The first volume of Thoroughbred Stud Book was published in England in 1791 [1], and the first volume was published in Korea in 1998. Domestic foals can be listed in the Korean Stud Book (KSB) through appearance screening and paternity verification. In Korea, the paternity of Thoroughbred horses was tested via blood type until the late 1990s but was changed to microsatellite DNA analysis in 2002 [2].

Microsatellite polymorphism, i.e., short tandem repeat (STR) in a horse, was first reported by Ellegren et al [3] and Marklund et al [4]. Microsatellites have been used for genetic diversity assessment, genetic maps constructions, quantitative trait loci mapping and parentage testing [5,6]. The STR became a valuable tool for horse parentage verification and pedigree registration [7]. In 1998, at the Equine Genetic and Thoroughbred parentage Testing workshop hosted by the International Society for Animal Genetics (ISAG), an international panel with nine STRs for horse DNA typing was created, in 2011, three STRs were added, with 12 STRs currently recommended by ISAG. The International Stud Book Committee (ISBC) recommends using these 12 STRs for registration of Thoroughbred horses. It also requires that the total probability of exclusion (PE) value of parentage testing for Thoroughbred horses exceeds 0.9995 [8].

In Korea, Thoroughbred horse parentage testing started in 2002 using 14 STRs, including the nine (AHT4, AHT5, ASB2, HMS3, HMS6, HMS7, HTG4, HTG10, VHL20) STRs recommended by ISAG. In total, 15 STRs, including 12 (9 STRs plus ASB17, ASB23, HMS2) recommended by ISAG, have been routinely used since 2013.

At present, in South Korea, ~1,000 donkeys and ~27,000 domestic horses exist, including 12,000 Thoroughbreds, 1,000 individuals from other horse breeds (e.g., Warmblood, Quarter horse), and 14,000 native horses (the Jeju Halla horse), of which ~5,000 Jeju horses which was designated as natural monument No. 347 by the government [9].

In Korea, ≥1,500 Thoroughbred foals are born annually. In order for domestic-born Thoroughbred horses to be used as racehorses, they must be identified through appearance tests or genetic tests to be listed in the KSB. In addition, the horse's microsatellite DNA marker used in Korea was recognized for the registration of Thoroughbred horses from ISAG.

Stallions in Korea, have been replaced a lot so far; hence genetic diversity is also presumed to have changed. Therefore, in this study, we investigated the recent changes such as allele frequencies and PE in Thoroughbred horses in Korea using STR parentage panels between 2006 and 2016.

Several microsatellite markers have been isolated from the horse genome [12], and the microsatellites showed multiple alleles and high heterozygosity among European horse breeds such as Thoroughbred horse. Several types of microsatellites are informative because of their high polymorphism, and they are useful in paternity testing of animals. In cattle, pig, horse, dog, and other populations, pedigree control has been performed on a routine basis in most countries [12–18]. These controls rely on microsatellite typing standardized through regular comparison tests with aid from the ISAG.

Blood typing tests of horses require fresh whole blood and include the costs of sampling by veterinarians, and transportation due to rapid transportation; the entire test process is manually conducted by humans. The results were also slightly inaccurate, with 97% to 99.5% in probability of parentage verification. However, since 2002, microsatellite DNA typing was introduced and used for the paternity assessment of horses, most of these deficiencies in existing blood typing tests have been resolved. In Korea, a comparative analysis of the number of alleles, frequency of alleles, Ho, He, and PIC with microsatellite markers used in 2006 and 2016 showed that many stallions and mares had been replaced, but genetic diversity did not change significantly because of the small numbers of mares and stallions raised in the country. The total PE of the STR panel has changed significantly. This trend continues after adding HMS2 in 2011. Nevertheless, the total PE values for 14 or 15 STRs in Thoroughbred horses in Korea have been greater than the ISBC recommended values (>0.9995) over the past decade.

In Korea, 15 STR markers are used to conduct parentage verification for approximately 1,500 Thoroughbred horses in a year. Parentage verification is determined using Mendel's genetic law. If a discrepancy occurs in one marker after the test judgment, it is assumed to be a mutation and additionally examined with three to five TKY marker; if two or more markers deviate from Mendel's genetic law, it is finally determined that they are not paternity. In general, approximately 10 to 12 heads (0.7% to 0.8%) per year are not paternity.

On the basis of the PIC of each marker, the validity and reliability of the marker can be estimated. If the PIC value is ≥0.5000, the reliability of the marker is valid for pedigree analysis. If it is ≥0.7000, it has universal validity for analysis and can get a highly reliable result can be obtained.

It is currently under discussion and research to introduce single nucleotide polymorphism (SNP) instead of microsatellite DNA markers for parentage verification and individual identification of Thoroughbred horses. However, the results of this study are expected to be valid until the introduction of the SNP in the Thoroughbred population in Korea.