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.
journal_name
BMC Genetjournal_title
BMC geneticsauthors
Väli U,Brandström M,Johansson M,Ellegren Hdoi
10.1186/1471-2156-9-8subject
Has Abstractpub_date
2008-01-22 00:00:00pages
8issn
1471-2156pii
1471-2156-9-8journal_volume
9pub_type
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