Single nucleotide polymorphisms (SNPs) distinguish Indian-origin and Chinese-origin rhesus macaques (Macaca mulatta)

Abstract

Background: Rhesus macaques serve a critical role in the study of human biomedical research. While both Indian and Chinese rhesus macaques are commonly used, genetic differences between these two subspecies affect aspects of their behavior and physiology, including response to simian immunodeficiency virus (SIV) infection. Single nucleotide polymorphisms (SNPs) can play an important role in both establishing ancestry and in identifying genes involved in complex diseases. We sequenced the 3' end of rhesus macaque genes in an effort to identify gene-based SNPs that could distinguish between Indian and Chinese rhesus macaques and aid in association analysis.

Results: We surveyed the 3' end of 94 genes in 20 rhesus macaque animals. The study included 10 animals each of Indian and Chinese ancestry. We identified a total of 661 SNPs, 457 of which appeared exclusively in one or the other population. Seventy-nine additional animals were genotyped at 44 of the population-exclusive SNPs. Of those, 38 SNPs were confirmed as being population-specific.

Conclusion: This study demonstrates that the 3' end of genes is rich in sequence polymorphisms and is suitable for the efficient discovery of gene-linked SNPs. In addition, the results show that the genomic sequences of Indian and Chinese rhesus macaque are remarkably divergent, and include numerous population-specific SNPs. These ancestral SNPs could be used for the rapid scanning of rhesus macaques, both to establish animal ancestry and to identify gene alleles that may contribute to the phenotypic differences observed in these populations.

Figure 1

Number of SNPs identified in the 3' end of 91 rhesus macaque genes. SNPs were identified in 20 Chinese and Indian rhesus macaques. There were no SNPs identified in 3 genes; between one and 18 polymorphisms were found in the other 91 genes.

Figure 2

Minor allele frequencies of SNPs in Chinese and Indian rhesus macaque populations. The number of SNPs found in Chinese (gray) and Indian (black) rhesus macaque populations, at differing minor allele frequencies (MAF), are shown.

Figure 3

Results of population-specific SNP Assay. The animal identification numbers are shown on the left: Chinese rhesus are highlighted in purple, Indian rhesus in blue and documented hybrid animals are in gray. The SNP loci included are listed across the top. Genotype results are shaded as follows (based upon all animals in both populations): homozygous major alleles are in green, homozygous minor alleles are in red, heterozygous alleles are shown in yellow, and no information is indicated by white.

Figure 4

SNP analysis workflow. The DNA sequence output was analyzed using PolyPhred software to identify SNPs and to report the relative quality score of the SNP calls. SNPs with low quality scores or with inconsistent reports were reviewed manually. The approved SNP data was deposited into a local database for population, frequency and genotype analysis. Based upon the statistical results, some SNPs were selected for inclusion in Sequenom iPlex SNP panel.