Genomics provide a pathway to improved performance in horses


Identifying and utilising genes in horses linked to fertility, conformation, durability and athleticism is a more sensible way to improve performance rather than simply seeking to limit inbreeding, according to scientists.

Geneticists Ernest Bailey, Ted Kalbfleisch and Jessica Petersen discuss equine inbreeding and genomics in the latest issue of Equine Disease Quarterly.

“Inbreeding has played a key role in the improvement of livestock breeds, resulting in more uniform populations with highly specialized performance traits,” they say.

“Selection for desirable traits entails identifying individuals with superior performance and often mating them to relatives (inbreeding) who possess the same superior traits.

“The goal of this practice is to increase the frequency of the desired characteristics and thus of the beneficial genes in the offspring.”

At the same time, negative consequences of inbreeding are well known.

“In small populations such as captive-bred species, the loss of diversity associated with inbreeding is a major concern, and significant losses of diversity may lead to extinction.”

The increased expression of recessive harmful genotypes can also lead to losses or other defects.

Inbreeding can also lead to a phenomenon called inbreeding depression. Common signs are poor outcomes for traits that are complex (due to contributions of many different genes), such as fertility and athleticism.

Mindful of the dangers inherent with inbreeding, breeders traditionally balance the benefits and dangers of inbreeding by monitoring their breeding stock, culling poor performers and avoiding matings of closely related individuals.

“Recently, genetic tools have become available that provide an alternative approach to unambiguously quantify and manage inbreeding relative to the traditional use of pedigrees.”

A genomic survey of a horse’s DNA may cost $US70 to $US180. A comprehensive whole-genome sequence, including analyses, may cost $US1000 to $US2500.

So far, more than 1000 horses have had their entire DNA sequenced in connection with research projects. Those have been used to identify the genetic bases of diseases, coat colors and even some performance traits.

“Nevertheless, the overall performance of horses is complex, involving over 20,000 genes and probably millions of other functional elements.

“Studying genes one at a time is unlikely to be effective to significantly improve performance.”

Calculating inbreeding levels

Genomic tools, however, make it possible to identify associations between the genome and traits that contribute to success or which may cause problems.

One of the areas in which genomics excels is in determining levels of inbreeding.

An animal’s inbreeding coefficient is the likelihood that both parents transmitted the same piece of DNA to their offspring that they each inherited from a common ancestor.

Traditionally, inbreeding is measured by identifying all common ancestors – those that appear in the paternal and maternal sides of an individual’s pedigree. After common ancestors are identified, the relationship between the parents of the individual in question can be calculated.

Using this method, on average, pedigree-based inbreeding coefficients for Thoroughbred horses are reported to be between 12.5% and 13.5%. However, individual horses may have values that range from less than 5% to over 20%.

The scientists noted that when genomic measures have been made in other species, geneticists discovered that inbreeding levels calculated from pedigrees are poorly correlated with genomic measures of inbreeding.

“This is not surprising since pedigrees inaccurately assume a random and equal transmission of genes each generation.

“Which variant of each gene is inherited, however, is not predictable. For example, full-siblings share, on average, 50% of their genes; however, at any particular part of the genome they may share 0, 50, or 100%.

“Further, genes are not randomly distributed in a breed since selection practices are applied in mating horses.

“If we are good breeders, the genetic constitution of our current generation is not a random representation of the ancestors, but rather, a selection of the genes contributing to their success.”

They say there are other ways to apply genomics to horse breeding.

“As noted above, both the genome and the traits we value are complex. Our genomic tools are powerful, and we can begin to seek genetic patterns correlated with measures valued by horse owners.

“The limitation for such studies is the quality and availability of data for traits related to fertility, conformation, durability and athleticism.

“Collecting these data and using genomics to identify genes associated with these complex traits would be a more sensible way to improve performance rather than simply seeking to limit inbreeding.”

Pattern recognition in horse breeding

Bailey, in a separate commentary in the same issue, describes the art of horse production as pattern recognition.

“The most obvious pattern is that offspring resemble their parents. These resemblances can be found in phenotypes such as size, conformation, durability, and performance.

“Using phenotypes and pedigrees, breeders have applied selection, resulting in profound changes in horses since their domestication 5500 years ago.”

Today, hundreds of breed registries exist, reflecting diverse goals among horse breeders.

“These interests span divergent phenotypes related to racing, pulling, jumping, dressage, performing special gaits, and characteristics associated with coat color or size.”

The commonality among these traits is they have a large genetic component, he says.

“Foundation stock were identified as exemplifying traits of interest. The path to improvement has been to identify quality breeding stock, cross them to foundation horses and select the best for future breeding stock.”

As a result, foundation stock is represented many times in horse pedigrees and contribute to distinctive characteristics within breeds.

He notes that scientists have identified genes for discrete traits such as coat colors and some hereditary diseases. “However, despite a great deal of research, no single gene has been found responsible for complex traits such as racing, jumping, and gait.

“This is not surprising since athletic performance involves a combination of muscle strength, cardiovascular capability, competitiveness, and coordination.

“Yes, a few genes have been identified that influence performance (eg, DMRT3 for gait and MSTN for sprinting); however the development of champions involves many other genes as well as the art of the trainer and skill of the rider.

“This relationship is remarkably complex since variation exists despite generations of selection.”

The resilience of genetic variation may reflect the diverse ways in which a horse can become a champion.

Northern Dancer and Secretariat were champion Thoroughbred racehorses. However, while Northern Dancer was relatively small in stature, Secretariat was renowned for his large size and stride length.

“While the old breeding adage is ‘breed the best to the best and hope for the best,’ the skill of the successful breeder is to identify hereditary patterns among the best and make judicious choices.

“There is no single genetic test that will replace the skill of the breeder.”

However, genomic tools have the potential to improve the recognition of useful patterns.

He says there is the potential to identify the specific genetic blocks inherited from each parent and relate those blocks to those found in the grandparents.

“Likewise, one might even discern the blocks back to the Foundation Stock.

“Unfortunately, such a tool does not yet exist for horses, but a similar commercial application is used by people to identify the origin of their ancestors.

“We anticipate horse breeders may seek to use such a tool one day.”

Bailey, a specialist in immunogenetics and genomics, is with the University of Kentucky’s Gluck Equine Research Center; as is Kalbfleisch, whose areas of interest are bioinformatics, genetics and genomics. Petersen, with the University of Nebraska-Lincoln, is a specialist in animal functional genomics.

Equine Disease Quarterly is funded by underwriters at Lloyd’s, London.

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