Single nucleotide polymorphisms (SNPs) distinguish Indian-origin and Chinese-origin rhesus macaques (Macaca mulatta)

Betsy Ferguson, Summer L. Street, Hollis Wright, Carlo Pearson, Yibing Jia, Shaun L. Thompson, Patrick Allibone, Christopher J. Dubay, Eliot Spindel, Robert B Norgren

Research output: Contribution to journalArticle

75 Citations (Scopus)

Abstract

Background: Rhesus macaques serve a critical role in the study of human biomedical research. While both Indian and Chinese rhesus macaques are commonly used, genetic differences between these two subspecies affect aspects of their behavior and physiology, including response to simian immunodeficiency virus (SIV) infection. Single nucleotide polymorphisms (SNPs) can play an important role in both establishing ancestry and in identifying genes involved in complex diseases. We sequenced the 3′ end of rhesus macaque genes in an effort to identify gene-based SNPs that could distinguish between Indian and Chinese rhesus macaques and aid in association analysis. Results: We surveyed the 3′ end of 94 genes in 20 rhesus macaque animals. The study included 10 animals each of Indian and Chinese ancestry. We identified a total of 661 SNPs, 457 of which appeared exclusively in one or the other population. Seventy-nine additional animals were genotyped at 44 of the population-exclusive SNPs. Of those, 38 SNPs were confirmed as being population-specific. Conclusion: This study demonstrates that the 3′ end of genes is rich in sequence polymorphisms and is suitable for the efficient discovery of gene-linked SNPs. In addition, the results show that the genomic sequences of Indian and Chinese rhesus macaque are remarkably divergent, and include numerous population-specific SNPs. These ancestral SNPs could be used for the rapid scanning of rhesus macaques, both to establish animal ancestry and to identify gene alleles that may contribute to the phenotypic differences observed in these populations.

Original languageEnglish (US)
Article number43
JournalBMC genomics
Volume8
DOIs
StatePublished - Mar 9 2007

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Macaca mulatta
Single Nucleotide Polymorphism
Genes
Population
Simian Immunodeficiency Virus
Genetic Association Studies
Virus Diseases
Biomedical Research
Alleles

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Single nucleotide polymorphisms (SNPs) distinguish Indian-origin and Chinese-origin rhesus macaques (Macaca mulatta). / Ferguson, Betsy; Street, Summer L.; Wright, Hollis; Pearson, Carlo; Jia, Yibing; Thompson, Shaun L.; Allibone, Patrick; Dubay, Christopher J.; Spindel, Eliot; Norgren, Robert B.

In: BMC genomics, Vol. 8, 43, 09.03.2007.

Research output: Contribution to journalArticle

Ferguson, B, Street, SL, Wright, H, Pearson, C, Jia, Y, Thompson, SL, Allibone, P, Dubay, CJ, Spindel, E & Norgren, RB 2007, 'Single nucleotide polymorphisms (SNPs) distinguish Indian-origin and Chinese-origin rhesus macaques (Macaca mulatta)', BMC genomics, vol. 8, 43. https://doi.org/10.1186/1471-2164-8-43
Ferguson, Betsy ; Street, Summer L. ; Wright, Hollis ; Pearson, Carlo ; Jia, Yibing ; Thompson, Shaun L. ; Allibone, Patrick ; Dubay, Christopher J. ; Spindel, Eliot ; Norgren, Robert B. / Single nucleotide polymorphisms (SNPs) distinguish Indian-origin and Chinese-origin rhesus macaques (Macaca mulatta). In: BMC genomics. 2007 ; Vol. 8.
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abstract = "Background: Rhesus macaques serve a critical role in the study of human biomedical research. While both Indian and Chinese rhesus macaques are commonly used, genetic differences between these two subspecies affect aspects of their behavior and physiology, including response to simian immunodeficiency virus (SIV) infection. Single nucleotide polymorphisms (SNPs) can play an important role in both establishing ancestry and in identifying genes involved in complex diseases. We sequenced the 3′ end of rhesus macaque genes in an effort to identify gene-based SNPs that could distinguish between Indian and Chinese rhesus macaques and aid in association analysis. Results: We surveyed the 3′ end of 94 genes in 20 rhesus macaque animals. The study included 10 animals each of Indian and Chinese ancestry. We identified a total of 661 SNPs, 457 of which appeared exclusively in one or the other population. Seventy-nine additional animals were genotyped at 44 of the population-exclusive SNPs. Of those, 38 SNPs were confirmed as being population-specific. Conclusion: This study demonstrates that the 3′ end of genes is rich in sequence polymorphisms and is suitable for the efficient discovery of gene-linked SNPs. In addition, the results show that the genomic sequences of Indian and Chinese rhesus macaque are remarkably divergent, and include numerous population-specific SNPs. These ancestral SNPs could be used for the rapid scanning of rhesus macaques, both to establish animal ancestry and to identify gene alleles that may contribute to the phenotypic differences observed in these populations.",
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