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

Ferguson B, Street SL, Wright H, Pearson C, Jia Y, Thompson SL, Allibone P, Dubay CJ, Spindel E, Norgren RB - BMC Genomics (2007)

Bottom Line: Of those, 38 SNPs were confirmed as being population-specific.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Genetics Research and Informatics Program, Oregon National Primate Research Center, Oregon Health and Sciences University, Beaverton, OR 97006, USA. fergusob@ohsu.edu

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.

Show MeSH

Related in: MedlinePlus

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC1803782&req=5

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.

Mentions: We analyzed the SNPs discovered within each rhesus macaque population. We identified 555 SNPs in the Chinese group, while the Indian animals had a total of 312 SNPs (Table 2; see Additional file 1 – Gene summary). The distribution of the minor allele frequencies of the SNPs within each population ranged from 0.04 to 0.5 (Figure 2). There were a higher percentage of rare alleles (MAF < 0.1) and a lower average minor allele frequency (0.15) in the Chinese animals than in the Indian rhesus (average MAF = 0.20), which is consistent with the Chinese population being more diverse.


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

Ferguson B, Street SL, Wright H, Pearson C, Jia Y, Thompson SL, Allibone P, Dubay CJ, Spindel E, Norgren RB - BMC Genomics (2007)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1803782&req=5

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.
Mentions: We analyzed the SNPs discovered within each rhesus macaque population. We identified 555 SNPs in the Chinese group, while the Indian animals had a total of 312 SNPs (Table 2; see Additional file 1 – Gene summary). The distribution of the minor allele frequencies of the SNPs within each population ranged from 0.04 to 0.5 (Figure 2). There were a higher percentage of rare alleles (MAF < 0.1) and a lower average minor allele frequency (0.15) in the Chinese animals than in the Indian rhesus (average MAF = 0.20), which is consistent with the Chinese population being more diverse.

Bottom Line: Of those, 38 SNPs were confirmed as being population-specific.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Genetics Research and Informatics Program, Oregon National Primate Research Center, Oregon Health and Sciences University, Beaverton, OR 97006, USA. fergusob@ohsu.edu

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.

Show MeSH
Related in: MedlinePlus