TY - JOUR
T1 - DNA-based Determination of Ancestry in Cynomolgus Macaques (Macaca fascicularis)
AU - Day, George Q.
AU - Ng, Jillian
AU - Oldt, Robert F.
AU - Houghton, Paul W.
AU - Smith, David Glenn
AU - Kanthaswamy, Sreetharan
N1 - Funding Information:
This study was supported by California National Primate Research Center (CNPRC) base grant (no. RR000169-48), ARRA supplement grant RR018144-07 to SK and Nick Lerche (CNPRC), and NIH grants RR005090 and RR025871 to DGS. We thank the staff of the Molecular Anthropology Laboratory at the University of California–Davis for their assistance with sample preparation.
Funding Information:
The research described in this article has been reported in George Day’s Masters of Science (Forensic Science) thesis, which was submitted to the University of California–Davis Office of Graduate Studies in August 2015. This research has also been presented at the Society of American Primate Veterinarians 40th Annual Workshop, which was held in St Paul, MN, 31 Oct through 3 Nov 2012. This study was supported by California National Primate Research Center (CNPRC) base grant (no. RR000169-48), ARRA supplement grant RR018144-07 to SK and Nick Lerche (CNPRC), and NIH grants RR005090 and RR025871 to DGS. We thank the staff of the Molecular Anthropology Laboratory at the University of California–Davis for their assistance with sample preparation. Samples were provided pro bono by Primate Products. Animals involved in this study were managed in compliance with the American Society of Primatologists (ASP) Principles for the Ethical Treatment of Nonhuman Primates and with the National Institutes of Health guidelines prescribing the humane care and use of laboratory animals.
Publisher Copyright:
Copyright 2018 by the American Association for Laboratory Animal Science.
PY - 2018
Y1 - 2018
N2 - 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.
AB - 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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U2 - 10.30802/AALAS-JAALAS-17-000147
DO - 10.30802/AALAS-JAALAS-17-000147
M3 - Article
C2 - 30165920
AN - SCOPUS:85054410211
SN - 1559-6109
VL - 57
SP - 432
EP - 442
JO - Journal of the American Association for Laboratory Animal Science
JF - Journal of the American Association for Laboratory Animal Science
IS - 5
ER -