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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.

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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.
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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.

Mentions: The 3' ends of 94 different genes were amplified and sequenced in this study, with the average amplicon length being 712 bp/gene (range: 334–905 bp). The 94 genes included at least one from every chromosome with the exceptions of 17 and Y (see Additional file 1 – Gene summary). In total we identified 661 SNPs in the rhesus macaques (see Additional file 2 – SNP identity and NCBI accession numbers). All except for three of the genes (AR, CHRM4, IL7R) identified at least 1 SNP, with the overall average being 7.3 SNPs/gene (Figure 1). Some genes were very polymorphic: 20 genes contained between 10 and 17 SNPs (Figure 1; see Additional file 1 – Gene summary). The overall minor allele frequency (MAF) of the SNPs was 0.127, with 281 SNPs having a MAF ≥ 0.2 in the sample population.


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)

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

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

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.
Mentions: The 3' ends of 94 different genes were amplified and sequenced in this study, with the average amplicon length being 712 bp/gene (range: 334–905 bp). The 94 genes included at least one from every chromosome with the exceptions of 17 and Y (see Additional file 1 – Gene summary). In total we identified 661 SNPs in the rhesus macaques (see Additional file 2 – SNP identity and NCBI accession numbers). All except for three of the genes (AR, CHRM4, IL7R) identified at least 1 SNP, with the overall average being 7.3 SNPs/gene (Figure 1). Some genes were very polymorphic: 20 genes contained between 10 and 17 SNPs (Figure 1; see Additional file 1 – Gene summary). The overall minor allele frequency (MAF) of the SNPs was 0.127, with 281 SNPs having a MAF ≥ 0.2 in the sample population.

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