Genetic influences behind today’s Quarter Horses | TSLN.com
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Genetic influences behind today’s Quarter Horses

If 100 Quarter Horse owners were asked to envision the ideal Quarter Horse, images would vary significantly. Some would visualize a structurally perfect halter horse, others would picture a horse suitable for ranch work, and many would see the perfect pleasure or trail horse. 

Most Quarter Horse owners familiarize themselves with the three-generation pedigree provided on the certificate of registration, but a further query of parentage, usually several more generations, reveals significant Thoroughbred influence on both sire and dam sides.  

It’s well-accepted that the Thoroughbred played a significant role in the development of the Quarter Horse and other modern horse breeds, but other than visually comparing extended pedigrees, there has been no definitive way to determine that breed’s influence. Advances in genetic research, including the sequencing of the horse genome to identify nearly three billion DNA base pairs, was the initial step in allowing closer examination of individual animals’ genetics. More recent research provided scientists with the tools to identify single nucleotide polymorphisms (SNPs), which are variations at a single position in the DNA sequence that measure genetic differences within a species. 



With the help of SNP technology, a team of researchers looked more closely at the Thoroughbred’s contributions to the modern Quarter Horse. Results of the study were published in Journal of Heredity (Petersen, Jessica L., et al. “The American Quarter Horse: Population Structure and Relationship to the Thoroughbred.” Journal of Heredity. 2014 Mar-Apr, pp. 148-162).  

The study included 200 top-performing horses in six performance groups as designated by AQHA: halter, western pleasure, reining, working cow horse (reined cow horse), cutting and racing. While the bloodlines behind the horses in these groups are different, they’re also the same – and all carry Thoroughbred blood. 



“The breed advertises themselves as, and they are, a versatile horse,” said Dr. Jessica Petersen, associate professor of Animal Functional Genomics at the University of Nebraska-Lincoln, who co-authored the paper. “We looked at the big picture – how different horse breeds are related to one another, and how subpopulations of Quarter Horses are related to one another.” In considering the primary characteristics of the six Quarter Horse performance groups, Petersen says the genotype (genetics) and phenotype (outward appearance) are distinct. “The genotype is one of the parts that makes the phenotype different,” she said. “If we see a physical difference, we expect to find a genetic difference. We now know what’s different and what’s the same. And when we look at the genes in parts of the genome that are different, we can then ask, what does that tell us about the biology?” 

Veterinarian, geneticist and lifelong Quarter Horse aficionado Dr. Molly McCue co-authored the paper. McCue is associate dean of research at the University of Minnesota College of Veterinary Medicine. “We know maintaining genetic diversity is really important,” said McCue. “And one thing about the Quarter Horse that stands out is that it’s a very diverse breed. When we measure diversity within a breed, we look at heterozygosity, and in a random group of Quarter Horses, regardless of performance type, we see they’re very diverse with high heterozygosity.” 

Heterozygosity is important because it’s the key to maintaining genetic diversity in domestic animals. “As we lose genetic diversity within a breed, it helps us fix the phenotype for certain traits,” said McCue. “But loss of genetic diversity can cause more homozygosity, which can lead to decreased longevity and an increase in deleterious traits in populations that are less diverse and more inbred.” 

Prior to genome mapping and SNP technology, the role of heterozygosity was an unproven theory. “Now we have the genetic markers to demonstrate that’s the case, and we’re showing quite clearly that it’s true,” said McCue. “When we compared the Quarter Horse to other horse breeds, one of the things that stood out is that Quarter Horses are one of the two most heterozygous of the nearly 40 domestic horse breeds we looked at.” 

Referencing the study, McCue says data from molecular genetics proved concepts that genetic theory had predicted. “For a long time, the thinking was ‘from what we know, it seems to be happening this way,’” she said. “How the genome replicates itself and some of the rules of biology are a little more complicated, but for the most part, what we think has been happening over time can be proven. Seeing the genetics behind phenotypic changes is pretty cool.” 

The Quarter Horse breed is diverse for a variety of reasons, one of which is the breed’s relatively new status. “We also know that within the breed, some inbreeding and linebreeding has happened; particularly for certain performance types,” said McCue. “So while there’s an overall QH phenotype, a halter horse looks quite different from a cutting Quarter Horse or a racing Quarter Horse.” 

While most Quarter Horse owners are aware that their horses’ lineage includes Thoroughbreds, both Petersen and McCue point out other breeds behind the modern Quarter Horse. “There were draft horses, and probably some Morgan influence,” said McCue. “The native American Indian Chocktaw and Chickasaw horses also were important.” 

Horses that arrived with the Spanish invasion and later released into the wild also contributed to the modern Quarter Horse. McCue says Native Americans bred horses over a period of time to achieve a different phenotype prior to the founding of the Quarter Horse breed. “In genetic terms we consider them an admixed breed,” she said, “created with an admixture of a lot of different breeds, and not that long ago.” 

The introduction and crossbreeding of various horse types and breeds resulted in a phenotype – a horse that fit the bill – that would eventually become the Quarter Horse. McCue says the stud book was created in the 1940s and filled with several hundred animals that fit the phenotype. 

However, the selection of horses that would eventually create the Quarter Horse occurred about 30 to 50 years prior to the original Quarter Horse stud book. “We selected for phenotype, and at some point decided ‘this’ phenotype is what we wanted,” said McCue. “Just prior to the Quarter Horse becoming a breed, the type was being defined. Those horses weren’t in the registry yet, but there was definitely a phenotype. When the (AQHA) registry was created, they looked at horses to determine which animals fit the type.”  

McCue points out what Quarter Horse owners already know: that within the Quarter Horse breed, there’s variation in phenotype. “Within those phenotypes, be it halter, cutting or racing or whatever performance category, we know the phenotype looks different,” she said. “If you’re familiar with them, you can pick them out relatively easily. We also know that within the subcategories there’s quite a bit of linebreeding/inbreeding.” 

Other than delving into pedigrees, the most obvious clue that Thoroughbreds played a major role in the development of the Quarter Horse is found in old photographs. McCue says reference photos of Thoroughbreds in early Quarter Horse lines, many of which are accessible via http://www.allbreedpedigree.com, shows horses that look quite different from today’s Thoroughbred.  

“It’s easy to see what early breeders were looking for in foundation horses,” said McCue, describing the appearance of Thoroughbreds in the early 1900s. “They’re shorter and look more like what a Quarter Horse would look like. They’ve become more refined over time, and if you look at how almost all modern horse breeds have changed between 1950 and now, they all have cleaner legs, prettier heads and are a little fancier. That’s definitely something horse people have selected for over time, but the general appearance is still the same.”  


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