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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.
©2023 Catalyst Unit.
Publication Date: 2023-08-09 PubMed ID: 37781568PubMed Central: PMC10534061DOI: 10.1294/jes.34.83Google Scholar: Lookup The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
- Journal Article
Summary
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This research article presents a study that successfully developed an identification panel for horses using insertion and deletion (INDEL) markers. This panel is primarily useful for identity confirmation, paternity testing, and urine-sample identification in Thoroughbred horses.
Selection of INDEL Markers and Panel Construction
- The researchers constructed an identification panel for horses using INDEL markers – genetic variations that occur when segments of DNA are inserted or deleted.
- 39 INDEL markers were chosen from a large INDEL database. They were then genotyped (analysed) in 89 Thoroughbreds.
- The markers showed polymorphisms – genetic differences or variations – with minor allele frequencies (MAFs) ranging from 0.180 to 0.489. This indicates a good level of genetic diversity which is helpful for differentiating between individuals.
Evaluation of the Identification Panel
- The panel was assessed for its potential in excluding incorrect parentages. The total probability of exclusion for paternity testing was astonishingly high at over 99.9%.
- Suitable for individual discrimination, the power of discrimination was also very high with a greater than 99.99999999% chance of correctly distinguishing between horses.
- The probability of identity (the likelihood of two randomly selected individuals having the same genotype) was also very high at about 99.99999987%.
Application of the Identification Panel
- The newly-developed panel was applied to 13 trios of sires (fathers), dams (mothers), and foals (offspring), with no inconsistencies found in genetic inheritance among them.
- When tested on false-father trios (52 in number), the panel successfully excluded false paternity with an average of 7.3 markers.
- Urinary DNA from six horses was also tested using the panel. Here, 6-28 markers were successfully genotyped, proving the panel’s utility for non-invasive testing.
Advantages of the Identification Panel
- The INDEL-marker-based panel possesses two major advantages. Firstly, it has a lower mutation rate compared to short tandem repeats, increasing its reliability for long term studies.
- Secondly, genotyping with this panel is as straightforward as with short tandem repeat typing, making it easier and more accessible.
Thus, this INDEL-marker-based panel has shown high potential for use in identifying individual horses, paternity determination, and non-invasive urine-sample identification in the horse racing industry, particularly in Thoroughbred horses.
Cite This Article
APA
Tozaki T, Ohnuma A, Kikuchi M, Ishige T, Kakoi H, Hirota KI, Nagata SI.
(2023).
Construction of an individual identification panel for horses using insertion and deletion markers.
J Equine Sci, 34(3), 83-92.
https://doi.org/10.1294/jes.34.83 Publication
Researcher Affiliations
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi 320-0851, Japan.
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi 320-0851, Japan.
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi 320-0851, Japan.
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi 320-0851, Japan.
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi 320-0851, Japan.
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi 320-0851, Japan.
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi 320-0851, Japan.
Conflict of Interest Statement
The authors declare no competing interests concerning this study, including patents, products in development, or marketed products.
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Citations
This article has been cited 1 times.- Muko R, Ojima Y, Matsuda H, Toishi Y, Oikawa MA, Shin T, Sato H, Tanaka A. Comparison of DNA extraction methods for genotyping equine histidine-rich glycoprotein insertion/deletion polymorphisms using oral mucosa swabs and feces. Vet Anim Sci 2024 Sep;25:100361.
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