Pyrosequencing as a method for SNP identification in the rhesus macaque (Macaca mulatta)
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 SNPs have many advantages over the simple tandem repeat (STR) loci currently used to assay genetic variation. However, the number of currently identified polymorphism is too small, for whole genome QTLstudies.
To that end, we tested a combination of methods to identify large numbers of high-confidence SNPs, and screen those with high MAFs.
Results: By testing our previously reported SNP loci, 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.
Conclusions: 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.
Author: Jessica A Satkoski, R S Malhi, S Kanthaswamy, R Y Tito, V S Malladi and D G Smith
Credits/Source: BMC Genomics 2008, 9:256
Published on: 2008-05-29
Copyright by the authors listed above - made available via BioMedCentral (Open Access). Please
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