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Genotyping single nucleotide polymorphisms (SNPs) across species in Old World Monkeys
Author(s) -
Malhi Ripan S.,
Trask Jessica Satkoski,
Shattuck Milena,
Johnson Jesse,
Chakraborty Debrapriyo,
Kanthaswamy Sree,
Ramakrishnan Uma,
Smith David Glenn
Publication year - 2011
Publication title -
american journal of primatology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.988
H-Index - 81
eISSN - 1098-2345
pISSN - 0275-2565
DOI - 10.1002/ajp.20969
Subject(s) - single nucleotide polymorphism , genotyping , biology , genetics , snp genotyping , locus (genetics) , population , phylogenetic tree , genotype , evolutionary biology , gene , medicine , environmental health
Abstract The development of DNA markers is becoming increasingly useful in the field of primatology for studies on paternity, population history, and biomedical research. In this study, we determine the efficacy of using cross‐species amplification to identify single nucleotide polymorphisms (SNPs) in closely related species. The DNA of 93 individuals representing seven Old World Monkey species was analyzed to identify SNPs using cross‐species amplification and genotyping. The loci genotyped were 653 SNPs identified and validated in rhesus macaques. Of the 653 loci analyzed, 27% were estimated to be polymorphic in the samples studied. SNPs identified at the same locus among different species (coincident SNPs) were found in six of the seven species studied with longtail macaques exhibiting the highest number of coincident SNPs (84). The distribution of coincident SNPs among species is not biased based on proximity to genes in the samples studied. In addition, the frequency of coincident SNPs is not consistent with expectations based on their phylogenetic relationships. This study demonstrates that cross‐species amplification and genotyping using the Illumina Golden Gate Array is a useful method to identify a large number of SNPs in closely related species, although issues with ascertainment bias may limit the type of studies where this method can be applied. Am. J. Primatol. 73:1031–1040, 2011. © 2011 Wiley‐Liss, Inc.