Breeding horses: how genetic variants pass to foals

How a mare and stallion each pass on a version of a gene

A gene is a stretch of DNA involved in how the body functions. A variant is a difference in its DNA sequence; different versions at the same genetic location are called alleles. In these examples, the genes are autosomal, meaning they are on chromosomes other than the sex chromosomes. A horse has two copies at the location studied, one from its dam and one from its sire. Their combination is its genotype.

When a parent has two different versions, it has a one-in-two chance of passing either one to each foal. If its two versions are identical, it passes that version to every foal. This explains why siblings from the same parents can inherit different combinations. The examples below concern one variant at a time; they do not describe every form of inheritance.

Sources [1]

HERDA: why two unaffected carriers can have an affected foal

HERDA is an inherited disease that makes the skin fragile. For the variant tested for, a horse with one copy is an unaffected carrier of HERDA; a horse with two copies develops the disease. Here, HRD denotes that variant and N denotes the version without it. N does not mean that the gene is missing.

If both the mare and stallion are N/HRD, either can pass N or HRD. Two of the four equally likely combinations give a foal with one copy, which is why the carrier probability is 50%. If one parent is confirmed N/N, the foal cannot inherit two copies of this HERDA variant. It can still inherit one copy from the other parent.

Sources [1] · [2]

PSSM1: a parent with a negative result does not prevent transmission

PSSM1 is a muscle disease associated with a variant in GYS1. It has dominant inheritance: one copy can already cause disease signs. In this example, P1 denotes the PSSM1 variant. A parent with genotype N/P1 has a 50% chance of passing it to each foal, even if the other parent is N/N.

A foal with one copy must therefore not be described as an unaffected carrier in the same sense as for HERDA. However, the severity and occurrence of visible signs vary. A 50% chance of inheriting the variant does not mean a 50% chance of a particular clinical outcome. The DNA result cannot predict exactly how the foal’s health will develop.

Sources [3] · [4]

Why the probabilities apply afresh to each pregnancy

For two N/HRD parents, a 25% chance of an affected foal means one chance in four at each conception. It does not mean that an affected foal must follow three unaffected foals, or that four foals will include exactly one affected foal.

An earlier foal’s result does not change the next foal’s probabilities when the same parents’ genotypes are confirmed. The 25% / 50% / 25% figures describe alternative genotypes for one variant and add up to 100%. Percentages for different diseases or traits cannot simply be added or multiplied to obtain an overall health risk.

Sources [1] · [2]

What can be concluded when a parent’s DNA result is unknown

An untested horse is not a horse with a negative result. Appearance, breed and the birth of a healthy foal do not establish whether a parent carries a recessive variant. If one HERDA parent is N/HRD and the other is untested, the examples above cannot establish a single probability of an affected foal.

For a recessive variant, a parent confirmed N/N rules out the foal inheriting two copies of that variant, even if the other parent’s result is unknown. It does not determine whether the foal carries one copy. Coat appearance is also insufficient for some variants: a horse carrying frame overo can have little visible white. Several genes and environmental factors can contribute to other conditions, which these single-variant examples cannot predict.

Sources [2] · [5] · [4]

Using both parents’ results to assess a planned mating

Compare reports for the same disease and the same variant, checking the horses’ identities and each laboratory’s notation. A result described as negative applies to the variants tested for. Discuss any uncertain result or disease-associated variant with a veterinarian before drawing a conclusion about the mating.

For HERDA, pairing an unaffected carrier with a parent tested N/N prevents the two-copy combination for the tested variant, but does not remove the variant from all offspring. A dominant variant such as PSSM1 requires different reasoning. Breeding decisions also need to consider the horses’ health, welfare and relatedness, and the population’s genetic diversity. A few negative tests cannot guarantee a healthy foal.

Sources [2] · [3] · [6]

Questions about inheritance and breeding

Sources on inheritance and breeding

These examples draw on university genetics resources and IFCE guidance. References appear beside the relevant explanations. The diagrams illustrate confirmed genotypes, rather than results from particular horses.

1. 1.University of Minnesota — Mendelian inheritance in horses
2. 2.UC Davis Veterinary Genetics Laboratory — HERDA and interpretation of DNA results
3. 3.UC Davis Veterinary Genetics Laboratory — PSSM1 and transmission of its variant
4. 4.University of Minnesota — Simple and complex genetic diseases
5. 5.UC Davis Center for Equine Health — Lethal white overo syndrome
6. 6.IFCE — Genetic diversity and choice of breeding horses