Single nucleotide polymorphisms for DNA typing in the domestic horse.
Abstract: Genetic markers are important resources for individual identification and parentage assessment. Although short tandem repeats (STRs) have been the traditional DNA marker, technological advances have led to single nucleotide polymorphisms (SNPs) becoming an attractive alternative. SNPs can be highly multiplexed and automatically scored, which allows for easier standardization and sharing among laboratories. Equine parentage is currently assessed using STRs. We obtained a publicly available SNP dataset of 729 horses representing 32 diverse breeds. A proposed set of 101 SNPs was analyzed for DNA typing suitability. The overall minor allele frequency of the panel was 0.376 (range 0.304-0.419), with per breed probability of identities ranging from 5.6 × 10 to 1.86 × 10 . When one parent was available, exclusion probabilities ranged from 0.9998 to 0.999996, although when both parents were available, all breeds had exclusion probabilities greater than 0.9999999. A set of 388 horses from 35 breeds was genotyped to evaluate marker performance on known families. The set included 107 parent-offspring pairs and 101 full trios. No horses shared identical genotypes across all markers, indicating that the selected set was sufficient for individual identification. All pairwise comparisons were classified using ISAG rules, with one or two excluding markers considered an accepted parent-offspring pair, two or three excluding markers considered doubtful and four or more excluding markers rejecting parentage. The panel had an overall accuracy of 99.9% for identifying true parent-offspring pairs. Our developed marker set is both present on current generation SNP chips and can be highly multiplexed in standalone panels and thus is a promising resource for SNP-based DNA typing.
© 2017 Stichting International Foundation for Animal Genetics.
Publication Date: 2017-09-13 PubMed ID: 28901559DOI: 10.1111/age.12608Google Scholar: Lookup
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- Journal Article
Summary
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This research tested a set of 101 single nucleotide polymorphisms (SNPs) to see how useful they’d be for DNA typing in horses. The researchers found that no two horses shared identical genotypes across all markers, and the set had a 99.9% accuracy rate for identifying parent-offspring pairs, suggesting that these SNPs are an excellent tool for horse DNA typing.
Investigating Single Nucleotide Polymorphisms (SNPs)
- The researchers started by exploring a publicly available SNP dataset of 729 horses representing 32 different breeds.
- From this dataset, they proposed a set of 101 SNPs to analyze for DNA typing suitability. SNPs are genetic variations that involve a change of just a single nucleotide, the building blocks of DNA.
- These SNPs were attractive because, unlike other DNA markers such as short tandem repeats (STRs), they can be highly multiplexed and automatically scored, simplifying standardization and sharing of data across labs.
Analyzing the SNP Set
- The researchers evaluated the proposed SNP set by looking at the overall minor allele frequency, or likelihood the less common form of a gene is present. This was found to have a frequency of 0.376, a decently high percentage that shows genetic variation within the population.
- The researchers also analyzed the probability of identity, or likelihood two randomly chosen individuals have identical genotypes. This ranged between 5.6×10 and 1.86×10, meaning there’s significant genetic variety within the sample.
- They also looked at the exclusion probabilities, the likelihood that an individual isn’t the parent of an offspring. Depending on whether one or both parents were available for comparison, exclusion probabilities ranged from 0.9998 to beyond 0.9999999.
Applying the SNP Set
- To test the SNP set, the researchers genotyped a set of 388 horses from 35 breeds that included 107 parent-offspring pairs and 101 full trios.
- The genotyping revealed that no horses shared identical genotypes across all markers, which indicates that the proposed SNP set could effectively differentiate individual horses.
- In terms of parent-offspring relationships, the researchers found an overall accuracy rate of 99.9%. This was determined following the International Society for Animal Genetics (ISAG) rules, with one or two excluding markers considered an accepted parent-offspring pair, while those with more excluded markers doubted or rejected the parentage relationship.
Conclusion
- This research showed the promise of the SNP set for DNA typing, as it can be used on current generation SNP chips and can be highly multiplexed in standalone panels.
- The success of this study suggests potential for SNP-based DNA typing not just in horses, but potentially in other animals and humans as well.
Cite This Article
APA
Holl HM, Vanhnasy J, Everts RE, Hoefs-Martin K, Cook D, Brooks SA, Carpenter ML, Bustamante CD, Lafayette C.
(2017).
Single nucleotide polymorphisms for DNA typing in the domestic horse.
