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Horse Breeding Realities – Reproductive Management

HWAC acknowledges with appreciation the cooperation and funding by the North American Equine Ranching Information Council (NAERIC) to facilitate the series of articles “HORSE BREEDING REALITIES – REPRODUCTIVE MANAGEMENT” composed by Judy Wardrope, JW Equine.

Articles Series

  1. Breeding Realities Introduction
  2. Breeding Realities and Basic Genetics
  3. Genetic Disorders – Part I
  4. Genetic Disorders – Part II
  5. The Selection Process and Breeding Theories

 

Breeding Realities Introduction

Breeding horses can be exciting, but it also means we must weigh our options and make decisions. Our hopes are elevated as we picture that perfect foal romping in our fields. Our pride swells, yet we have to be realistic.

Being Realistic

In order to have a reasonable expectation of producing a quality foal, we need to ask ourselves some serious questions. Should we breed or not breed? Which mare to which stallion? What criteria should we use to make our selections? The path to suitable options may resemble a minefield, but with some forethought, research, and honest analysis, we may avoid some of the traps, and the resulting foal may be just what we hoped.

Part of the process is deciding the intended purpose of the foal. Will the resultant foal be retained or be destined for the commercial market? Commercial foals need to meet certain specifications in order to attain higher selling prices. Although commercial appeal may not be part of the equation for the homebred, quality remains important. Since breeders are taking on Mother Nature’s role, the goal should be to produce structurally sound horses that are free of genetic disorders.

For many people contemplating breeding, one of the major factors in the decision process is finance. Therefore, for those who have this consideration, dollar-value is key. We can find some very reasonably priced if not downright cheap mares; however, that does not necessarily mean they are good dollar value as breeding stock. This same reasoning applies to stallions judged solely by their stud fees. In addition, if the mare is to be sent out for breeding, the breeder will need to budget for the costs of transportation, board and veterinarian fees (ultrasound and/or palpation to determine ovulation or pregnancy) on top of the stud fee.

Even if finances are not an issue, some of the information provided by research and analysis will be helpful in deciding on short and long-term breeding plans. Is the breeding and production history of the mare known? If we have an in-house stallion, knowing the mare’s breeding history makes the task of getting her pregnant easier, and if the history is not promising, perhaps that will sway the decision in a different direction. If we have chosen to breed using shipped semen (fresh or frozen), knowing the mare’s history of production can save a considerable amount of money and frustration. We can either prepare for the needs of that particular mare or eliminate her as a poor candidate for insemination. This is why it is advisable to consult a veterinarian. It would be wonderful if we could all order one dose of semen from our chosen stallion, have the mare inseminated and a few weeks later, pronounced in foal. But alas, that seldom happens.

With the advent of frozen semen and improving technology, we can breed to any of thousands of stallions that are alive and many that are not. The mind boggles at the possibilities. Sure, the horses we are exposed to on television, in magazine articles and at the big competitions are wonderful, but imagine the percentage of horses that we never see because they just weren’t good enough. The reality is that not all breedings result in the foals we envision. That doesn’t mean the foals, if bred with an eye to overall quality, are without merit. Many horses didn’t make it in the venue or at the level that was intended, but with the right blood and proper functional conformation, they found a niche or excelled in another venue or at another level.

Being Responsible

Sir Robert Baker is quoted as saying, “A breeder is one who leaves the breed with more depth of quality than when he started. All others are but multipliers of the breed.” People should show accountability to individual animals and to the relevant gene pools since many welfare problems can be prevented through responsible breeding.

When interviewed for an article about the retirement of horses, Canadian-born actor and long-time horseman, William Shatner, said, “All horse owners need to realize that when they have a horse, they are assuming a responsibility – not just to grow them, exercise them or train them fairly and kindly… It is like being a parent. You may like the idea of having a baby in the house, watching it grow, become a teenager and then leave the house, but your obligation does not end there. Your obligation is over the length of their lifetime. Putting a horse down is as sorrowful as losing a member of the family.”

Numerous criteria can be used alone or in combination to make responsible breeding selections. One school of thought bases breeding plans on the assessment of phenotype (appearance, size, type, temperament, and ability). When the mare and the stallion complement each other, a mating may be considered. If one of the parents has a perceived weakness we can seek a mate that has considerable strength in that area to compensate.

Have we made a true and honest assessment of mare and stallion? If not, we should seek the advice of a veterinarian or a non-biased industry professional. Simply saying that the mare is pretty, tall, or has some other quality, and that the stallion looks big and powerful, are not evaluations on which to base breeding. If, after close scrutiny, we can say that the mare and the stallion truly complement each other for the desired purpose or use, then a mating could be considered. Remember that if both potential parents are short necked and have offset cannons, the offspring may well be short necked or have offset cannons. That does not mean that if you breed a long-necked horse to a short-necked horse that you will end up with a medium-length necked foal, or that a straight-legged horse bred to one with offset cannons will produce a foal with slightly offset cannons. Genetics do not work that way.

To further complicate the picture, one or both of the parents may not display a trait, but may carry a recessive gene for it, and if both parents contribute their recessive genes, the foal will display the trait. So, as mentioned before, knowing the breeding and production history of both horses is very important. Generally, if you breed “like” to “like,” the result should be close to the “type” of the parents.

