Evaluation of parentage testing using single nucleotide polymorphism markers for draft horses in Japan.
Abstract: We evaluated the utility of single nucleotide polymorphism (SNP) markers for parentage testing in Breton (BR) and Percheron (PR) horses in Japan using the proposed International Society for Animal Genetics (P-ISAG) 147 SNP panel and 414 autosomal SNPs. Genomic DNA was extracted from 98 horses of two breeds, BR (n = 47) and PR (n = 51), and sequenced using next-generation sequencing. The average minor allele frequencies for the P-ISAG panel for BR and PR were 0.306 and 0.301, respectively. The combined probabilities of exclusion (PEs) given two parents and one offspring: exclude a relationship (PE01) and given one parent and one offspring: exclude their relationship (PE02) were over 0.9999 for both breeds. Using the P-ISAG panel, no exclusion or doubtful cases were identified in 35 valid parent-offspring pairs, suggesting that the P-ISAG panel is helpful for parentage verification in both breeds. In contrast, as 0.18% of falsely accepted parentages were observed in the parentage discovery cases, additional markers such as the combination of the P-ISAG panel and 414 autosomal SNPs (561-SNP set) presented here should be used to identify valid parent-offspring pairs of horses with unknown parentage relationships.
© 2023 Japanese Society of Animal Science.
Publication Date: 2023-07-10 PubMed ID: 37427667DOI: 10.1111/asj.13854Google Scholar: Lookup
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- Journal Article
Summary
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This research tests the effectiveness of single nucleotide polymorphism (SNP) markers for determining the parentage of Breton and Percheron draft horses in Japan.
Study Purpose and Methodology
- By using single nucleotide polymorphism (SNP) markers, the researchers evaluated the potential of parentage testing in two breeds of draft horses in Japan: Breton and Percheron.
- The researchers ensured to use a resourceful 147 SNP panel recommended by the International Society for Animal Genetics (P-ISAG), as well as 414 other autosomal SNPs.
- This was done by extracting genomic DNA from 98 horses from both breeds (47 Breton horses and 51 Percheron horses), and then sequencing this DNA using next-generation sequencing methodologies.
Findings
- The researchers found that in both breeds, the average minor allele frequencies for the P-ISAG panel were around 0.3.
- The probabilities of exclusion (PEs)—statistics that demonstrate the chance of excluding an incorrectly assigned parent—were incredibly high. In situations where two parents and one offspring are given (PE01) or one parent and one offspring are given (PE02), these probabilities were over 0.9999 for both breeds.
- These findings suggest that the P-ISAG panel can efficiently exclude incorrect parent-offspring relationships in both of these breeds, making it an effective tool for parentage verification.
Implications
- Whilst the results from this study are promising, the researchers noted that in some cases there was a small chance of false acceptance of parentage (0.18% of cases).
- Because of this limitation, the researchers recommend using the P-ISAG panel in combination with other marker sets, such as the 414 other autosomal SNPs (forming a 561-SNP set), for more accurate parentage identification in situations where the parent-offspring relationship is not known.
Cite This Article
APA
Ishige T, Kikuchi M, Kakoi H, Hirota KI, Ohnuma A, Tozaki T, Hirosawa Y, Tanaka S, Nagata SI.
(2023).
Evaluation of parentage testing using single nucleotide polymorphism markers for draft horses in Japan.
Anim Sci J, 94(1), e13854.
https://doi.org/10.1111/asj.13854 Publication
Researcher Affiliations
- Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Japan.
- Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Japan.
- Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Japan.
- Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Japan.
- Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Japan.
- Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Japan.
- National Livestock Breeding Center Tokachi Station, Otofuke, Japan.
- National Livestock Breeding Center Tokachi Station, Otofuke, Japan.
- Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Japan.
MeSH Terms
- Horses / genetics
- Animals
- Polymorphism, Single Nucleotide / genetics
- Japan
- Gene Frequency / genetics
- Base Sequence
- DNA
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Citations
This article has been cited 1 times.- Valera M, Karlau A, Anaya G, Bugno-Poniewierska M, Molina A, Encina A, Azor PJ, Demyda-Peyrás S. The Use of Genomic Screening for the Detection of Chromosomal Abnormalities in the Domestic Horse: Five New Cases of 65,XXY Syndrome in the Pura Raza Español Breed. Animals (Basel) 2024 Sep 3;14(17).
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