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tional information from relatives, weighted properly according to each relative’s relationship to the animal being selected, will increase the selection accuracy regardless of the heritability for that trait.

The selection differential is the difference between the selected individual and the population average.

Breeders who cannot predict (many economically important traits may not be measurable until the animal matures) or recognize superior animals probably will not make a lot of genetic change or may end up with the wrong type of change for their goals.

Also, breeders who have only a limited number of horses to utilize in their breeding program are at a disadvantage for this factor.

More intense selection, through retaining only the highest quality animals, allows breeders to increase the mean genetic level of their herd.

Breeders with a limited number of breeding animals often do not want to intensely cull animals because it may reduce their herd size to a number that is not economically viable.

However, producing animals of limited usefulness to the horse industry probably is not economically viable either.

The long generation interval of horses also reduces the rate of genetic change in horse breeding.

The generation interval is the average time from the birth of one generation to the birth of the next, and in horses the generally accepted generation interval is about 10 years.

Genetic change can occur more rapidly with shorter generation intervals.

The long generation interval also means that the average horse breeder has very few opportunities to influence genetic change in horses in his or her lifetime.

Poor selection decisions or constantly changing breeding goals will negatively influence the amount of genetic change a breeder can realize.

Also, when the long generation interval is combined with poor reproductive efficiency (only about 50 percent of mares bred produce a foal), this factor can greatly retard genetic change.

Increasing the reproductive efficiency can decrease the generation interval and increase selection intensity in a herd, resulting in more rapid genetic change.

Finally, the very nature of the horse industry can influence the amount of genetic change made by individual breeders.

Historically, many desirable stallions were accessible to only a few breeders due to factors such as high cost and geographical location.

This did not retard the genetic change of the breed, but it did slow the genetic change realized by the average breeder.

With the increased use of shipped semen in the horse industry, this problem is beginning to be alleviated in most breeds.

Through the use of artificial insemination, selection intensity from the male side can be greatly improved. Evaluating Individuals Breeding stock selection is usually based on a variety of individual preferences of the breeder.

Some breeders put more weight on pedigree, some on performance of the horse or its relatives, and some on appearance of the horse.

Are some of these considerations more important than others? It depends on the trait in question.

Highly heritable traits (0.4 or higher heritability) respond well to selection procedures based on individual performance, assuming that environmental effects are minimized.

Individual performance is also a useful selection criterion for economically important traits and when genetic turnover is fast.

Traits with low heritabilities (less than 0.2) respond well to selection based on family background (pedigree, performance of relatives) because the individual’s own performance is not an accurate assessment of the animal’s genetic merit.

Pedigree also can be a useful selection tool for a young horse that has not had a chance to prove itself or for a horse that was injured prior to proving itself.

Pedigree also may be a useful tool when dealing with genetic abnormalities, traits expressed later in life, or traits expressed by only one sex.

However, breeders should realize that the pedigree decreases in value in the selection process as the individual animal gains performance and progeny records.

In addition, breeders should remember that the individual horse will not have any genes that its parents did not have.

So, when utilizing the pedigree as a selection tool, breeders should emphasize the individual’s parents and grandparents.

The genetic contribution of more distant relatives such as great grandparents is very minor.

Performance tests, in which horses are put into a common environment for a period of time before traits are measured and compared, and progeny tests, in which a stallion is bred to number of mares to evaluate his offspring relative to those of other stallions for certain traits, have been used as selection tools.

Other livestock species commonly evaluate potential breeding animals using this scheme.

The performance test commonly is used as a selection tool for young stallions of warmblood breeds. Basic Horse Genetics 7 Basic Breeding Schemes Breeding schemes of outcrossing and inbreeding do have genetic consequences that may be either good or bad, depending on the goals of the breeder.

Outcrossing is mating unrelated families within a breed.

It tends to increase heterozygosity, strengthen traits related to fitness (such as fertility), and cover up recessive genes.

Crossbreeding is a more extreme form of outcrossing in which horses from different breeds are mated.

Crossbreeding has the same genetic effects as outbreeding, plus it decreases genetic purity.

Crossbreeding is common with some types and uses of horses.

Many of our modern light horse breeds were formed by crossbreeding, and it is still used today to introduce desirable genetics into horse populations.

For example, Thoroughbred and Arabian genes were introduced into native horse populations to refine the appearance and increase the athletic ability of warmblood breeds.

Outcrossing is sometimes used for corrective mating—for example, breeding a splay-footed mare to a pigeon-toed stallion.

These two conditions potentially are caused by two separate genetic mechanisms, and it is difficult to predict what type of leg structure would result from the breeding.

A far better strategy would be to breed the mare to a stallion with the most correct structure that fits into the breeder’s economic restraints and other selection criteria.

Inbreeding is breeding closely related individuals (father-daughter, brother-sister).

The genetic consequences of inbreeding are to increase homozygosity of both dominant and recessive genes.

Inbreeding does not create undesirable genes, but it does increase the possibility that recessive genes will be paired and expressed phenotypically.