An examination of genotype (genetic makeup, pedigree and factors in the lineage) helps identify characteristics that may or may not be displayed in the individual. Many qualities are deemed worth knowing in the ancestry, such as a genetic tendency to pass on a particular trait (good or bad) or a genetic mutation. In some cases, the idea of crossing two individuals may have to be abandoned due to the risk factors. But, by the same token, genetic factors may lead us to choose a mating that could produce our wonder horse. If, for instance, the genetic background of either parent shows a tendency to throw a bad disposition, susceptibility to a particular disease, or a conformational defect, then the genetic makeup of the other becomes even more important. The breeding and production history of the families can also be used to gauge which horses tend to be more prepotent in stamping their offspring. Unfortunately, most traits cannot be guaranteed because of the nature of genes. Witness the degree of difference in full siblings.

Being Objective

As a noun ‘objective’ refers to the intended goal, and, as an adjective, it means undistorted by emotion, bias or interpretation and is the opposite of subjective. Both definitions can be advantageous when choosing a suitable mate for our mares and our stallions.

Objectively evaluating the functional aspects of conformation of both mare and stallion perfectly supplements pedigree evaluation, performance records, production history, genetic testing and such. It also compliments financial choices, allowing the bargain hunter to get the most value for their budget as well as decreasing the likelihood of producing a substandard offspring no matter the costs.

Consider what happens to the foal with the fabulous pedigree that lacks the physical abilities suggested by the lineage. It will likely be pushed – at its own peril – to reach human expectations based on its ancestry.

Code of Practice

The National Farm Animal Care Council’s Code of Practice for the Care and Handling of Equines states: “Horses, donkeys and mules are bred for multiple purposes. Established breeders generally follow a specific breeding program producing quality offspring for a specific market.”

It goes on to define responsible breeding and recommended practices. It can be found in its entirety here: www.nfacc.ca/codes-of-practice/equine
 

Breeding Realities and Basic Genetics

Although this article is about basic genetics, that should not be taken to mean that genetics are simple. In fact, genetics are anything but simple; they are actually quite complex.

David Trus, geneticist in the Animal Industry Division of Agriculture and Agri-Food Canada, said, “I typically like to work from simple to more complex, especially with genetics, which rapidly befuddles people. Simple principles work.” He went on to add, “The biggest complexity though, may be in how people insert themselves in the process.”

But don’t be deterred. If you have a little understanding of human or any other form of genetics, it may come as a relief to know that the same basic principles apply to horses…and other species.

Mendel’s Milestones

Many people have heard of Gregor Mendel, his basic principles of genetics and his book, Origin of Species. His ideas were published in 1866, but he died in 1884, some six years before his work was recognized as truly meaningful.

Mendel came to three important conclusions based on his experiments with peas:

  1. The inheritance of each trait is determined by “units” or “factors” (now called genes) that are passed on to descendants unchanged
  2. An individual inherits one such unit from each parent for each trait
  3. A trait may not show up in an individual but can still be passed on to the next generation.

Based on the seven traits he studied in pea plants, he found that one form appeared dominant over the other (or masked the presence of the other). For example, when the genotype for pea seed color is YG (heterozygous), the phenotype (physical trait) is yellow. However, the dominant yellow allele does not alter the recessive green one in any way. In fact, either allele can be passed on to the next generation unchanged.

Mendel’s observations from experiments can be summarized in two principles:

  1. The principle of segregation
  2. The principle of independent assortment

According to his principle of segregation, for any particular trait, the pair of alleles of each parent separate and only one allele passes from each parent on to an offspring. Which allele in a parent’s pair of alleles is inherited is a matter of chance. We now know that this segregation of alleles occurs during the process now called meiosis.

And according to his principle of independent assortment, different pairs of alleles are passed to offspring independently of each other. The result is that new combinations of genes present in neither parent are possible. Today, we know this is due to the fact that the genes for independently assorted traits are located on different chromosomes.

Mendel’s principles of inheritance, along with the understanding of unit inheritance and dominance, were the basis of modern genetics. However, Mendel did not realize there were exceptions to the rules, and he certainly did not foresee the discovery of DNA and its double-helix structure in the 1950s.

Beyond Mendel

By the 1960s another leap in genetic research brought Mitochondrial DNA (mtDNA) and its unique method of transfer to the mix. Mitochondrial DNA is vital to life at the cellular level and is only passed from mother to offspring. While males inherit mitochondrial DNA from their mother, they cannot pass it on to any of their offspring.

As we will see in subsequent articles, there are several modes of inheritance beyond Mendel’s foundation and that genes/alleles may be influenced by other factors, including modifiers.

Due to the complexity of equine genetics, coat colour is often used to provide examples of, and parallels for, how genes work. One excellent online source is the UC Davis Veterinary Genetics Laboratory. www.vgl.ucdavis.edu/services/coatcolor.php

The site states, “For every living thing millions of instructions called genes are used for its growth, appearance and maintenance. It is not possible to see a gene, even with the most sophisticated microscope available. We recognize the presence of genes because of their effects on the organism in ways that we can see or measure.

