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A microarray system for Y chromosomal and mitochondrial single nucleotide polymorphism analysis in chimpanzee populations
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine.
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2008 (English)In: Molecular Ecology Notes, ISSN 1471-8278, E-ISSN 1471-8286, Vol. 8, no 3, 529-539 p.Article in journal (Refereed) Published
Abstract [en]

Chimpanzee populations are diminishing as a consequence of human activities, and as a result this species is now endangered. In the context of conservation programmes, genetic data can add vital information, for instance on the genetic diversity and structure of threatened populations. Single nucleotide polymorphisms (SNP) are biallelic markers that are widely used in human molecular studies and can be implemented in efficient microarray systems. This technology offers the potential of robust, multiplexed SNP genotyping at low reagent cost in other organisms than humans, but it is not commonly used yet in wild population studies. Here, we describe the characterization of new SNPs in Y-chromosomal intronic regions in chimpanzees and also identify SNPs from mitochondrial genes, with the aim of developing a microarray system that permits the simultaneous study of both paternal and maternal lineages. Our system consists of 42 SNPs for the Y chromosome and 45 SNPs for the mitochondrial genome. We demonstrate the applicability of this microarray in a captive population where genotypes accurately reflected its large pedigree. Two wild-living populations were also analysed and the results show that the microarray will be a useful tool alongside microsatellite markers, since it supplies complementary information about population structure and ecology. SNP genotyping using microarray technology, therefore, is a promising approach and may become an essential tool in conservation genetics to help in the management and study of captive and wild-living populations. Moreover, microarrays that combine SNPs from different genomic regions could replace microsatellite typing in the future.

Place, publisher, year, edition, pages
2008. Vol. 8, no 3, 529-539 p.
Keyword [en]
chimpanzee, conservation genetics, microarray, minisequencing, population genetics, sex-linked SNPs
National Category
Medical and Health Sciences
URN: urn:nbn:se:uu:diva-110437DOI: 10.1111/j.1471-8286.2007.02000.xISI: 000254810300007OAI: oai:DiVA.org:uu-110437DiVA: diva2:277096
Available from: 2009-11-16 Created: 2009-11-16 Last updated: 2013-09-25Bibliographically approved
In thesis
1. Analysis of Nucleotide Variations in Non-human Primates
Open this publication in new window or tab >>Analysis of Nucleotide Variations in Non-human Primates
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Many of our closest relatives, the primates, are endangered and could be extinct in a near future. To increase the knowledge of non-human primate genomes, and at the same time acquire information on our own genomic evolution, studies using high-throughput technologies are applied, which raises the demand for large amounts of high quality DNA.

In study I and II, we evaluated the multiple displacement amplification (MDA) technique, a whole genome amplification method, on a wide range of DNA sources, such as blood, hair and semen, by comparing MDA products to genomic DNA as templates for several commonly used genotyping methods. In general, the genotyping success rate from the MDA products was in concordance with the genomic DNA. The quality of sequences of the mitochondrial control region obtained from MDA products from blood and non-invasively collected semen samples was maintained. However, the readable sequence length was shorter for MDA products.

Few studies have focused on the genetic variation in the nuclear genes of non-human primates. In study III, we discovered 23 new single nucleotide polymorphisms (SNPs) in the Y-chromosome of the chimpanzee. We designed a tag-microarray minisequencing assay for genotyping the SNPs together with 19 SNPs from the literature and 45 SNPs in the mitochondrial DNA. Using the microarray, we were able to analyze the population structure of wild-living chimpanzees.

In study IV, we established 111 diagnostic nucleotide positions for primate genera determination. We used sequence alignments of the nuclear epsilon globin gene and apolipoprotein B gene to identify positions for determination on the infraorder and Catarrhini subfamily level, respectively, and sequence alignments of the mitochondrial 12S rRNA (MT-RNR1) to identify positions to distinguish between genera. We designed a microarray assay for immobilized minisequencing primers for genotyping these positions to aid in the forensic determination of an unknown sample.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2007. 41 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 263
Molecular genetics, SNP, genotyping, primate, chimpanzee, whole genome amplification, multiple displacement amplification, minisequencing, microarray, Y-chromosome, mitochondria, Genetik
urn:nbn:se:uu:diva-7904 (URN)978-91-554-6904-7 (ISBN)
Public defence
2007-06-01, Rudbecksalen, Rudbecklaboratoriet, Dag Hammarskjölds väg 20, Uppsala, 13:15
Available from: 2007-05-10 Created: 2007-05-10 Last updated: 2013-09-25Bibliographically approved

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Syvänen, Ann-Christine
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