, see below.

RUSSIAN TANGO (f. by Nijinsky II). 4 wins at 3 and 4, $92,390, The Very One H. [L] (GP, $30,000). Dam of--

EUROSILVER (c. by Unbridled's Song). 4 wins, 2 to 4, 2005, $622,310, Lane's End Breeders' Futurity [G2] (KEE, $248,000), Skip Away H. [G3] (GP, $60,000), 2nd Stephen Foster H. [G1] (CD, $165,600), Swale S. [G3] (GP, $30,000), Perryville S. [L] (KEE, $22,520).

limitations of stallion indexes
Limitations of stallion indexes
  • Average of all offspring is unknown
    • only superior animals compete
  • Mare contributions hard to quantify
    • stallion managers screen superiority
  • Points, $$’s, and purse size influences
  • Miles and resources give advantage
    • Honor roll vs world champion
heritability estimate
Heritability Estimate
  • Definition
    • Percentage of a horse's expressed trait (phenotype) that is due to genetics
    • Due to genetics indicates the probability of trait being passed on from one generation to the next
    • Specifically, ability to select horses to mate based on superior performance for the trait and to predict the improvement in the offspring
selection process
Selection process
  • Greater progress when keeping # of selected traits to a minimum
  • Low heritabilty est. traits: increase success by controlling environment and management regimes
two basic types of genetic action
Two basic types of genetic action
  • Qualitative
    • Particular trait is influenced by a single pair of genes (or maybe 2 or 3 pairs)
two basic types of genetic action21
Two basic types of genetic action
  • Quantitative
    • Trait that is influenced by numerous different genes
    • Effects of many genes are added together to produce trait
    • Each gene only has small effect of trait
    • Most traits are quantitative
type of qualitative
Type of Qualitative
  • Dominance: ability of gene to mask or cover up its recessive allele
    • Only one dominant gene is required to display a particular trait
    • Two recessive genes are required for a recessive trait to be exhibited
types of qualitative
Types of Qualitative
  • Co-dominance
    • Gene action results in an intermediate state between two parents example: blood type
    • Each blood type is different, known, and indicates genotype
horse gtg idiogram
Horse GTG Idiogram
  • E. caballus
    • 64 chromosomes
  • E. assinus
    • 62 chromosomes
  • Odd hybrids are sterile
    • Mule
    • Hinny
    • zorse
parentage testing
Parentage Testing
  • Blood type group - AB on RBC surface
    • electrophoresis of 8 proteins - very specific
    • used to detect NI (neonatal isoerthyyhtolysis) - like Rh factor in humans - dam makes AB against foal blood type
    • blood type is example of co-dominance
parentage testing26
Parentage Testing
  • DNA Testing - uses microsatalite allele length variants - uses hair follicles
  • Polymerase Chain Reactions (PCR) & tag with florescent dye and sized by gel electrophoresis
  • Breeds all contract labs - need dam, sire, and foal
qualitative example
Qualitative example


  • Deficiency of B & T lymphocytes - susceptible to adenoviral pneumonia
    • Arabian & part-Arabian horses
    • Autosomal recessive - homozygous
    • cid cid - diseased
    • CID cid - carrier; CID CID – normal
  • Normal foal at birth.
  • Illness 2-5 months of age.
  • Die of infection
qualitative example28
Qualitative example
  • HYPP - Hyperkalemic periodic paralysis
    • sporadic attacks of muscle tremors, collapse
    • hyperexcitable muscle from voltage-gated K channel
    • Gene mutation in Impressive (QH)
    • Autosomal dominant - not sex linked
    • H/H and H/h are affected and hh - normal
    • Industry refers to hh as N/N
    • Hair follicle test
  • AQHA - Foals born January 1, 2007, and testing positive for the H/H status of HyPP, will no longer be eligible for registry.
qualitative example color related allele partial dominance
Qualitative example Color related allele - partial dominance
  • Ww - White
  • WW: Lethal
  • Ww: Horse typically lacks pigment in skin, hair and eyes and appears to be white.
  • ww: Horse is fully pigmented.
qualitative example lethal white in overo paint horses
  • Colon is formed but its nerve supply is missing - gut is paralyzed.
  • Atresia Coli - Sections of colon are missing.
  • Lethal White Overo (LWO) - not selective to the paint color overo pattern
  • extreme co-dominant - not really dominance/recessive
  • use allele specific PCR hair test
  • if O is sequence for overo gene, then
    • OO is lethal
    • ON is paint color pattern
    • NN is solid color “breeding stock”
  • colored x colored gives 25% lethal
quantitative example
Quantitative example
  • Racing
    • Affected by: size, length of leg, coordination, efficiency of heart, lungs, muscles, mental traits that affect the desire and determination of horse
  • 2 components involved
    • Heredity: genetic component
    • Environment: nutrition, training
      • Combination of many genes
what s new
  • Juntional Epidermolysis Bullosa (JEB)
    • Belgians
    • Moderate-severe blistering of skin & mouth & sloughing of hooves in newborns
glycogen branching enzyme deficiency gbed
Glycogen Branching Enzyme Deficiency (GBED)
  • Glycogen branching enzyme - protein necessary to build glycogen
  • Mutation in the GBE gene on chromosome 26
  • Autosomal recessive
  • Quarter Horse related breeds
  • Fatal in all cases by time foals reach 8 wks of age
glycogen branching enzyme deficiency gbed34
Glycogen Branching Enzyme Deficiency (GBED)

Biopsies from normal (left) and GBED-affected (right) horses stained with PAS.

  • Abortion or still birth of a foal
  • Weakness, low body temperature at birth.
  • Sudden death on pasture from the heart stopping or from seizures
  • High respiratory rate & weakness of the muscles used to breathe
  • Contracted tendons in all four legs
polysaccharide storage myopathy pssm
Polysaccharide Storage Myopathy (PSSM)
  • Muscle disease in Quarter Horses, Paint Horses & Appaloosas.
  • Another form of PSSM occurs in Draft, Draft crossbreds, warmbloods.
  • Enhanced insulin sensitivity & accumulation of glycogen
  • Severe muscle damage
  • Signs of tying-up
  • Muscle stiffness, sweating & reluctance to move
  • First noticed in horses when they are put into training or after a lay-up period
  • Episodes begin after very light exercise such as 10-20 min of walking and trotting.

A normal biopsy (left) and a biopsy from a horse with PSSM (right) stained with PAS. Note the lack of a uniform texture in the PSSM biopsy. The darker areas in the PSSM biopsy indicate the accumulation of excess glycogen and abnormal polysaccharide.

exertional rhabdomyolysis
Exertional Rhabdomyolysis
  • Most racing Quarter Horses, Thoroughbreds, Standardbreds and Arabians with tying-up suffer from a separate disease from PSSM called recurrent exertional rhabdomyolysis
hyperelastosis cutis hc herda
Hyperelastosis Cutis (HC/HERDA)
  • Lack of adhesion within the dermis due to a collagen defect
  • Recessive
  • Poco Bueno’s bloodline