4040 SNPs for genomic analysis in the rhesus macaque (Macaca mulatta)

Abstract

Although the rhesus macaque (Macaca mulatta) is commonly used for biomedical research and becoming a preferred model for translational medicine, quantification of genome-wide variation has been slow to follow the publication of the genome in 2007. Here we report the properties of 4040 single nucleotide polymorphisms discovered and validated in Chinese and Indian rhesus macaques from captive breeding colonies in the United States. Frequency-matched measures of linkage disequilibrium were much greater in the Indian sample. Although the majority of polymorphisms were shared between the two populations, rare alleles were over twice as common in the Chinese sample. Indian rhesus had higher rates of heterozygosity, as well as previously undetected substructure, potentially due to admixture from Burma in wild populations and demographic events post-captivity.

Figure 1

Distribution of minor allele frequencies in the Chinese and Indian samples. Mean minor allele frequency is significantly different (p<0.01).

Figure 2

Histograms of observed heterozygosity in the Chinese and Indian samples. The mean heterozygosities for the two samples are statistically significantly different (p<0.01).

Figure 3

The decay of linkage disequalibrium in the Indian and Chinese samples. R² values are calculated for frequency-matched markers located on the same chromosome. The x intercept of each line marks the complete disintegration of linkage disequilibrium.

Figure 4

Principal component analysis of Indian and Chinese rhesus macaques. Principal component (PC) 1 separates Indian from Chinese individuals with the exception of sample Orhs22375.

Figure 5

Differentiation within the Indian samples shown by PC2 and PC3 in the principal component analysis.