“Every cell contains a duplicate set of genes. Each set is derived from the single gene sets contributed at conception by both the mother and the father. The gene sets contain similar, but not necessarily identical, information. For example, both sets may contain a gene determining hair structure, but one set may contain the instructions for straight hair and the other for curly hair. The alternative forms of each gene are called alleles. If both alleles are identical, then the animal is said to be homozygous at that gene; if the alleles are dissimilar, then the animal is said to be heterozygous at that gene. Information about the homozygosity or heterozygosity for various genes can be inferred from information about parents and/or progeny and can be used for predicting the outcome of matings.

“Both sets of genes function simultaneously in the cell. Often when the gene pair is heterozygous, one allele may be visibly expressed but the other is not. The expressed allele in a heterozygous pair is known as the dominant allele, the unexpressed one as the recessive allele. The term dominant is given an allele only to describe its relationship to related alleles, and is not to be taken as an indication of any kind of physical or temperamental strength of the allele or the animal possessing it. Likewise, possession of a recessive allele does not connote weakness.

“In any animal expressing the dominant allele of a gene, it cannot be determined by looking at the animal whether the second allele is a dominant or a recessive one. The presence of a recessive allele may be masked by a dominant allele, which leads to the expression ‘hidden recessive.’ Dominant alleles are never hidden by their related recessive alleles.”

This is one of the most concise yet informative writings that this scribe has seen on the subject. It will be well worth your time to go to the site and read further.

Big-Picture Thinking

Mr. Trus notes that the responsibility of breeders is not just to the individual animal, but to the greater population as well. “Animals always exist within the context of a larger population. Each animal is the genetic result of a random combination of the genetics of its sire and dam following reproduction, producing a unique assortment of genes and genetic makeup. This process carries on from generation to generation. The resulting genetic variation from all breeding events is essential to the overall genetic health of populations, which must be maintained in sufficiently large numbers and genetic diversity to ensure their well-being, utility and survival.”

You have likely observed that within most human families, full siblings (unless they are maternal twins) are quite different from each other, yet there are often common traits that run through a family. The same is true in horses and is explained by the random combinations referenced by Mr. Trus. Thus, despite marketing attempts to make us believe otherwise, it is rather uncommon for two equine siblings to perform the same job at the same level.

Trus also emphasized, “Modern animal breeding seeks to direct the natural evolutionary process. Rather than fitness for survival in the wild, breeders seek to breed animals which are productive and excel at certain functions, are manageable, fit and healthy for the desired usage. Good breeding is most effectively achieved as a collective undertaking of many breeders having common goals, typically within a breed. In the end, good breeding should be directed towards the collective goals of breeders, be beneficial to the well-being of individual animals, and be positive for the fitness and survival of the population.”

New Directions

DNA testing as a form of parentage verification was introduced and quickly became the norm among breeds and registries. Now an ever-increasing number of genetic tests are available. And, as the horse genome was mapped, tests became available for more and more genetic disorders that affect horses, including some that affect certain breeds specifically. The question is not whether to test, but rather what one does with the information provided.

Ernie Bailey, PhD of MH Gluck Equine Research Center at the University of Kentucky and former chair of the Horse Genome Project, observes, “Every month some new test is developed or proposed. Which ones make it to commercial application? Hard to say.”

Does that mean there are actually more genetic disorders now? “I think that we are just more aware of them,” responds Dr. Bailey. “In the past it was a cost of doing business. Today we can use the information and therefore talking about it is useful. The impact of testing is to reduce the number of affected individuals.”

Domestic equines will continue to evolve based upon pressures for superior performance and certain physical characteristics (phenotype). Hopefully the registries, studbooks and individual breeders will provide sufficient guidance and stewardship (which was easier when the number of horses was smaller) so that the horses meet market needs and are noted for usability, soundness and longevity.

Sir Robert Baker is quoted as saying, “A breeder is one who leaves the breed with more depth of quality than when he started. All others are but multipliers of the breed.” Breeders should be accountable, both to the individual animals they produce and to the relevant gene pools, since many welfare problems can be prevented through responsible breeding.

As breeders, we all have a responsibility to think of the long term as well as the short term. After all, we are the true guardians of the gene pool as it moves into the future.
 

Genetic Disorders – Part I

In the previous article, we delved just below the surface of equine genetics. But, as stated in that Basic Genetics piece, the inheritance of traits is a complex subject. In this article we will dig a little deeper and begin to examine genetic disorders in the horse as well as types of genetic expression.

Categories

Understanding the difference between dominant and recessive gives us a start, but as Ernie Bailey, PhD of MH Gluck Equine Research Center at the University of Kentucky and former chair of the Horse Genome Project, observes, “It’s always tricky to categorize things. The subject is mode of inheritance and people have used the following terms: dominant, recessive, multigenic, complex, sex-linked, sex-limited, co-dominance, partial dominance, etc. The terms arise with respect to the array of phenotypes (physical traits) that result from different gene actions.”

Just one example that proves Dr. Bailey’s point is the gene for milk production in mares. While both males and females have genes for milk production, they are only expressed in females, making those specific genes sex-limited.

Dr. Bailey opines, “My own thinking about categories is 1) phenotype is caused by action of a single gene (dominant, recessive, partial dominant, sex-linked, etc.) such that a diagnostic test is developed that confirms diagnosis, or 2) phenotype is complex and caused by a combination of genes, or genes plus environment.”

