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Breeding Realities and Basic Genetics

This is the second in a series of five articles aimed at providing knowledge and resources to horse breeders and buyers as well as discussing the thought processes involved in breeding horses. Subsequent articles will touch on genetic disorders (in two parts) and the selection process and breeding theories.

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


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.

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.

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