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Open Access Highly Accessed Open Badges Research article

Insertion-deletion polymorphisms (indels) as genetic markers in natural populations

Ülo Väli12, Mikael Brandström1, Malin Johansson1 and Hans Ellegren1*

Author Affiliations

1 Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden

2 Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia

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BMC Genetics 2008, 9:8  doi:10.1186/1471-2156-9-8

Published: 22 January 2008



We introduce the use of short insertion-deletion polymorphisms (indels) for genetic analysis of natural populations.


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 were highly correlated.


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.