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Introduction and Definitions

A. Congenital Defects: Congenital defects include all undesirable traits and pathologic conditions present at birth whether they are genetic or due to intra-uterine events that results from extra-uterine influences. Congenital defects do not necessarily indicate inheritance; they simply indicate that the defect was present at birth.

B. Inherited Tendencies: There are characteristics in horses that are influenced by a wide variety of genes, whose pattern of inheritance is complex and whose expression has strong environmental influences. Horses have been selectively bred for centuries to promote or discourage these characteristics. The selection for or against these inherited tendencies is the basis for our current breed registries. Size, power, color, speed, conformation and many other characteristics that are genetically influenced are selected for or against by certain breed registries. Variations from ideal may be
undesirable but they are not deemed to be genetic defects.

C. Genetic Defects: Genetic defects are pathologic conditions of proven genetic origin. These may be the result of a mutation in a gene of major effect or mutations in multiple genes (polygenic) whose effects combine to produce a deleterious or undesirable result. The degree to which some traits are expressed in horses carrying particular mutations can be influenced by environmental factors. This is called incomplete penetrance. 

D. Undesirable Traits: An undesirable trait, as designated by certain breed registries, is a condition or behavior which may or may not be present at birth, may develop over time, may or may not be a genetic defect, but precludes registration of that animal. A variation in color is an example of a characteristic that may be considered by a breed to be undesirable. Concealment of such undesirable traits by any means, including surgery, is prohibited by breed registry. It is therefore unethical for a veterinarian to perform such treatments, except when the treatment is intended to improve the health of the horse, and when the veterinarian reports the treatment to the breed registry.

Genetic Tests Available for Horses

As of February 2012, tests for mutations in single genes are currently available for 12 diseases. 

Autosomal Dominant
Hyperkalemic Periodic Paralysis (HYPP) in the Quarter Horse
Type 1 Polysaccharide Storage Myopathy (PSSM) in numerous breeds
Malignant Hyperthermia (MH) in Quarter Horse related breeds

Autosomal Recessive
Overo Lethal White Syndrome (OLWS) in the Paint Horse
Severe Combined immunodeficiency (SCID) in Arabian Horses
Glycogen Branching Enzyme Deficiency (GBED) in Quarter Horse related breeds
Junctional Epidermolysis Bullosa (JEB) in Belgians
JEB in Saddlebred horses
Hereditary Equine Regional Dermal Asthenia (HERDA) in Quarter Horse-related breeds
Lavender Foal Syndrome in Arabians
Cerebellar Abiotrophy (CA) in Arabians
Fell Pony Syndrome

New information in equine genetics is being generated very quickly and this list will be updated as it becomes available.
 

Surgical Correction of Undesirable Traits and Genetic Defects

According to the American Veterinary Medical Association, surgical correction of “genetic defects” for the purposes of concealing the defect is unethical. If surgical correction is undertaken for the purpose of improving the health of the individual, then it should be accompanied by sterilization to prevent the perpetuation of the genetic defect. The AAEP agrees with the intent of this position. Further, surgical correction of any characteristic specifically named by the breed organization as being prohibited, for the purpose of concealing the characteristic for obtaining registration, would be considered fraudulent and unethical. Such procedures offer no benefit to the horse and are intended only to deceive the breed organization. The AAEP does support surgical correction of conditions that are in the best interest of individual horses.
 

Identification of Genetic Traits

AAEP supports the use of genetic testing by veterinarians or breed associations to identify genetic mutations in animals so that owners can make informed decisions about breeding, purchase and specific
treatments. Breed associations should be contacted to determine if  there are any restrictions on registration of horses with genetic defects. Licensed laboratories should be used for genetic testing.
More information on equine genetic diseases is available at these websites:

http://www.vdl.umn.edu/
http://www.cvm.msu.edu/research/faculty-research/valberg-laboratory
http://www.vgl.ucdavis.edu/services/horse.php
http://vetsci.ca.uky.edu
http://www.uky.edu/Ag/Horsemap/