He adds, “Dominant/recessive are flip sides of a phenotype. Consider hair color in horses: Black phenotype is dominant and chestnut is recessive. The gene is MC1R. The gene isn’t dominant or recessive; its alleles causing the colors are. Animals have two copies of all genes, except some genes on the sex chromosomes. In most cases a single functioning gene is all that is needed for health. Black hair color is the result of a receptor binding melanocortin. If half the receptors on the cell surface cannot bind melanocortin, the cell still has enough functional receptors to produce black pigment. Red hair color is the absence of any receptor binding function; [in other words, it requires] two defective copies of MC1R.

“I think that as far as the breeders are concerned the main question is this: Does a single allele cause a change in phenotype?” One way to find out is through genetic tests, but not all traits have tests attached to them…yet.

Genetic Testing

With the ever-increasing number of genetic tests available for horses, breeders have access to information that was previously only available through trial and error. Unfortunately, and with some regularity, the ‘error’ portion resulted in death or suffering in the resultant offspring. In the case of a number of genetic disorders, there is a laboratory test to determine if a horse will be affected by the disorder, is a non-affected carrier of the disorder or is clear of the disorder.

According to Dr. Bailey, “Every month some new test is developed or proposed. Which ones make it to commercial application? Hard to say.” Beyond genetic test results, it is important to know whether any particular disorder is dominant, recessive or has some different mode of expression when it comes to making informed breeding decisions. It is also advisable to know which disorders and/or syndromes affect the type or breed of horses we are contemplating breeding. (We will look more fully at breed-related syndromes and disorders in the next article.)

Mode of Inheritance

Inheritance of genetic disorders depends on the transmission of dominant genes and recessive genes. Genetic defects include any abnormality that is due to a change in the DNA that affects development, such as a new mutation occurring in the embryo’s DNA that causes a problem, but that is not inherited from either parent.

Not all horses that possess a mutated gene express clinical signs of a disease or defect. Genes occur in pairs that perform the same function (i.e. determine coat color or some other trait) but the activity of one gene may dominate the activity of the other (recessive) gene. A pair of genes may also be co-dominant, meaning that each contributes equally to the resulting trait.

When a disorder or syndrome is classified as dominant, only one copy of the dominant gene is necessary for expression of the trait. When a horse with a dominant trait for a disorder is bred to a horse that is clear of the gene for that disorder, there is a 50% chance of the resulting offspring developing the disorder or syndrome. In other words, about half of that first horse’s offspring will exhibit the defect, and that half of the affected offspring of that first horse will pass the defect to their offspring even if bred to horses clear of the gene for that disorder. The numbers can multiply quickly, so consideration must be given to that fact when contemplating breeding with horses with dominant genes for a disorder.

If the gene for a particular disorder is recessive, two copies (one from the sire and one from the dam) are required for the offspring to express the disorder. Any offspring with only one copy of the mutated gene will be completely normal; however, he/she will be a genetic carrier of the disorder. But when he/she reproduces, there will be a 50% chance that he/she will pass the mutated gene on to his/her offspring. If the foal of two carriers receives a recessive gene from both parents (each parent has a 50% of passing their recessive gene), the foal will have the disorder. If the disorder is not life-threatening, then the foal could mature and enter the gene pool, but that mature animal would pass on one gene for the disorder 100% of the time because both its genes are associated with expression of the disorder, even though the gene has a recessive role when paired with its dominant counterpart.

If a carrier (one normal gene and one recessive gene) is mated with a non-carrier (two normal genes), each foal has a 50% chance of becoming a new carrier by inheriting a recessive gene from the carrier and a 50% chance of becoming a non-carrier by inheriting two healthy genes. However, when two carriers are mated, the resulting foal has a 50% chance of becoming a new carrier of one recessive gene, a 25% chance of getting both mutations and acquiring the disorder and only a 25% chance of becoming a non-carrier.

But it is not always so simple. As Dr. Bailey points out, “The overo/OLWFS (Overo Lethal White Foal Syndrome) trait is tricky because the mutation causing overo is the same as the one causing OLWFS. It would seem the allele has both aspects. The classification of the alleles would seem dependent upon the genotype. I just read a review where the author objected to referring to the genetics of OLWFS as recessive since the EDNRB gene has a dominant effect causing frame-overo. Interesting. EDNRB exhibits both: recessive for lethal white foals and dominant for overo color pattern.”

Breeding Considerations

It is clear that although testing may provide an answer concerning a horse’s status in regards to a syndrome/disorder, breeders will carry the responsibility regarding the propagation and numbers of affected horses, carriers and non-carriers in the gene pool.

Dr. Bailey says, “If there is a test for a gene causing a disease, then one could eliminate that gene from the population in a single generation. Just require testing and refuse registration to carriers. However, that practice would eliminate a lot of good genes to get rid of one bad one. Breeders have selected horses for generations to increase performance genes in the population. We need to keep these genes in the population. If we outlawed horses that carry deleterious genes, pretty soon we would have a very small population and not one selected for performance. Since some disease genes are recessive and carriers are normal and healthy, the most intelligent approach is to test and set up matings to be sure that affected foals are not produced. Breeders should select for performance, not against disease.”

If given the choice between two horses of equal genetic merit where one is a carrier of a genetic disorder/syndrome or some form of unsoundness and one is not, it seems obvious that using the non-carrier would help reduce the number of carriers in the gene pool over the long term.

