Can Genetics Turn the Art of Stallion Selection into a Science?

February 03, 2016

Can Genetics Turn the Art of Stallion Selection into a Science_Horse ChromosomesThe horse genome contains all the information required to direct the growth and function of a foal, from conception to death. This enormous “text” is organized into chromosomes, much like the volumes of an encyclopedia. The domesticated horse possesses 32 unique chromosomes, and most cells carry two copies of each chromosome for a total of 64. Gametes of course are the exception, carrying just one of each of the chromosome pairs to the future offspring. This article will discuss information about genotype vs. phenotype, genetic testing, recent genetic studies performed on stallions, and current genetic research being performed on the "freezability" of stallion sperm.

The X and the Y

Just like humans, horses use two mismatched sex chromosomes, the X and the Y to determine sex: XX for females, XY for males. In every animal the two copies of each chromosome are not identical, creating “alleles” that control a diverse set of traits like temperament, height or fertility. Different interactions and combinations of the “alleles” lead to simple inheritance patterns like “dominant” and “recessive” that are frequently used to describe genetic traits like coat color.

Genotype vs. Phenotype

Geneticists call the information written in the DNA sequence a “genotype”, and the physical trait you can measure on the horse a “phenotype”. Genotypes, interactions among genes, and factors from the environment can significantly alter most phenotypes. As a result, an exceptional horse may have only average genes, or an average horse may have exceptional genes but suffered in a subpar developmental environment. For example, a colt may have the genetic potential for superb fertility, but an intervention like gelding can completely negate his fertility. Only the genes are passed from sire to offspring, not the alterations due to the environment. Therefore, it makes sense to examine the genes of a potential stallion with at least as much scrutiny as one might use to evaluate his conformation or performance record.

Genetic Testing

Can Genetics Turn the Art of Stallion Selection into a Science_Dr. Samantha Brooks Breeders today have an unprecedented number of genetic tests to select from. Recent success in mapping the genetic variants responsible for important traits is a direct result of the completion of the equine genome sequence in 2009. With novel tools developed from the genome sequence we now have the power to determine the genetic component of complex conditions like disease resistance or athletic performance. To date there are approximately 132 known genetic markers for 61 unique traits in the horse. However, getting these valuable tests in to the hands of breeders has been a slow process.

Unlike genetic testing in human medicine, DNA based diagnostics in the horse do not require a prescription from a health care professional. While this lack of regulation allows widespread access to testing services, it also means there is little motivation in the industry to regulate the quality of services offered by commercial animal genetic testing companies. One bad experience with a less than reputable company may discourage horse owners from investing in genetic testing in the future.

Likewise, although the costs of traditional individual genetic tests have remained low, around $20 a test, when this cost is multiplied times the dozens or hundreds of markers required to predict exciting new complex traits like racing performance the costs to horse owners rise steeply, especially if they have a large herd.

Luckily, new breakthroughs in the chemistry and equipment used to determine genotypes is lowering the cost of these tests quickly and large multi-marker panels at very affordable prices are now entering the market. Emerging new companies will increase competition in the market, driving the quality of customer service up as horse owners have the power to take their business elsewhere.

Recent Genetic Studies

Recent genetic studies have described traits of particular interest to the owners of promising young stallions.

  • Research coordinated by Dr. Ottmar Distl, University of Veterinary Medicine in Hannover, describes new markers in a single gene called PLCz1 contributing to the pregnancy rate per estrus cycle in Hanoverian Stallions [1].
  • Exciting new work on a gene named FKBP6 by the Raudsepp lab at Texas A&M revealed that a genetic change created a high risk of developing Impaired Acrosome Reaction, a condition that can render a stallion infertile [2]. 
  • Later work illustrated new alleles at this same gene contributing to other parameters for fertility, suggesting that the FKBP6 gene is of particular importance to reproductive fitness in the stallion [3].

Current Research on “Freezability”

Can Genetics Turn the Art of Stallion Selection into a Science_stallion In partnership with SBS, the Brooks Equine Genetics Lab (Dr. Samantha Brooks pictured above) has just begun an exciting new study to investigate genes contributing to semen quality after freezing, aka “freezability”. Theories on the cause of sperm cryodamage and poor-freezing are diverse. Certainly osmotic damage to sperm membranes, toxic effects of cryoprotectants, and loss of mitochondrial function may all play a role in disrupting the quality of semen after the freezing process. Trends in the quality of sperm cells after freezing are noted within breeds and specific bloodlines, suggesting a heritable genetic contribution to “freezability” in the stallion. Notably, membrane integrity and post-thaw motility could be improved, not by altering sperm morphology, but by replacing the seminal plasma in poor-freezing stallions with plasma from good freezers. This suggests that a secreted component of plasma, not a characteristic of individual sperm cells, could play a role in sperm cryosurvival [4].

Secreted components to seminal plasma are often difficult to identify or quantify using analytical chemistry, yet genetic mapping provides the opportunity to quickly discover the genes controlling this variation in composition. Discovery of genetic changes impacting “freezabilty” could be applied immediately for genotype assisted selection of stallions with the potential to pass on superior semen cryopreservation characteristics. However, identification of genes will also highlight potential new cryoprotectants or additives to specifically improve the quality of preservation in semen from poorly-freezing stallions.

Conducted by Dr. Laura Patterson-Rosa, a Brazilian veterinarian pursuing her PhD in the Brooks lab (group photo below), sample collection for our genetic study on “freezabilty” is currently ongoing. Please encourage your stallion owners to participate in this study if they are contacted, the success of this work depends on getting a large sampling of stallions. Can Genetics Turn the Art of Stallion Selection into a Science_Group Photo It is our hope that this work will benefit not only the stallions in service today, but also the next generation of sires.

Stallion owners are by nature in the business of selling genetic content, we believe they should be among those most motivated to use new genomic technologies to provide the best possible future foal crops. Recent, and on-going research focuses on developing predictive tests for traits of performance, health, and of course, fertility. The technology allowing mare owners to “shop by genotype” for their next stallion is already here, it won’t be long before the industry “takes the reins” and fully applies these new tools to the benefit of the horse.


1. Schrimpf R, Dierks C, Martinsson G, Sieme H, Distl O. Genome-wide association study identifies phospholipase C zeta 1 (PLCz1) as a stallion fertility locus in Hanoverian warmblood horses. PLoS One. 2014;9(10):e109675. doi: 10.1371/journal.pone.0109675. PubMed PMID: 25354211; PubMed Central PMCID: PMCPMC4212906.

2. Raudsepp T, McCue ME, Das PJ, Dobson L, Vishnoi M, Fritz KL, et al. Genome-wide association study implicates testis-sperm specific FKBP6 as a susceptibility locus for impaired acrosome reaction in stallions. PLoS Genet. 2012;8(12):e1003139. doi: 10.1371/journal.pgen.1003139. PubMed PMID: 23284302; PubMed Central PMCID: PMCPMC3527208.

3. Schrimpf R, Metzger J, Martinsson G, Sieme H, Distl O. Implication of FKBP6 for male fertility in horses. Reprod Domest Anim. 2015;50(2):195-9. doi: 10.1111/rda.12467. PubMed PMID: 25495881.

4. Aurich JE, Kühne A, Hoppe H, Aurich C. Seminal plasma affects membrane integrity and motility of equine spermatozoa after cryopreservation. Theriogenology. 1996;46(5):791-7. PubMed PMID: 16727943

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