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Open Access DNA-based Determination of Ancestry in Cynomolgus Macaques (Macaca fascicularis)

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Interest in the genetic composition of cynomolgus macaques (Macaca fascicularis) has increased due to the rising demand for NHP models in human biomedical research. Significant genetic differences among regional populations of cynomolgus macaques can confound interpretations of research results because they do not solely reflect differences in experimental treatment effects. Therefore, the common origin of cynomolgus macaques used as research subjects should be verified by using region-specific genetic markers to minimize the influence of underlying genetic variation among animals selected as research subjects on phenotypes under study. We compared the effectiveness of 18 short tandem repeat (STR) markers with that of 83 single-nucleotide polymorphism (SNP) markers to differentiate the ancestry of cynomolgus macaques from 6 different populations (Cambodia, Sumatra, Mauritius, Singapore, and the islands of Luzon and Zamboanga in the Philippines). Genetic diversity indices such as allele numbers and expected heterozygosity based on SNP were lower and exhibited lower standard errors than those provided by STR, probably because, unlike STR, most SNP are biallelic and consequently exhibit maximal expected heterozygosity values of 0.50. However, the standard error of estimates of observed heterozygosity based on SNP was higher than that for STR, perhaps reflecting sampling errors. Only 27 SNP were required to match the resolving power of 17 STR to detect population structure, that is, 1.6 SNP:1 STR. Whereas STR only differentiated the Mauritian population from all other populations, SNP detected 4 genetically distinct groups (Cambodia, Singapore-Sumatra, Mauritius, and Zamboanga). SNP are poised to become as valuable as STR for understanding and detecting genetic structure among cynomolgus macaques. Although STR will remain an important tool for cynomolgus macaque population studies, SNP have the potential to become the mainstream marker type.

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Document Type: Research Article

Affiliations: 1: Molecular Anthropology Laboratory, University of California, Davis, California 2: Molecular Anthropology Laboratory, University of California, Davis, California, School of Mathematics and Natural Sciences, Arizona State University at the West Campus, Glendale, Arizona 3: Primate Products, Immokalee, Florida 4: Molecular Anthropology Laboratory, California National Primate Research Center, University of California, Davis, California 5: California National Primate Research Center, University of California, Davis, California, School of Mathematics and Natural Sciences, Arizona State University at the West Campus, Glendale, Arizona;, Email: [email protected]

Publication date: September 1, 2018

This article was made available online on August 30, 2018 as a Fast Track article with title: "DNA-based Determination of Ancestry in Cynomolgus Macaques (Macaca fascicularis)".

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  • The Journal of the American Association for Laboratory Animal Science (JAALAS) serves as an official communication vehicle for the American Association for Laboratory Animal Science (AALAS). The journal includes a section of refereed articles and a section of AALAS association news. The mission of the refereed section of the journal is to disseminate high-quality, peer-reviewed information on animal biology, technology, facility operations, management, and compliance as relevant to the AALAS membership. JAALAS accepts research reports (data-based) or scholarly reports (literature-based), with the caveat that all articles, including solicited manuscripts, must include appropriate references and must undergo peer review.

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