David Trus adds, “Disorders should really be discussed in the context of good breeding practices, such as limiting inbreeding, maintaining sufficiently diverse lines within a breed, selection based on multiple traits (e.g. health, growth, performance, temperament, [which] are determined by very different genes) rather than single trait emphasis. So if we acknowledge there are potentially many deleterious genes in a population, getting rid of them no longer makes that much sense – as most people tend to think. Rather, good breeding practices are key. Only a very limited number of disorders will be worthwhile targeting. On the other hand, the appearance of new genetic disorders could be looked on suspiciously as the possible result of poor breeding practices.”

Breeder Responsibility

It is the breeder’s responsibility to know which disorders their horses are predisposed to propagate, and to take the appropriate steps to ensure the welfare of the foals they will be producing as well as the gene pool at large. Such consideration applies to purebreds, cross-breds and grade horses whether they are registered or not.

In the next article in this series we will look at some breed-specific or type-specific disorders as well as resources for accessing information about them.
 

Genetic Disorders – Part II

This article will touch on some of the known genetic diseases, disorders and/or syndromes in horses. It will also suggest resources for further investigation. Naturally, other sources of information are available, especially through breed organizations and registries.

HYYP – hyperkalemic periodic paralysis (from aqha.com) “The most-common symptoms of HYPP include muscle tremors, weakness, muscle cramping, yawning, depression, an inability to relax the muscles, sweating, prolapse of the third eyelid, noisy breathing and/or abnormal sounds or whinnies.

“In 1996, AQHA designated HYPP a genetic defect and undesirable trait. Two years later, the Association added that all Impressive-descendent foals born after January 1, 1998, were required to be tested for the disease and parentage verified for registration, with the results placed on the registration certificate. Since 2007, any horses tested as H/H are not accepted for registration with AQHA.”

Impressive, a foal of 1969, became a dominant influence in halter horses in the Quarter Horse, Paint and Appaloosa breeds. It wasn’t until 1992 that this stallion was identified as the propagator of HYPP. Not all descendants of Impressive have HYPP, but all horses with HYPP descended from Impressive. A genetic test became available in 1994.

Further info on HYPP can be found here: https://www.aqha.com/hypp

The AQHA has required a five-panel test for all breeding stallions since 2015. The panel includes testing for GBED (glycogen branching enzyme deficiency), HERDA (hereditary equine regional dermal asthenia), HYPP (hyperkalemic periodic paralysis), MH (malignant hyperthermia) and PSSM (polysaccharide storage myopathy).

OLWFS – overo lethal white foal syndrome is also known as Lethal white syndrome (LWS), overo lethal white syndrome (OLWS) and lethal white overo (LWO). Affected foals are delivered looking normal and healthy. They are all white or nearly so and have blue eyes, but their colons do not function, meaning they colic within hours and will die within a few days if not euthanized.

SCID – “Severe Combined Immunodeficiency (SCID) is a lethal genetic disorder that results in an affected foal being born with a severely weakened immune system. SCID is caused by a mutation in the coding for the enzyme DNA-protein kinase catalytic subunit (DNA-PKcs) located on chromosome 9, which is responsible for the formation of key immune defense molecules. Because the foal’s natural defense system against infection is not functioning properly, by the time they are five months of age, they die of an opportunistic infection (such as pneumonia) or they are euthanized.

VetGen, LLC states, “SCID is known to be an autosomal recessive trait. ‘Autosomal’ means that there is no sex linkage, so both males and females can be equally affected. ‘Recessive’ means that in order for a foal to be affected, it must have received two copies of the mutated gene, inheriting one copy from each parent. Horses that have one copy of the mutated gene, in combination with one copy of the normal gene, are physically normal but are considered carriers and have a 50% probability, each time they are bred, of passing the mutation along to their offspring. Although the first veterinary publication on SCID appeared in 1973 and the mode of inheritance was determined in 1980, it wasn’t until 1997 that a direct DNA test became commercially available. The use of this test allows breeders to make informed breeding choices and avoid ever breeding an affected foal.”

Other Breed-Related Diseases

The Connemara and the Warmblood have two entirely different diseases/syndromes and two entirely different issues concerning them. The Connemara has to contend with a small gene pool, while the warmblood gene pool is vast and horses often ‘migrate’ from registry to registry or are approved by several.

HWSD – Statement re Hoof Wall Separation Disease (HWSD) in Connemaras as shared by the registrar: “In an effort to reduce the number of foals affected by HWSD, the American Connemara Pony Society (ACPS) has adopted the following breeding policy: All breeding stallions must be tested with UC-Davis lab, and the test results reported to the ACPS Registrar. The foals of 2016 by untested stallions will not be registered until the foal is tested for HWSD.

“The ACPS also strongly supports the importance of testing all breeding mares prior to covering. The simple test will be a breeder’s best tool to avoid producing foals affected by the Hoof Wall disease. This policy will reduce the possibility of affected foals if the test results are used responsibly by both the stallion and mare owners.

“The subsequent edit of sentence 2 will be: The foals by untested stallions will not be registered until the foal is tested for HWSD.

