Halla horse is crossbreed between Jeju and Thoroughbred horses and is used for riding, racing and meat production. Thus, molecular genetic studies are needed to establish and preserve the industrially valuable Halla horses. This study aimed to analyses the genetic diversity and population structure through 12 microsatellite (MS) markers for Halla and putatively related 3 breeds (Jeju, Mongolian and Thoroughbred horses). On average, the number of alleles, observed heterozygosity (Hobs), expected heterozygosity (Hexp), and polymorphic information content (PIC) among all horses were 10, 0.767, 0.799, and 0.771, respectively. Neighbor-joining tree and STRUCTURE analysis showed that Halla horses were between Thoroughbred and Jeju horses, tend to more influenced by Thoroughbred horses. Therefore, these results could be considered for use as the basic genetic breed relationships resource among the horse breeds (Jeju, Mongolian, and Thoroughbred horses) related to the origins of the Halla horse.

The conformational characteristics and performance of the horse breed should be evaluated to establish the breeding goals for a riding horse breed. Halla horses are cross-bred from Thoroughbred horses and Jeju ponies. Halla horses have been bred for speed as racing horses in Jeju Island in South Korea. However, some horses have also been used for riding purposes. Thus, the main purpose of this study was to evaluate the characteristics of Halla horses for riding purposes, which can be used as a guideline to define the breeding goals of Halla horses. Therefore, we evaluated the athletic performance of Halla horses by analyzing 3-year records of dressage (from S-3 Class to F Class) and show-jumping competitions (from S-2 Class to G Class) held in South Korea. We also examined the conformational characteristics of 15 Halla horses and compared them with those of 15 Thoroughbred and 15 Warmblood horses. In the results of dressage competitions over 3 years, Halla horses were awarded in D Class dressage only. In contrast, in the show-jumping competition, Halla horses were awarded in the D, E, F, and G classes. Overall, most body parts measured were smaller than those of Thoroughbred and Warmblood horses. When the rate of body parts per the average height of each breed was compared, Halla horses showed a higher rate of head length, head perimeter, and lumbar back length and croup length. In contrast, Halla horses had a shorter neck length. Based on the results of horse competition and conformation analysis, it is concluded that Halla horses are suitable for youth show-jumping competitions and have the potential to be representative riding horses in South Korea.