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

TitleCharacterization of single-nucleotide variation in Indian-origin rhesus macaques (Macaca mulatta).
Publication TypeJournal Article
Year of Publication2011
AuthorsFawcett, GL, Raveendran, M, Deiros, DRio, Chen, D, Yu, F, Harris, RA, Ren, Y, Muzny, DM, Reid, JG, Wheeler, DA, Worley, KC, Shelton, SE, Kalin, NH, Milosavljevic, A, Gibbs, RA, Rogers, J
JournalBMC Genomics
Date Published2011 Jun 13
KeywordsAnimals, Genetic Variation, India, Macaca mulatta, Polymorphism, Single Nucleotide, Sequence Analysis, DNA, Species Specificity

BACKGROUND: 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.RESULTS: 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 SOLiD™ 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.CONCLUSIONS: 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.

Alternate JournalBMC Genomics
PubMed ID21668978
PubMed Central IDPMC3141668
Grant ListP30 HD003352 / HD / NICHD NIH HHS / United States
R01 HG004009 / HG / NHGRI NIH HHS / United States
5P50-MH84051 / MH / NIMH NIH HHS / United States
U01 DA025956 / DA / NIDA NIH HHS / United States
5R01-MH081884 / MH / NIMH NIH HHS / United States
2 U54 HG003273 / HG / NHGRI NIH HHS / United States
NIH-R24-RR15383 / RR / NCRR NIH HHS / United States
R01 MH046729 / MH / NIMH NIH HHS / United States
5R01-MH046729 / MH / NIMH NIH HHS / United States
U54 HG003273 / HG / NHGRI NIH HHS / United States

Similar Publications

Wojcik MH, Reuter CM, Marwaha S, Mahmoud M, Duyzend MH, Barseghyan H, et al.. Beyond the exome: What's next in diagnostic testing for Mendelian conditions. Am J Hum Genet. 2023;110(8):1229-1248.
Schlosser P, Zhang J, Liu H, Surapaneni AL, Rhee EP, Arking DE, et al.. Transcriptome- and proteome-wide association studies nominate determinants of kidney function and damage. Genome Biol. 2023;24(1):150.
Lu J, Zheng KQ, Bertrand RElaine, Quinlan J, Ferdous S, Srinivasan T, et al.. Gene augmentation therapy to rescue degenerative photoreceptors in a Cwc27 mutant mouse model. Exp Eye Res. 2023;234:109596.
Calame DG, Guo T, Wang C, Garrett L, Jolly A, Dawood M, et al.. Monoallelic variation in DHX9, the gene encoding the DExH-box helicase DHX9, underlies neurodevelopment disorders and Charcot-Marie-Tooth disease. Am J Hum Genet. 2023;110(8):1394-1413.
Qian X, Srinivasan T, He J, Lu J, Jin Y, Gu H, et al.. Ceramide compensation by ceramide synthases preserves retinal function and structure in a retinal dystrophy mouse model. Dis Model Mech. 2023;16(7).
Yang L, Chen X, Lee C, Shi J, Lawrence EB, Zhang L, et al.. Functional characterization of age-dependent p16 epimutation reveals biological drivers and therapeutic targets for colorectal cancer. J Exp Clin Cancer Res. 2023;42(1):113.
Shao Y, Zhou L, Li F, Zhao L, Zhang B-L, Shao F, et al.. Phylogenomic analyses provide insights into primate evolution. Science. 2023;380(6648):913-924.
Kuderna LFK, Gao H, Janiak MC, Kuhlwilm M, Orkin JD, Bataillon T, et al.. A global catalog of whole-genome diversity from 233 primate species. Science. 2023;380(6648):906-913.
Gao H, Hamp T, Ede J, Schraiber JG, McRae J, Singer-Berk M, et al.. The landscape of tolerated genetic variation in humans and primates. Science. 2023;380(6648):eabn8153.
Sørensen EF, Harris RA, Zhang L, Raveendran M, Kuderna LFK, Walker JA, et al.. Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons. Science. 2023;380(6648):eabn8153.