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The Selection Process and Breeding Theories

This is the last 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.

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


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.


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.


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.


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.

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