Individual identification and paternity testing are important for avoiding inbreeding in
the management of small populations of wild and domestic animals. In horse racing
industries, they are extremely important for identifying and registering individuals and
doping control to ensure fair competition. In this study, we constructed an individual
identification panel for horses by using insertion and deletion (INDEL) markers. The panel
included 39 INDEL markers selected from a whole-genome INDEL database. Genotyping of 89
Thoroughbreds showed polymorphisms with minor allele frequencies (MAFs) of 0.180–0.489 in
all markers. The total probability of exclusion for paternity testing, power of
discrimination, and probability of identity were 0.9994271269, >0.9999999999, and
0.9999999987, respectively. The panel was applied to 13 trios (sires, dams, and foals),
and no contradictions were observed in genetic inheritance among the trios. When this
panel was applied to the trios (52 trios) containing false fathers, an average of 7.3
markers excluded parentage relationships. In addition, genomic DNA extracted from the
urine of six horses was partially genotyped for 39 markers, and 6–28 markers were
successfully genotyped. The newly constructed panel has two advantages: a low marker
mutation rate compared with short tandem repeats and a genotyping procedure that is as
simple as short tandem repeat typing compared with single nucleotide variant typing. This
panel can be applied for individual identification, paternity determination, and
urine-sample identification in Thoroughbred horses.