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20 TheHorse.com THE HORSE June 2017 Differences in the genomic DNA sequence between individual horses are called single nucleotide polymorphisms (SNPs, or "snips"). If SNPs are located near each other on a chromosome, they will likely be inherited together; this proximity enables researchers to investigate specific regions of the genome that vary in fre- quency between horses. Samantha Brooks, PhD, assistant professor and founder of the University of Florida's Brooks Equine Genetics Lab, in Gainesville, says SNPs aren't the only reason for genome variation. Much of it is also due to sequence rearrangements or changes. "Genes that have flipped or duplicated may be responsible for varia- tion in phenotype (observable character- istics)," she says. For instance, a sequence change is responsible for tobiano color (white hair on a base coat color) in pinto horses, says Brooks. While most rearrangements are benign, some are fatal, such as the overo lethal white gene responsible for a disease that suppresses intestinal activity. Let's look at some of the harmless (and even desirable!) genetic variations that create horses' unique characteristics. Coat Color's Link to Behavior You've probably heard people describe chestnuts, or "redheads" as they're fondly called, as excitable and reactive. It turns out there might be some biological truth to this stereotype, says Brooks. In one study in humans, researchers compared pain responses in redheads to those of nonredheads. Subjects rated their pain in response to small electric shocks from electrodes attached to their shins. The re- searchers then administered an analgesic (morphine) and asked the participants to rerate the pain. The redheads consistently perceived the electrical shocks as more painful than nonredheads did, but they reported relief from analgesia. It turns out that both people and horses have mutations in the MC1R (melanocor- tin receptor 1) gene. This gene is respon- sible for signaling cells called melanocytes to produce the pigment melanin and establish base coat color. Redheads (both human and horse) have a variant of this gene that prevents them from producing the black pigment and allows them to produce only red pigments. In humans the MC1R loss-of- function mutation results in red hair, along with increased sensitivity to the sun and a lower pain tolerance. In horses, a similar mutation produces a chestnut coat color. "The melanocortin receptors in the brain are in part responsible for trans- lating a signal from that opioid class of chemicals (which the brain produces and uses for signaling), and the same recep- tors on melanocytes are responsible for receiving signals for when to turn black pigment on or off," Brooks explains. "This mutation in both chestnut horses and redheaded women creates a defec- tive receptor that doesn't receive a signal for pigment control or for pain relief." This might make a chestnut-coated horse more sensitive to environmental stimuli. Another base coat color gene, ASIP (agouti-signaling protein), is associated with behavior in horses. The ASIP gene works in the same signaling pathway to suppress the effect of the MC1R gene. Brooks and her colleagues surveyed owners of 215 Tennessee Walking Horses to compare 20 temperament traits with DNA information extracted from the base of their hair follicles. Horses with a loss-of-function mutation in ASIP, which results in a black coat color, tended to have more self-reliant and independent temperaments than those with bay coats. This particular mutation might also keep the adrenal gland from releasing natural steroid hormones in response to stress, thereby leading to a calmer temperament. Spooking and the Startle Response You've always known your spooky gelding is a bit of a scaredy-cat, but did you know he might be genetically wired to react to things the way he does? University of Florida researchers recently studied Quarter Horse weanlings to map the genes for spooking behavior. "The initiation of a spook begins with a startle response, which is a neurologic reflex, not a conscious effort," Brooks says. "Some genetic changes result in an alteration in the neurologic pathway controlling the startle response." All study horses received uniform envi- ronmental training (e.g., they were halter- broke at the same time, etc.). All also experienced the same experimental setup: Once the weanlings were accustomed to being fed from a pan in a round pen, a researcher would pop open a brightly col- ored umbrella nearby while they ate. The team catalogued the responses—ear flick, increased heart rate, defecation, distance traveled, and the likelihood and speed of return to the feed pan. Some weanlings continued eating, some refused to return to the feed pan, and others exhibited behaviors across the spectrum. The re- searchers used a statistical model to score each individual's likelihood to startle. "To map something, you must first be able to precisely measure it," says Brooks. Now the researchers will investi- gate each weanling's genetic makeup and look for genomic markers that correlate with its score. "A practical objective of this work is to create a genetic test for the tendency to spook, based on a population-wide aver- age," says Brooks. "Recreational riders often want a quiet horse, whereas a show jumper may desire a horse with lightning- fast reflexes. A DNA sample submitted for genetic testing may help people decide if a young horse will be appropriate for their athletic endeavors." It's in the GENES COURTESY DR. SAMANTHA BROOKS Researchers are comparing weanlings' genetic makeup to their tendency to spook.