Unlocking the potential of a validated single nucleotide polymorphism array for genomic monitoring of trade in cheetahs (Acinonyx jubatus)

Michelle Magliolo, Stefan Prost, Pablo Orozco-terWengel, Pamela Burger, Anna S. Kropff, Antoinette Kotze, J. Paul Grobler, Desire Lee Dalton

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Pages (from-to)171-181
Number of pages11
JournalMolecular Biology Reports
Issue number1
Early online date4 Dec 2020
Publication statusPublished - 31 Jan 2021

Bibliographical note

Funding Information:
D.L.D. and P.B. acknowledge the Scientific & Technological Cooperation Austria, from the Austrian Agency for International Cooperation in Education and Research and the National Research Foundation (NRF) of South Africa. This work is based on the research supported in part by the National Research Foundation of South Africa (Grant Number 116055).

Publisher Copyright:
© 2020, Springer Nature B.V.


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