“The policy in 2017 became – no foal will be registered until the HWSD [status] is known and recorded. If both parents are N/N, no testing will be done. If either parent is N/HWSD or a carrier, the foal must be tested. The results of the tests will be printed on each registration certificate.”

WFFS – Warmblood Fragile Foal Syndrome: According to Animal Genetics Inc., Warmblood Fragile Foal Syndrome (WFFS) is an autosomal recessive trait, meaning a foal can only be affected if that foal inherits the disease from both parents. Parents that are carriers do not have any symptoms associated with WFFS. However, they will pass on a copy of the defective gene 50% of the time whether bred to a carrier or a non-carrier and regardless of the foal’s gender. If two carriers are bred, the foal has a 25% chance of being affected (a death sentence if carried to term and a likely cause of aborted fetuses), a 50% chance of being a carrier and only a 25% chance of being clear of the defective gene.

In March of 2012, a mare that gave birth to a foal with all the symptoms currently associated with WFFS was at first thought to be a carrier for a different genetic disease, such as Hereditary Equine Regional Dermal Asthenia (HERDA, which was discovered in 2007). When she was found to not be a carrier, exploration of her and some of her relatives led to the identification of the genetic anomaly responsible for WFFS.

A genetic test for Warmblood Fragile Foal Syndrome Type 1 (WFFS), developed by N. Winand, became commercially available in 2013, but there wasn’t that much public talk about the syndrome until 2018.

Now most, if not all, of the warmblood registries have issued statements promoting testing. However, advice regarding choices based on test results is usually not given.

Additional Resources

Dr. Bailey, who is quoted in the previous articles, advises that there is a compendium: Online Mendelian Inheritance in Animals. http://omia.org/home/ “It is a database in Sydney, Australia that attempts to keep track of all single genes that have an effect on phenotype in all species. Horses are well represented there.”

Genetic Testing for Horses: What is available and when to use it is available as a pdf document. https://vvma.org/resources/Conferences/2016%20VVC%20Notes/Valberg-%20Equine%20Genetic%20Diseases.pdf. Disorders, modes of inheritance as well as the estimated percentages of the population affected are included and the list of breeds is quite extensive, making it well worth the time to read.

This online article – https://westernhorseman.com/horsemanship/eight-known-genetic-diseases/ – discusses some of the common genetic diseases from a breed-specific perspective and includes: GBED, HERDA, HYPP and MHS in stock horse breeds; JEB in Belgians and Saddlebreds; LWFS in Paint horses; PSSM1 in stock horse and draft breeds; SCID in Arabians; etc.

Another great article

The article found here https://thehorse.com/111370/genetic-disorders-breed-by-breed/ includes: CA, JES, LFS and SCID in Arabians; FIS in Fell and Dales ponies; HERDA and HYPP in Quarter Horses; JEB in draft horses; OLWS in Paints; PSSM1 in Quarter Horses and Draft Horses; etc.

This particular article makes several excellent points worth including here: “Because the mass institution of equine chastity belts isn’t feasible, the best way to minimize the perpetuation of genetic disorders is testing. A wide range of tests is currently available and, as we’ve noted, some breed associations…demand proof of certain test results before you can register your horse. Such groups have demonstrated the benefits to this practice.

“’The goal is not to stop breeding carrier horses—and, thus, lose their gene pool—altogether,’ notes the World Arabian Horse Organization. Rather, testing can help breeders avoid crossing carriers with carriers while still retaining those bloodlines’ desirable pedigrees and associated traits.

“In 2013 British researchers highlighted the benefits of genetic testing when they reported that they had identified the genetic mutation responsible for foal immunodeficiency syndrome (FIS) and successfully reduced disease incidence. This disorder, not to be confused with SCID, occurs in Fell and Dales ponies and is caused by a fatal recessive mutation that results in the lack of B lymphocytes. Scientists subsequently developed a test that revealed 38% of tested Fell ponies and 18% of breeding Dales were FIS carriers. After testing and avoiding carrier-to-carrier breeding, the number of affected foals decreased dramatically in just two to three years.” Here’s part of the article’s very important take-home message: It behooves all horse owners to breed responsibly, research a horse’s genetic disease potential prior to purchase, and consider the importance of testing.

Partbreds, Crossbreds and Unregistered

Purebreds are not the only horses to consider when contemplating testing for genetic diseases. Numerous types of crossbreds are commonplace in the horse world: Thoroughbred/Arabian crosses, Quarter Horse/Paint crosses, Thoroughbred/Quarter Horse crosses, Arabian/Saddlebred crosses, Thoroughbred/Connemara crosses, Warmblood/Thoroughbred crosses, etc. And whether a registry offers part-bred papers or not, knowing the ancestry of all horses – even grade horses – is important when it comes to assessing genetic risk factors.

Discussion

By all means do your own research. You might even want to look at what has happened in the past regarding both dominant and autosomal-recessive syndromes in horses. Pay particular attention to what has happened once a condition was identified, tests were made available, education was provided and the governing bodies either did or did not impose immediate and firm rules. See how many of those that were identified decades ago are still in the afflicted gene pools today. Consider whether the percentages are acceptable and whether best practices were applied.

If the registry or governing body does not have a stated policy regarding test results, it is up to the owners and breeders to decide how to precede once the test results are known. Accountability falls squarely on the shoulders of the people involved whenever a mating happens. Remember what Sir Robert Baker said: “A breeder is one who leaves the breed with more depth of quality than when he started. All others are but multipliers of the species.”

