We scanned the rhesus macaque genome, using the recently completed rhesus macaque genome map, and identified 23,000 single nucleotide polymorphisms (SNPs) randomly distributed throughout the rhesus macaque genome. The locations of these SNPs in the rhesus macaque genome are identified on our web-site. To identify these SNPs DNA from a rhesus macaque from Sichuan Province, China, was pyrosequenced and the resulting fragments were compared with the rhesus genome map (based on a rhesus macaque from India) using bioinformatics tools we developed in collaboration with the UC Davis Genome Center. We propose to verify approximately 5,000 of these SNPs by high through-put genotyping in a sample of geographically heterogeneous Indian and Chinese rhesus macaques and in a sample of longtail macaques representing five different geographic regions. These SNPs will be evaluated for their usefulness for genetic management in each of these regional populations and are also likely to contain vital information on immune competence to pathogens that will have major impacts on the results of laboratory research with rhesus macaques. The 100 most informative of these SNPs for genetic management (GM) will be selected as a GM panel and adapted to a suitable platform for rapid genotyping, such as those of Illumina or Sequenom, at a cost not to exceed $25 per sample. By the end of this grant period, genotyping using this panel will be provided as a service to NlH investigators at a laboratory to be established at the California National Primate Research Center. In the interim, genetic management services based on microsatellite (STR) loci will continue to be provided to NIH investigators on a cost-recovery basis. Rhesus macaques will also be trapped in their wild habitat in seven different provinces of China and near Bombay, India and genotyped for 21 STR loci and the panel of 100 SNPs. These genotypes will be compared with those of captive-bred Chinese origin rhesus macaques imported from breeding centers in the same provinces as the wild caught rhesus were sampled and Indian rhesus macaques originating in their northern range that comprise the existing domestic supply of rhesus macaque breeding stock to determine whether or not Chinese and Indian rhesus macaques are genetically subdivided. Longtail macaques from five different geographic regions will also be genetically characterized using these markers and evaluated for their potential genetic subdivision.
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