Inbreeding also decreases traits related to fitness, such as fertility, disease resistance, and longevity.

Linebreeding is a mild form of inbreeding that breeds horses related to a common ancestor, and it has the same genetic consequences of inbreeding.

Inbreeding and linebreeding are used to set phenotypic type in qualitative (morphological) traits, to concentrate the influence of an outstanding ancestor, and to form lines for future outcrossing purposes.

Neither outcrossing nor inbreeding is “good” or “bad.” The use of these breeding schemes depends on what is appropriate to reach the breeding goals set by the breeder. Selection Methods After setting goals and examining performance records, pedigrees, relationships between animals, and test results as appropriate, horse breeders can use a variety of methods of multiple trait selection.

Before getting started, breeders need to realize that as the number of traits selected for increases, the possible amount of change in a single trait decreases.

One method is to select for one trait exclusively until the goal for that trait is reached, then start selecting for the next trait.

This is termed tandem selection and is probably the least effective method of selection because traits often are correlated genetically.

That is, one gene may affect more than one trait.

So, selecting for each individual trait separately may alter, either positively or negatively, the genetic change made for the previous trait(s).

A second selection procedure is to set minimum standards for several traits, and if a horse does not measure up to one of those standards, it is culled.

This method is called an independent culling level and is used to some degree by most breeders and breed associations.

The problem with this method is that a horse that is outstanding in one trait may be culled if it does not meet the standards for another trait.

This type of selection is most useful if the breeder is dealing with only a small number of traits and a small percentage of the offspring are needed to replace the parents.

Neither of these requirements is common to the horse population.

A selection index is a more effective method of trait selection than tandem selection or setting independent culling levels, but it is more difficult to set up.

Selection indices are mathematical formulas that utilize information from traits of importance and weight those traits according to importance.

Information is obtained from the animal itself and from its relatives to calculate a single score for an animal, and selection is based on the score.

If multitrait evaluations are used, the selection index method simply weighs the traits by their relative economic values and sums them.

Drawbacks to the selection index are that it is difficult to formulate, and it often is difficult to obtain the information needed.

Also, what may be important for one horse breeder and be weighted heavily in his or her index would not necessarily be a highly important trait to another breeder.

However, formulating a selection index may be a useful exercise because assigning a relative economic value to each trait allows the breeder to realize which traits are of true economic importance to his or her breeding goals. 8 Alabama Cooperative Extension System Another method of selection that is commonly used in other livestock species and is beginning to be available for horses in Europe is the expected progeny difference (EPD).

In this method, all available information about a trait from the individual and its pedigree, properly weighed according to the relationships to the animal being evaluated, is used to calculate the expected difference in the offspring’s performance for that trait.

That is, an EPD is the expected difference in performance from future offspring of a sire compared to the performance of the base population.

The EPD combines into one figure a measurement of the genetic potential for a particular trait based on the individual’s performance and performance of related animals.

In other species, EPDs are reported as positive or negative values for each trait of importance.

For example, a beef bull may have an EPD of -0.4 for birth weight (slightly below the average of his peers), a weaning weight EPD of +38 (38 points above the average of his peers), and a yearling weight EPD of +82.

So, if a particular breeder were looking for a bull that sires calves of average birth weight that will grow rapidly after birth, this might be a bull to consider.

Also, the procedure can be used to rank the bull on traits that cannot be measured directly from him, such as maternal ability traits and carcass traits.

The EPD scores come with an accuracy score attached.

The more offspring the sire has, the more accurate the EPD score and the more the breeder can rely on it to remain relatively unchanged with additional data. In horse breeding, the EPD would be a good selection tool.

Most breeders have too few mares to cull them intensely.

Instead, they correctly put more emphasis on selection of the stallion.

With the use of transported semen, stallions are able to have more offspring in many different herds.

Properly recording the performance of these offspring would allow for EPD estimation so that the stallions could be compared more objectively by the breeder.

Whether the breeding goal is to produce a palomino foal or to produce the next Olympic winner, the same basic genetic principles should guide the selection process. References for this publication and further reading materials are as follows: Bowling, A.T. 1996.

Horse Genetics.

CAB International, New York.

Harrington, R.B. 1995.

Animal Breeding – An Introduction.

Interstate Publ.

Danville, IL Sponenberg, D.P. 2003.

Equine Color Genetics.

Iowa State Press.


Veterinary Genetics Laboratory.

University of California, Davis.

Http:// coatcolorhorse.php.

Accessed June 30, 2011.

Cook, D., Brooks S., Bellone, R., Bailey, E. 2008. “Missense Mutation in Exon 2 of SLC36A1 Responsible for Champagne Dilution in Horses.” PLoS Genetics 4(9):e1000195 Cindy McCall, Extension Specialist, Professor Animal Sciences, Auburn University For more information, call your county Extension office.

Look in your telephone directory under your county’s name to find the number.

Published by the Alabama Cooperative Extension System (Alabama A&M University and Auburn University), an equal opportunity educator and employer.

Web Only, New March 2012, ANR-1420

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