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Insertion-deletion polymorphisms (indels) as genetic markers in natural populations
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. (Conservation genetics)
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. (Molecular evolution)
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. (Conservation Genetics)
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
2008 (English)In: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156, Vol. 9, 8- p.Article in journal (Refereed) Published
Abstract [en]

BACKGROUND: We introduce the use of short insertion-deletion polymorphisms (indels) for genetic analysis of natural populations. RESULTS: Sequence reads from light shot-gun sequencing efforts of different dog breeds were aligned to the dog genome reference sequence and gaps corresponding to indels were identified. One hundred candidate markers (4-bp indels) were selected and genotyped in unrelated dogs (n=7) and wolves (n=18). Eighty-one and 76 out of 94 could be validated as polymorphic loci in the respective sample. Mean indel heterozygosity in a diverse set of wolves was 19%, and 74% of the loci had a minor allele frequency of >10%. Indels found to be polymorphic in wolves were subsequently genotyped in a highly bottlenecked Scandinavian wolf population. Fifty-one loci turned out to be polymorphic, showing their utility even in a population with low genetic diversity. In this population, individual heterozygosity measured at indel and microsatellite loci, respectively were highly correlated. CONCLUSIONS: With an increasing amount of sequence information gathered from non-model organisms, we suggest that indels will come to form an important source of genetic markers, easy and cheap to genotype, for studies of natural populations.

Place, publisher, year, edition, pages
2008. Vol. 9, 8- p.
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Biological Sciences
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URN: urn:nbn:se:uu:diva-15694DOI: 10.1186/1471-2156-9-8ISI: 000254049400001PubMedID: 18211670OAI: oai:DiVA.org:uu-15694DiVA: diva2:43465
Available from: 2008-03-03 Created: 2008-03-03 Last updated: 2017-12-08Bibliographically approved

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Johansson, MalinEllegren, Hans

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