MamuSNP: A Resource for Rhesus Macaque (Macaca mulatta) Genomics

Ripan S Malhi,Raul Y Tito,Dawei Lin,Brad Sickler,Sreetharan Kanthaswamy,Jessica Satkoski,Debbie George,David Glenn Smith,Jean-Nicolas Volff

doi:10.1371/journal.pone.0000438

Ripan S Malhi, Raul Y Tito + Show 7 more

Open Access

https://doi.org/10.1371/journal.pone.0000438

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Abstract

We developed a novel method for identifying SNPs widely distributed throughout the coding and non-coding regions of a genome. The method uses large-scale parallel pyrosequencing technology in combination with bioinformatics tools. We used this method to generate approximately 23,000 candidate SNPs throughout the Macaca mulatta genome. We estimate that over 60% of the SNPs will be of high frequency and useful for mapping QTLs, genetic management, and studies of individual relatedness, whereas other less frequent SNPs may be useful as population specific markers for ancestry identification. We have created a web resource called MamuSNP to view the SNPs and associated information online. This resource will also be useful for researchers using a wide variety of Macaca species in their research.

Highlights

Rhesus macaques (Macaca mulatta) are a widely used and valuable model for biomedical research and understanding the etiology of human diseases
With the completion of a draft sequence of the rhesus macaque genome [1], the ability to identify genetic polymorphisms throughout the entire genome will vastly improve the utility of rhesus macaques for investigating the heritable components of complex diseases
The average read length received from 454 Life ScienceTM was 103.92 bases

Summary

INTRODUCTION

Rhesus macaques (Macaca mulatta) are a widely used and valuable model for biomedical research and understanding the etiology of human diseases. Due to the nature of the sequencing method, these sequences are distributed randomly across the entire genome This wide range of coverage makes it advantageous to discover unlinked common SNPs in coding and non-coding regions by screening one or only a few animals. This method of SNP identification is unique because it can be used to identify SNPs distant from any genes. Many of the SNPs identified in rhesus macaques and reported on the MamuSNP website may be polymorphic in cynomolgus macaques and other closely related primates These SNPs would exhibit a significant ascertainment bias in cynomolgus macaques, they may still be useful as markers for QTL analyses

RESULTS

DISCUSSION

MATERIALS AND METHODS