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Conservation genetics resources2022; 14(2); 203-213; doi: 10.1007/s12686-022-01259-2

Targeted genome-wide SNP genotyping in feral horses using non-invasive fecal swabs.

Abstract: The development of high-throughput sequencing has prompted a transition in wildlife genetics from using microsatellites toward sets of single nucleotide polymorphisms (SNPs). However, genotyping large numbers of targeted SNPs using non-invasive samples remains challenging due to relatively large DNA input requirements. Recently, target enrichment has emerged as a promising approach requiring little template DNA. We assessed the efficacy of Tecan Genomics' Allegro Targeted Genotyping (ATG) for generating genome-wide SNP data in feral horses using DNA isolated from fecal swabs. Total and host-specific DNA were quantified for 989 samples collected as part of a long-term individual-based study of feral horses on Sable Island, Nova Scotia, Canada, using dsDNA fluorescence and a host-specific qPCR assay, respectively. Forty-eight samples representing 44 individuals containing at least 10 ng of host DNA (ATG's recommended minimum input) were genotyped using a custom multiplex panel targeting 279 SNPs. Genotyping accuracy and consistency were assessed by contrasting ATG genotypes with those obtained from the same individuals with SNP microarrays, and from multiple samples from the same horse, respectively. 62% of swabs yielded the minimum recommended amount of host DNA for ATG. Ignoring samples that failed to amplify, ATG recovered an average of 88.8% targeted sites per sample, while genotype concordance between ATG and SNP microarrays was 98.5%. The repeatability of genotypes from the same individual approached unity with an average of 99.9%. This study demonstrates the suitability of ATG for genome-wide, non-invasive targeted SNP genotyping, and will facilitate further ecological and conservation genetics research in equids and related species. Unassigned: The online version contains supplementary material available at 10.1007/s12686-022-01259-2.
© The Author(s) 2022.
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Publication Date: 2022-03-16 PubMed ID: 35673611PubMed Central: PMC9162989DOI: 10.1007/s12686-022-01259-2Google Scholar: Lookup
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  • Journal Article

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 article focuses on a new technique in wildlife genetics involving targeted genome-wide single nucleotide polymorphisms (SNPs) genotyping, specifically in feral horses via non-invasive fecal swabs. This approach, using the Tecan Genomics’ Allegro Targeted Genotyping (ATG) method, is effective at generating SNP data, and offers a promising and versatile method that can be adopted for ecological and conservation genetics research.

Research Objectives and Methodology

  • The study aimed to evaluate the efficacy of the Tecan Genomics’ Allegro Targeted Genotyping (ATG) method for generating genome-wide SNP data using non-invasive fecal swabs.
  • The researchers collected 989 samples from a long-term individual-based study of feral horses on Sable Island, Nova Scotia, Canada. Specific DNA fluorescence and qPCR assays were used to quantify total and host-specific DNA in these samples.
  • Then, a custom multiplex panel targeting 279 SNPs was used to genotype 48 samples, each containing at least 10ng of host DNA, representing 44 individuals. This amount of host DNA is the recommended minimum input for the ATG method.

Results and Findings

  • The study found that 62% of the swabs yielded the minimum recommended amount of host DNA necessary for the ATG method.
  • Disregarding samples that failed to amplify, ATG recovered an average of 88.8% targeted sites per sample.
  • The genotype concordance (agreement) between ATG and SNP microarrays was notably high at 98.5%.
  • The repeatability of genotypes from the same individual was also extremely high, with an average of 99.9%.

Conclusion and Implications

  • The ATG method demonstrated a high level of suitability for non-invasive targeted SNP genotyping. This suggests a promising future for the application of ATG in wildlife genetics research, particularly in ecological and conservation studies.
  • Therefore, the researchers conclude that the ATG method could be adopted for further genetic research in equids and related species, showcasing the potential and versatility of the approach.

Cite This Article

APA
Gavriliuc S, Reza S, Jeong C, Getachew F, McLoughlin PD, Poissant J. (2022). Targeted genome-wide SNP genotyping in feral horses using non-invasive fecal swabs. Conserv Genet Resour, 14(2), 203-213. https://doi.org/10.1007/s12686-022-01259-2

Publication

Conservation genetics resources
ISSN: 1877-7252
NlmUniqueID: 101505405
Country: Netherlands
Language: English
Volume: 14
Issue: 2
Pages: 203-213

Researcher Affiliations

Gavriliuc, Stefan
  • Department of Ecosystem and Public Health, University of Calgary, 3280 Hospital Drive, Calgary, AB T2N 4Z6 Canada.
Reza, Salman
  • Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4Z6 Canada.
Jeong, Chanwoori
  • Department of Ecosystem and Public Health, University of Calgary, 3280 Hospital Drive, Calgary, AB T2N 4Z6 Canada.
Getachew, Fitsum
  • Department of Ecosystem and Public Health, University of Calgary, 3280 Hospital Drive, Calgary, AB T2N 4Z6 Canada.
McLoughlin, Philip D
  • Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2 Canada.
Poissant, Jocelyn
  • Department of Ecosystem and Public Health, University of Calgary, 3280 Hospital Drive, Calgary, AB T2N 4Z6 Canada.

Conflict of Interest Statement

Conflict of interestNA.

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