Unlocking the potential of a validated single nucleotide polymorphism array for genomic monitoring of trade in cheetahs
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ORIGINAL ARTICLE
Unlocking the potential of a validated single nucleotide polymorphism array for genomic monitoring of trade in cheetahs (Acinonyx jubatus) Michelle Magliolo1,2 · Stefan Prost1,4 · Pablo Orozco‑terWengel5 · Pamela Burger3 · Anna S. Kropff1 · Antoinette Kotze1,2 · J. Paul Grobler2 · Desire Lee Dalton1,2 Received: 31 March 2020 / Accepted: 24 November 2020 © Springer Nature B.V. 2020
Abstract Cheetahs (Acinonyx jubatus) are listed as vulnerable on the International Union for Conservation of Nature Red List of Threatened Species. Threats include loss of habitat, human-wildlife conflict and illegal wildlife trade. In South Africa, the export of wild cheetah is a restricted activity under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), however, limited legal trade is permitted of animals born to captive parents. To effectively monitor the legal and illegal trade in South Africa, it was thus essential to develop a validated molecular test. Here, we designed a single nucleotide polymorphism (SNP) array for cheetah from Double Digest Restriction Associated DNA sequencing data for individual identification and parentage testing. In order to validate the array, unrelated individuals and 16 family groups consisting of both parents and one to three offspring were genotyped using the Applied Biosystems™ QuantStudio™ 12K Flex Real-Time PCR System. In addition, parentage assignments were compared to microsatellite data. Cross-species amplification was tested in various felids and cheetah sub-species in order to determine the utility of the SNP array in other species. We obtained successful genotyping results for 218 SNPs in cheetah (A. j. jubatus) with an optimal DNA input concentration ranging from 10 to 30 ng/µl. The combination of SNPs had a higher resolving power for individual identification compared to microsatellites and provided high assignment accuracy in known pedigrees. Cross-species amplification in other felids was determined to be limited. However, the SNP array demonstrated a clear genetic discrimination of two cheetah subspecies tested here. We conclude that the described SNP array is suitable for accurate parentage assignment and provides an important traceability tool for forensic investigations of cheetah trade. Keywords Single nucleotide polymorphism · Parentage · Forensics · Cheetah
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11033-020-06030-0) contains supplementary material, which is available to authorized users. * Desire Lee Dalton [email protected] 1
South African National Biodiversity Institute, P.O. Box 754, Pretoria 0001, South Africa
2
Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
3
Department of Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, Vetmeduni Vienna, Vienna, Austria
4
LOEWE‑Centre for Translational Biodiversity Genomics, Senckenberg Nature Research Society, Frankfurt, Germany
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