Abstract
BackgroundRhesus macaques (Macaca mulatta) are the primate most used for biomedical research, but phenotypic differences between Indian-origin and Chinese rhesus macaques have encouraged genetic methods for identifying genetic differences between these two populations. The completion of the rhesus genome has led to the identification of many single nucleotide polymorphisms (SNPs) in this species. These single nucleotide polymorphisms have many advantages over the short tandem repeat (STR) loci currently used to assay genetic variation. However, the number of currently identified polymorphisms is too small for whole genome analysis or studies of quantitative trait loci. To that end, we tested a combination of methods to identify large numbers of high-confidence SNPs, and screen those with high minor allele frequencies (MAF).ResultsBy testing our previously reported single nucleotide polymorphisms, we identified a subset of high-confidence, high-MAF polymorphisms. Resequencing revealed a large number of regionally specific SNPs not identified through a single pyrosequencing run. By resequencing a pooled sample of four individuals, we reliably identified loci with a MAF of at least 12.5%. Finally, we found that when applied to a larger, geographically variable sample of rhesus, a large proportion of our loci were variable in both populations, and very few loci were ancestry informative. Despite this fact, the SNP loci were more effective at discriminating Indian and Chinese rhesus than STR loci.ConclusionPyrosequencing and pooled resequencing are viable methods for the identification of high-MAF SNP loci in rhesus macaques. These SNP loci are appropriate for screening both the inter- and intra-population genetic variation.
Highlights
Rhesus macaques (Macaca mulatta) are the primate most used for biomedical research, but phenotypic differences between Indian-origin and Chinese rhesus macaques have encouraged genetic methods for identifying genetic differences between these two populations
While the single nucleotide polymorphism (SNPs) identified by Ferguson et al [36] and Hernandez et al [35] will be extremely useful as AIMs for differentiating between rhesus macaques originating in India and China and for estimating the level of admixture in hybrid rhesus macaques with ancestry from both regions, they might be unsuitable for studies of the structure of the rhesus macaque genome if they prove to be unrepresentative of this structure
We replicated several of the pyrosequenced fragments with varying Phred scores, to both check for sequencing error and to screen for additional, regionally specific polymorphisms
Summary
Rhesus macaques (Macaca mulatta) are the primate most used for biomedical research, but phenotypic differences between Indian-origin and Chinese rhesus macaques have encouraged genetic methods for identifying genetic differences between these two populations. Rhesus macaques (Macaca mulatta) are used more extensively as animal models for the study of human disease than any other primate species They provide the primary model for research in infectious diseases, reproductive biology, behavior, neuroscience and immunology. The severe shortage of rhesus macaques as subjects for biomedical research prompted the establishment of national centers for breeding them in the US [46]. The particular shortage of Indianderived rhesus macaques available for use as subjects in biomedical research and their desirability over Chinese rhesus macaques have led to efforts to acquire Indian-like rhesus macaques from sources outside India, such as Nepal and Bangladesh [7], and to establish close relationships with the National Center for Primate Breeding and Research currently under construction in Bombay, India
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