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Equine veterinary journal2019; 52(2); 290-297; doi: 10.1111/evj.13158

A novel 13-plex STR typing system for individual identification and parentage testing of donkeys (Equus asinus).

Abstract: Previous studies investigating donkey parentage and genetic diversity used horse-specific multiplex systems. However, several mis-allele and null-allele issues were found with some of the horse primers when used in donkeys. In 2017, the International Society for Animal Genetics (ISAG) recommended 13 dinucleotide short tandem repeats (STRs) (AHT4, ASB23, HMS2, HMS3, HMS6, HMS7, HMS18, HTG7, HTG10, TKY297, TKY312, TKY337 and TKY343) as a core panel that should be used to identify individuals and to test for parentage in donkeys. To date, no single multiplex STR typing system containing all 13 donkey STRs recommended by the ISAG has been reported. Objective: To establish a novel and donkey-specific multiplex STR typing system containing all 13 recommended STRs. Methods: Assay development and validation in field population. Methods: Primers for seven of the STRs were redesigned and conditions for polymerase chain reaction (PCR) were optimised. We analysed the allele sequences, sensitivity, species-specificity and stutter ratios of this new system. Results: A 13-plex STR typing system for donkey was established. A full profile could be generated from a single PCR reaction using as little as 5 ng of DNA template with the 13 pairs of primers labelled with fluorescent dyes. An allele ladder, containing 101 alleles from the 13 STRs, was generated. No full genotype profile was generated with these primers if DNA from humans, or 11 other commonly encountered animals, was used. Genotypes could be generated for the horse and horse-donkey hybrids (mule and hinny). Stutter ratios and population genetic parameters were calculated based on samples from 150 donkeys. The combined probabilities of paternity exclusion for this system were 0.988907326 (CPEduo) and 0.999665018 (CPEtrio). Conclusions: This system cannot detect sex. Conclusions: Our results indicate that our donkey-specific 13-plex STR typing system is sensitive, species-specific and robust for individual identification, paternity testing and population genetic analysis in donkeys, and has potential forensic applications.
© 2019 EVJ Ltd.
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Publication Date: 2019-09-05 PubMed ID: 31398262DOI: 10.1111/evj.13158Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research paper presents a novel 13-plex short tandem repeats (STR) typing system designed to improve the identification and parentage testing process in donkeys, achieving a high probability of paternity exclusion.

Objective and Need for the Research

  • The research aimed to introduce a novel donkey-specific 13-plex STR typing system targeting more accurate identification and parentage testing.
  • The need for this research originated from the issues related to the use of horse-specific multiplex systems in donkeys, including the occurrence of mis-allele and null-allele problems encountered with some horse primers.

Methods Used

  • In developing and validating the proposed 13-plex STR typing system, the research team optimised polymerase chain reaction (PCR) conditions.
  • They performed a detailed analysis of allele sequences, sensitivity and species-specificity, and calculated stutter ratios of the new system on DNA samples of 150 donkeys.
  • Primers labelled with fluorescent dyes were used in a single PCR reaction with as minimal as 5 ng of DNA template to obtain a full profile.

Results and Findings

  • The research successfully established a 13-plex STR typing system specifically for the identification and parentage testing of donkeys.
  • In the case of DNA derived from humans or any of 11 other commonly encountered animals, their primers did not generate a full genotype profile. Horse DNA and horse-donkey hybrid DNA (from mules and hinnies) were exceptions, showing resultant genotypes.
  • They were able to generate a ladder of 101 alleles from the 13 STRs and calculated the combined probabilities of paternity exclusion as 0.988907326 (CPEduo) and 0.999665018 (CPEtrio).

Conclusion

  • The novel 13-plex STR system for donkeys does not have the ability to detect sex.
  • The results indicate the system as a sensitive, robust, and species-specific method for individual identification, paternity testing, and genetic population analysis in donkeys. Moreover, there is potential for forensic applications.

Cite This Article

APA
Dang W, Shang S, Zhang X, Yu Y, Irwin DM, Wang Z, Zhang S. (2019). A novel 13-plex STR typing system for individual identification and parentage testing of donkeys (Equus asinus). Equine Vet J, 52(2), 290-297. https://doi.org/10.1111/evj.13158

Publication

Equine veterinary journal
ISSN: 2042-3306
NlmUniqueID: 0173320
Country: United States
Language: English
Volume: 52
Issue: 2
Pages: 290-297

Researcher Affiliations

Dang, W
  • Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China.
Shang, S
  • Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China.
Zhang, X
  • Liaoning Province Engineering Center of Modern Agricultural Production Base, Shenyang, China.
Yu, Y
  • Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China.
Irwin, D M
  • Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
Wang, Z
  • Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China.
Zhang, S
  • Institute of Equine Sciences, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China.

MeSH Terms

  • Alleles
  • Animals
  • Equidae
  • Genotype
  • Horses
  • Humans
  • Microsatellite Repeats
  • Polymerase Chain Reaction / veterinary

Grant Funding

  • 2016YFD0500300 / Ministry of Science and Technology of the People's Republic of China
  • 2019416032 / Department of Science and Technology of Liaoning Province of China

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Citations

This article has been cited 2 times.
  1. Wang Y, Tang C, Xue P, Yang N, Sun X, Serik K, Assanbayer T, Shamekova M, Kozhanov Z, Sapakhova Z, Khurramovich JK, Zhou X, Kairat I, Muhatai G. Identification of Genetic Relationships and Group Structure Analysis of Yanqi Horses. Genes (Basel) 2025 Feb 27;16(3).
    doi: 10.3390/genes16030294pubmed: 40149446google scholar: lookup
  2. Shang S, Wang Y, Yu X, Zhang D, Luo R, Jiang R, Zhao G, Du X, Zhang J, Irwin DM, Wang Z, Zhang S. Development of a 17-plex STR typing system for the identification of individuals and parentage testing in cattle. Sci Rep 2024 Oct 23;14(1):24998.
    doi: 10.1038/s41598-024-76547-ypubmed: 39443655google scholar: lookup
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