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

BMC Genetics
Ulo VäliHans Ellegren

Abstract

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.

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Citations

Sep 14, 2012·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Bo LiuJian Wu
Jun 21, 2012·International Journal of Legal Medicine·M FondevilaP M Vallone
Jul 25, 2008·Genetica·Patrícia H Brito, Scott V Edwards
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Sep 3, 2016·BMC Genomics·Mohammad Shabbir Hasan, Liqing Zhang

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Methods Mentioned

BETA
genotyping
PCR
light shot-gun
Profiler

Software Mentioned

Genetic Profiler
Microsatellite Toolkit for MS Excel
BLAST
Primer3

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