Anim Genet, 48(6), 669-676.
https://doi.org/10.1111/age.12608 Publication
Researcher Affiliations
- Etalon Inc., Menlo Park, CA, 94025, USA.
- Agena Bioscience, San Diego, CA, 92121, USA.
- Agena Bioscience, San Diego, CA, 92121, USA.
- Etalon Inc., Menlo Park, CA, 94025, USA.
- Etalon Inc., Menlo Park, CA, 94025, USA.
- Etalon Inc., Menlo Park, CA, 94025, USA.
- Etalon Inc., Menlo Park, CA, 94025, USA.
- Etalon Inc., Menlo Park, CA, 94025, USA.
- Etalon Inc., Menlo Park, CA, 94025, USA.
MeSH Terms
- Animals
- Breeding
- DNA Fingerprinting
- Gene Frequency
- Genetic Markers
- Genotype
- Horses / genetics
- Polymorphism, Single Nucleotide
Citations
This article has been cited 11 times.- Tozaki T, Ohnuma A, Kikuchi M, Ishige T, Kakoi H, Hirota KI, Takahashi Y, Nagata SI. Short Insertion and Deletion Discoveries via Whole-Genome Sequencing of 101 Thoroughbred Racehorses. Genes (Basel) 2023 Mar 3;14(3).
- Cardinali I, Giontella A, Tommasi A, Silvestrelli M, Lancioni H. Unlocking Horse Y Chromosome Diversity. Genes (Basel) 2022 Dec 2;13(12).
- Nolte W, Alkhoder H, Wobbe M, Stock KF, Kalm E, Vosgerau S, Krattenmacher N, Thaller G, Tetens J, Kühn C. Replacement of microsatellite markers by imputed medium-density SNP arrays for parentage control in German warmblood horses. J Appl Genet 2022 Dec;63(4):783-792.
- Tozaki T, Ohnuma A, Nakamura K, Hano K, Takasu M, Takahashi Y, Tamura N, Sato F, Shimizu K, Kikuchi M, Ishige T, Kakoi H, Hirota KI, Hamilton NA, Nagata SI. Detection of Indiscriminate Genetic Manipulation in Thoroughbred Racehorses by Targeted Resequencing for Gene-Doping Control. Genes (Basel) 2022 Sep 4;13(9).
- Luttman AM, Komine M, Thaiwong T, Carpenter T, Ewart SL, Kiupel M, Langohr IM, Venta PJ. Development of a 17-Plex of Penta- and Tetra-Nucleotide Microsatellites for DNA Profiling and Paternity Testing in Horses. Front Vet Sci 2022;9:861623.
- de Groot M, Anderson H, Bauer H, Bauguil C, Bellone RR, Brugidou R, Buckley RM, Dovč P, Forman O, Grahn RA, Kock L, Longeri M, Mouysset-Geniez S, Qiu J, Sofronidis G, van der Goor LHP, Lyons LA. Standardization of a SNP panel for parentage verification and identification in the domestic cat (Felis silvestris catus). Anim Genet 2021 Oct;52(5):675-682.
- von Thaden A, Nowak C, Tiesmeyer A, Reiners TE, Alves PC, Lyons LA, Mattucci F, Randi E, Cragnolini M, Galián J, Hegyeli Z, Kitchener AC, Lambinet C, Lucas JM, Mölich T, Ramos L, Schockert V, Cocchiararo B. Applying genomic data in wildlife monitoring: Development guidelines for genotyping degraded samples with reduced single nucleotide polymorphism panels. Mol Ecol Resour 2020 May;20(3).
- Kim D, Lee S, Oyungerel B, Cho G. Evaluation of the Effectiveness of Single-Nucleotide Polymorphisms Versus Microsatellites for Parentage Verification in Horse Breeds. Vet Sci 2025 Sep 15;12(9).
- Jaito W, Singchat W, Patta C, Thatukan C, Kumnan N, Chalermwong P, Budi T, Panthum T, Wongloet W, Wattanadilokchatkun P, Thong T, Muangmai N, Han K, Duengkae P, Phatcharakullawarawat R, Srikulnath K. Shared alleles and genetic structures in different Thai domestic cat breeds: the possible influence of common racial origins. Genomics Inform 2024 Jul 31;22(1):12.
- 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.
- Lee SY, Kim SM, Oyungerel B, Cho GJ. Single nucleotide polymorphisms for parentage testing of horse breeds in Korea. Anim Biosci 2024 Apr;37(4):600-608.
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