Open Access Open Badges Research article

Characterization of single-nucleotide variation in Indian-origin rhesus macaques (Macaca mulatta)

Gloria L Fawcett12, Muthuswamy Raveendran1, David Rio Deiros1, David Chen1, Fuli Yu12, Ronald Alan Harris2, Yanru Ren1, Donna M Muzny12, Jeffrey G Reid12, David A Wheeler12, Kimberly C Worley12, Steven E Shelton4, Ned H Kalin45, Aleksandar Milosavljevic2, Richard Gibbs12 and Jeffrey Rogers123*

Author Affiliations

1 Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA

2 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA

3 Southwest National Primate Research Center, San Antonio, Texas 78245, USA

4 Department of Psychiatry, the HealthEmotions Research Institution, University of Wisconsin-Madison, Madison, Wisconsin, 53719, USA

5 Department of Psychology, Waisman Laboratory for Brain Imaging and Behavior, University of Wisconsin-Madison, Madison, Wisconsin, 53719, USA

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BMC Genomics 2011, 12:311  doi:10.1186/1471-2164-12-311

Published: 13 June 2011



Rhesus macaques are the most widely utilized nonhuman primate model in biomedical research. Previous efforts have validated fewer than 900 single nucleotide polymorphisms (SNPs) in this species, which limits opportunities for genetic studies related to health and disease. Extensive information about SNPs and other genetic variation in rhesus macaques would facilitate valuable genetic analyses, as well as provide markers for genome-wide linkage analysis and the genetic management of captive breeding colonies.


We used the available rhesus macaque draft genome sequence, new sequence data from unrelated individuals and existing published sequence data to create a genome-wide SNP resource for Indian-origin rhesus monkeys. The original reference animal and two additional Indian-origin individuals were resequenced to low coverage using SOLiDâ„¢ sequencing. We then used three strategies to validate SNPs: comparison of potential SNPs found in the same individual using two different sequencing chemistries, and comparison of potential SNPs in different individuals identified with either the same or different sequencing chemistries. Our approach validated approximately 3 million SNPs distributed across the genome. Preliminary analysis of SNP annotations suggests that a substantial number of these macaque SNPs may have functional effects. More than 700 non-synonymous SNPs were scored by Polyphen-2 as either possibly or probably damaging to protein function and these variants now constitute potential models for studying functional genetic variation relevant to human physiology and disease.


Resequencing of a small number of animals identified greater than 3 million SNPs. This provides a significant new information resource for rhesus macaques, an important research animal. The data also suggests that overall genetic variation is high in this species. We identified many potentially damaging non-synonymous coding SNPs, providing new opportunities to identify rhesus models for human disease.

single nucleotide polymorphism; common variants; SOLiDâ„¢; genetic variation; rhesus macaque