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; Allibone, Patrick; Dubay, Christopher; Spindel, Eliot R.; Norgren, Robert B.

doi:10.1186/1471-2164-8-43

Cited by 89 publications

(72 citation statements)

References 19 publications

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“…Only about one-third of SNPs were shared between the two geographic populations, which indicates that most variation is region-specific. Similar results were obtained in a survey of 3’ UTR sequences in a small number of macaques 37 . A study of whole genome sequences for three Indian-origin rhesus macaques found >3 million variants present in at least two of the datasets examined 33 .…”

Section: Genetic Variation Within Primate Speciessupporting

confidence: 87%

Comparative primate genomics: emerging patterns of genome content and dynamics

2014

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Preface Advances in genome sequencing technologies have created new opportunities for comparative primate genomics. Genome assemblies have been published for several primates, with analyses of several others underway. Whole genome assemblies for the great apes provide remarkable new information about the evolutionary origins of the human genome and the processes involved. Genomic data for macaques and other nonhuman primates provide valuable insight into genetic similarities and differences among species used as models for disease-related research. This review summarizes current knowledge regarding primate genome content and dynamics and offers a series of goals for the near future.

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Section: Genetic Variation Within Primate Speciessupporting

confidence: 87%

Comparative primate genomics: emerging patterns of genome content and dynamics

2014

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“…Another advantage of using these non-human primates is that rhesus monkeys of different geographical origin (Indian and Chinese) have been shown to be genetically different, with a number of SNPs distinguishing the two subspecies from one another [23]. Therefore, utilizing both subspecies of monkeys in carotenoid research provides a unique opportunity for studying the nutrigenomics of xanthophyll absorption, deposition, and storage/metabolism in neural tissue.…”

Section: Introductionmentioning

confidence: 99%

Brain xanthophyll content and exploratory gene expression analysis: subspecies differences in rhesus macaque

et al. 2017

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BackgroundThe dietary xanthophylls, lutein and zeaxanthin, accumulate in primate retina and brain, and emerging evidence indicates neural lutein content may be beneficial for cognition. Neural xanthophyll content in primates varies greatly among individuals, and genetic factors are likely to be significant contributors. Subspecies of rhesus macaques originating from different geographic locations are known to differ genetically, but the effect of origin on gene expression and carotenoid status has not been determined. The study objective was to determine whether xanthophyll status and expression of carotenoid-related genes, as well as genes with known variants between subspecies, differ between the brains of adult rhesus monkeys of Indian and Chinese origin.MethodsSamples of prefrontal cortex, cerebellum, and striatum were collected from adult monkeys (n = 9) fed a standard stock diet containing carotenoids. Serum and brain carotenoids were determined using reverse-phase high-performance liquid chromatography. For each brain region, RNA sequencing and real-time quantitative polymerase chain reaction were used to determine differentially expressed genes between the subspecies.ResultsIndian-origin monkeys had higher xanthophyll levels in brain tissue compared to Chinese-origin monkeys despite consuming similar amounts of dietary carotenoids. In a region-specific manner, four genes related to carotenoid and fatty acid metabolism (BCO2, RPE65, ELOVL4, FADS2) and four genes involved in the immune response (CD4, CD74, CXCL12 LTBR) were differentially expressed between Indian- and Chinese-origin monkeys. Expression of all four genes involved in carotenoid and fatty acid metabolism were correlated with brain xanthophyll concentration in a region-specific manner.ConclusionsThese results indicate that origin is related to differences in both gene expression and xanthophyll content in the brain. Findings from this study may have important implications regarding genetic diversity, lutein status, and cognition in primates.Electronic supplementary materialThe online version of this article (doi:10.1186/s12263-017-0557-3) contains supplementary material, which is available to authorized users.

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“…Previous studies of microsatellite (STR) markers [43], mtDNA sequence [22] and SNPs in the 3’ ends of rhesus macaque genes [3] and ENCODE regions [33] have reported higher levels of heterozygosity in Chinese than in Indian rhesus macaques. While the majority of the Indian-origin animals sampled by Hernandez et al [33] came from the Yerkes National Primate Research Center, most of the Indian-origin animals in the present study were selected from the Caribbean Primate Research Center (CPRC).…”

Section: Discussionmentioning

confidence: 99%

“…The National Center for Research Resources (NCRR) at the NIH currently sponsors six rhesus macaque Working Groups (WGs), one of which, the Genetics and Genomics WG, has assumed the stated goal of instituting uniform SNP-based genetic characterization protocols for parentage testing, ancestry determination and population genetic assessments [2]. In addition, several research groups are in the process of quantifying genomic variation in captive populations of rhesus macaques [3–5]. The data presented here were collected as part of a larger project to discover, quantify and validate single nucleotide polymorphisms (SNPs) in regional populations of rhesus macaques included in captive breeding populations in the US.…”

Section: Introductionmentioning

confidence: 99%

4040 SNPs for genomic analysis in the rhesus macaque (Macaca mulatta)

et al. 2011

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Although the rhesus macaque (Macaca mulatta) is commonly used for biomedical research and becoming a preferred model for translational medicine, quantification of genome-wide variation has been slow to follow the publication of the genome in 2007. Here we report the properties of 4040 single nucleotide polymorphisms discovered and validated in Chinese and Indian rhesus macaques from captive breeding colonies in the United States. Frequency-matched measures of linkage disequilibrium were much greater in the Indian sample. Although the majority of polymorphisms were shared between the two populations, rare alleles were over twice as common in the Chinese sample. Indian rhesus had higher rates of heterozygosity, as well as previously undetected substructure, potentially due to admixture from Burma in wild populations and demographic events post-captivity.

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

Cited by 89 publications

References 19 publications

Comparative primate genomics: emerging patterns of genome content and dynamics

Comparative primate genomics: emerging patterns of genome content and dynamics

Brain xanthophyll content and exploratory gene expression analysis: subspecies differences in rhesus macaque

4040 SNPs for genomic analysis in the rhesus macaque (Macaca mulatta)

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