title: Single nucleotide polymorphisms (SNPs) distinguish Indian-origin and Chinese-origin rhesus macaques (Macaca mulatta).
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Genetics Research and Informatics Program, Oregon National Primate Research Center, Oregon Health and Sciences University, Beaverton, OR 97006, USA. fergusob@ohsu.edu
authors.forename: Betsy
authors.initials: B
authors.lastname: Ferguson
authors.forename: Summer L
authors.initials: SL
authors.lastname: Street
authors.forename: Hollis
authors.initials: H
authors.lastname: Wright
authors.forename: Carlo
authors.initials: C
authors.lastname: Pearson
authors.forename: Yibing
authors.initials: Y
authors.lastname: Jia
authors.forename: Shaun L
authors.initials: SL
authors.lastname: Thompson
authors.forename: Patrick
authors.initials: P
authors.lastname: Allibone
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Dubay
authors.forename: Eliot
authors.initials: E
authors.lastname: Spindel
authors.forename: Robert B
authors.initials: RB
authors.lastname: Norgren
mesh_terms: D000818:Animals; D002681:China; D005828:Genetics, Population; D005838:Genotype; D007194:India; D008253:Macaca mulatta / Q000235:genetics*; D008954:Models, Biological; D020641:Polymorphism, Single Nucleotide; D013045:Species Specificity