For information and opinion regarding the art of culling, please visit: www.jwequine.com and read the post entitled The Art of Culling.
 

The Selection Process and Breeding Theories

Based on the previous articles, it is clear that the breeding of horses should not be taken lightly, which may explain why people have developed and gravitate towards various breeding theories. It is human nature to look for the simple answers. But are there any simple answers?

Undoubtedly a myriad of genetic factors is required to produce an exceptional athlete, and a lot of people are looking for a way to breed such a horse. Breeding theories are tools that can be used to analyze and narrow the search for optimal lineage; however, none of them carry guarantees of success.

Unfortunately, breeding theories can be far more complex than they appear on the surface, and, genetics being genetics, nothing is absolute. Pedigree research and applying the various theories can be rewarding, but they can just as easily lead to disappointment, since judging pedigrees is not the same as judging individuals.

Inbreeding and Linebreeding

The term inbreeding is usually used to signify duplicated ancestors that appear in the 3rd generation or closer. The term linebreeding usually signifies duplicated ancestors in the 4th generation and beyond.

The purpose of inbreeding is to cement some of the traits of the duplicated ancestor. The degree and closeness of the linebreeding will also affect the probability of the trait being homozygous (present on both alleles of the gene). Homozygous traits, by definition, must be displayed.

If inbreeding is done indiscriminately, a lack of vigor, decreased size at maturity, poor fertility, physical deformities, and lowered performance levels are the most common ramifications.

In the case of recessive traits, especially those deemed undesirable, they may do no direct harm in a heterozygous (having dissimilar alleles at corresponding chromosomal loci) state, but in a homozygous state, they have no alternative but to be expressed. This homozygous state is exactly what most breeding theories attempt to create, but for positive or favorable traits. Unfortunately poor traits can just as easily be cemented as good traits unless breeders act responsibly.

Although the average breeder does not attempt to produce offspring displaying homozygous recessive traits that are undesirable, much can be learned from matings that have that potential. It is theorized that if the offspring of several close-breeding matings do not display unfavorable traits, it is unlikely that the horse being “tested” carries the recessive trait and, therefore, should breed true. Such close inbreeding will quickly uncover any hidden or recessive genes. Some horse breeders have been known to deliberately breed full siblings and/or a stallion to his daughters or his dam as a means of progeny testing in order to manage their breeding selections in the future. If the stallion passes and therefore appears to be of superior gene type, he can be used successfully for both outcrossing and further inbreeding (to further cement desirable traits). That was mostly done in the past, and such breeders had a strong plan for culling. Nowadays, however, many genetic tests are available to provide genetic information quickly and reduce the risk of producing an afflicted foal.

Because homozygosity increases prepotency, inbreeding is not entirely without merit. We all want our top performers to be prepotent (having the ability to stamp the offspring with particular traits with a high degree of predictability) when they are used for breeding, and we certainly hope that the stallions we chose will pass on their best qualities to the foals from our mares. The trick, of course, is having homozygosity for the desirable traits without cementing undesirable ones. Therefore, linebreeding carries less risk than inbreeding.

In the horse industry, we have seen traits that were once considered desirable become undesirable as time revealed the consequences. For example, a muscular phenotype was desired for Quarter Horse halter classes, and then HYPP was discovered. Controversy ensued, but meanwhile many horses were adversely affected.

As stated in previous articles, Agriculture Canada’s David Trus notes that the responsibility of breeders is not just to the individualanimal, but to the greater population as well. “Animals always exist within the context of a larger population. Each animal is the genetic result of a random combination of the genetics of its sire and dam following reproduction, producing a unique assortment of genes and genetic makeup. This process carries on from generation to generation. The resulting genetic variation from all breeding events is essential to the overall genetic health of populations, which must be maintained in sufficiently large numbers and genetic diversity to ensure their well-being, utility and survival.

“Modern animal breeding seeks to direct the natural evolutionary process. Rather than fitness for survival in the wild, breeders seek to breed animals which are productive and excel at certain functions, are manageable, fit and healthy for the desired usage. Good breeding is most effectively achieved as a collective undertaking of many breeders having common goals, typically within a breed. In the end, good breeding should be directed towards the collective goals of breeders, be beneficial to the well-being of individual animals, and be positive for the fitness and survival of the population.

“Disorders should really be discussed in the context of good breeding practices, such as limiting inbreeding, maintaining sufficiently diverse lines within a breed, selection based on multiple traits (e.g. health, growth, performance, temperament, [which] are determined by very different genes) rather than single trait emphasis.” Breeds with limited genepools have to constantly guard against too much inbreeding and/or linebreeding.

What the overall linebreeding picture represents to me is a pattern that I see with increasing frequency. In successful horses in all sorts of competition (racing, cutting, jumping, dressage, barrel racing, eventing, reining, driving, endurance, etc.), I see an inbred (or linebred) horse bred to a horse that predominately represents an outcross, save for at least one common (between mare and stallion) ancestor (other than the originally duplicated ancestor) farther back in the lineage. In other words, it is not uncommon to see a stallion linebred to “A” bred to a mare that is either linebred to “B” or is not linebred, but both sire and dam have “C” in their pedigrees. This pattern seems to hold true in other species as well, but I have not found it identified by any particular name. It is important to mention that the sires and dams referred to in this pattern were superior athletes as well as very similar in phenotype, which also fits with the breed-like-to-like breeding theory.

