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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2008-12

AUTHORS

Ülo Väli, Mikael Brandström, Malin Johansson, Hans Ellegren

ABSTRACT

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 were highly correlated. CONCLUSION: 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. More... »

PAGES

8

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2156-9-8

DOI

http://dx.doi.org/10.1186/1471-2156-9-8

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1051357965

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/18211670


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49 schema:description 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 were highly correlated. CONCLUSION: 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.
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