Construction of an individual identification panel for horses using insertion and deletion markers

Abstract

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.

Comparison of DNA extraction methods for genotyping equine histidine-rich glycoprotein insertion/deletion polymorphisms using oral mucosa swabs and feces

“…Research on genes has also progressed in the field of veterinary science, and genetic testing is now commonly used to assess the risks of certain diseases and for drug selection of mast cell tumors in dogs ( Giantin et al, 2012 ; Gil, 2015 ; Vozdova et al, 2019 ). Particularly in equine science, genetic testing is increasingly used for parent-child identification, individual identification, and doping determination in racehorses ( Holl et al, 2017 ; Tozaki et al, 2022 ; 2023 ). However, the collection of genes from animals that do not provide consent sometimes poses problems from an animal welfare perspective.…”