High-Throughput SNP Discovery and the Search for Candidate Genes for Long-Term SIVmac Nonprogression in Chinese Rhesus Macaques (Macaca mulatta)

Genetic differences between Indian and Chinese rhesus macaques contribute to the phenotypic variance of clinical trials, including experimental infection with SIVmac. The completion of the rhesus genome has facilitated the discovery of several thousand markers. Although the marker density necessary for whole genome association mapping of phenotypes has not yet been achieved, a SNP map will help researchers investigate variation in candidate genes. We developed a genome-wide SNP map for rhesus macaques containing 3,869 validated markers with an average distance of 0.88 megabases. We used the program VarLD to identify genomic areas with significant differences in linkage disequilibrium (LD) between Indian-derived and Chinese rhesus macaques, assuming that these areas provide the greatest potential for differential selection in these regional populations. These genomic areas provide entry to more detailed study of gene function. This method is also applicable to the study of differences in biomarkers between regional populations of other species.