Pyrosequencing as a method for SNP identification in the rhesus macaque (Macaca mulatta)

Abstract

Background: Rhesus macaques (Macaca mulatta) are the primate most used for biomedical research, but phenotypic differences between Indian-origin and Chinese rhesus macaques have encouraged genetic methods for identifying genetic differences between these two populations. The completion of the rhesus genome has led to the identification of many single nucleotide polymorphisms (SNPs) in this species. These single nucleotide polymorphisms have many advantages over the short tandem repeat (STR) loci currently used to assay genetic variation. However, the number of currently identified polymorphisms is too small for whole genome analysis or studies of quantitative trait loci. To that end, we tested a combination of methods to identify large numbers of high-confidence SNPs, and screen those with high minor allele frequencies (MAF).

Results: By testing our previously reported single nucleotide polymorphisms, we identified a subset of high-confidence, high-MAF polymorphisms. Resequencing revealed a large number of regionally specific SNPs not identified through a single pyrosequencing run. By resequencing a pooled sample of four individuals, we reliably identified loci with a MAF of at least 12.5%. Finally, we found that when applied to a larger, geographically variable sample of rhesus, a large proportion of our loci were variable in both populations, and very few loci were ancestry informative. Despite this fact, the SNP loci were more effective at discriminating Indian and Chinese rhesus than STR loci.

Conclusion: Pyrosequencing and pooled resequencing are viable methods for the identification of high-MAF SNP loci in rhesus macaques. These SNP loci are appropriate for screening both the inter- and intra-population genetic variation.

Figure 1

Sanger re-sequencing of the 454 pyrosequenced DNA fragments. Although few of the identified SNPs are geographically informative, many of the resequenced individuals contain unique SNPs (marked in dark grey).

Figure 2

Number of SNPs in each MAF class. Expressed as a percent of the total for that sample, to account for differing numbers of variable SNPs in each population.

Figure 3

Principle Component Analysis. A comparison of principle components 1 and 2 for 80 individuals assayed at 23 STR loci (left) and 92 SNP loci (right).