Sex-Balanced

In its simplest form, sex-balanced means that a duplicated ancestor appears through a son (or sons) and a daughter (or daughters). This becomes particularly important if one is trying to replicate the attributes of a particular stallion in the ancestry. Having the potential to have both the X and the Y-chromosomes (daughter and son) from a duplicated stallion present within a pedigree increases the chances of his having a more significant influence on his descendant. Remembering that the X chromosome carries more genetic information than the Y-chromosome, a daughter of the duplicated stallion (or perhaps his dam or even his sister) would need to be present if you hoped to recreate his qualities. In addition, if that stallion passes an imprinted gene, only his daughters can perpetuate it.

Nicks

Simply put, nicks are the result of a propensity for certain bloodlines to produce above average percentages (certainly not a 100% guarantee) when crossed with certain other specific bloodlines. At one time, in large part due to the success of Secretariat on the track, the Bold Ruler/Princequillo cross was considered a successful nick. For Secretariat, that may have been true, but for his full-sister, The Bride, it was definitely not true. Incidentally, according to the ‘Large Heart’ theory, both Secretariat and The Bride should have inherited a large-heart gene, but it only benefitted one of them on the track.

Breed the Best to the Best

This is likely the simplest of the breeding theories. If one breeds a mare that was successful at a particular sport to a stallion that was successful at that same sport, the odds of producing a successful offspring are increased. However, breeders should take into consideration the soundness and longevity of the sire as well as the dam. The parents may have been successful, but were they sound? Breeding an unsound stallion – no matter his earnings or accolades – to an unsound mare – no matter her earnings or accolades – sets a trap for the resulting foal. Such a foal will grow up with huge expectations placed upon it. It will be pressured to perform, and if it cannot and breaks down, it will go into the genepool because it is seen as valuable and it will likely propagate the unsoundness. Valuable to the genepool and valuable to the pocketbook may not be the same in such cases.

Breed the Young to the Old

This theory is based in logic. If you breed a young mare to a young stallion, which horse do you credit or blame for the traits of the offspring? If they are good traits and you own the mare or the stallion, you will give credit to the one you own. If they are poor traits, you will blame the horse you do not own. That’s just human nature.

However, if you breed a young mare to a stallion with several crops on the ground, you can make a better assessment of what the mare added to the mix. Conversely, if you breed a young stallion to a mare that has had several foals, you can make a better assessment of his contributions.

Researching

One certainly gets the feeling that by the time a mating that produced any great horse was made, there was ample research done. There may have been proof that the bloodlines worked well together or that the phenotypes complimented each other. Rarely is a superior individual produced by sheer luck. If that were the case, we should all be so lucky!

Even without the “luck” however, we can do our homework, research the bloodlines, assess the individuals’ traits and make a long-range breeding (or production) plan. Several pedigree and performance resources are available on the internet or through registries and breed associations. Form your own opinions based on your own research since following the crowd may take you and your horses down the wrong path.

Where does the talent come from? Well, he is who he is or she is who she is because of the genes he or she inherited – just like everything else on this fine earth. But, when the “right” genes come together, the result is enviable. The trick is replicating the desirable qualities.

The downside is that you can breed the same mare to the same sire and never get another champion. The upside, which of course is much more elusive, is that you may hit just the right combination of dominant and recessive genes from the cross, and end up with a series of top horses. The odds of the latter situation occurring are astronomical when you think of it. As you know, if you have siblings (unless you are a maternal twin), appearance and abilities are not consistent, even in full siblings. And how like your cousins are you?

This is where the inbreeding/outcrossing-balancing act and knowing what to expect from the bloodlines come to the forefront. Such knowledge does not guarantee a world champion or even a sound, reliable mount, but it certainly improves the odds.

Whether a horse has the best looking match on paper or not, the horse still has to be built to do the job. Horses simply do not perform on pedigree alone – neither in competition nor in breeding.

Going Forward

Accountability includes everything from disposition to conformation to genetic diseases and encompasses the individual horses as well as the gene pool of the breed or registry. Breeding horses should not be taken lightly.

Unfortunately, health and quality of life can easily be compromised when not closely guarded in the gene pool, and selecting for specific performance traits without considering the soundness and longevity of the horses produced is compromising.

Breeding is a responsibility. The kindest thing you can ever do is not breed horses that will produce foals that for genetic, conformational or behavioral reasons will be mistreated for what they cannot do – through no fault of their own. It is the breeder’s responsibility to know which disorders, soundness issues or bad dispositions their horses are predisposed to propagate, and to take the appropriate steps to ensure the welfare of the foals they will be producing as well as the gene pool at large. Such consideration applies to purebreds, cross-breds and grade horses whether they are registered or not. Responsible breeders consider it an ethical obligation. Accountability falls squarely on the shoulders of the people involved whenever a mating happens.

Remember what Sir Robert Baker said: “A breeder is one who leaves the breed with more depth of quality than when he started. All others are but multipliers of the species.” People should show accountability to individual animals and to the relevant gene pools since many welfare problems can be prevented through responsible breeding.