Abstract
BackgroundWe introduce the use of short insertion-deletion polymorphisms (indels) for genetic analysis of natural populations.ResultsSequence 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.ConclusionWith 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.
Highlights
We introduce the use of short insertion-deletion polymorphisms for genetic analysis of natural populations
Preceding and subsequently in parallel to this, non-repetitive DNA sequence variation has been assessed through various approaches, including DNA sequencing, restriction fragment length polymorphism (RFLP) analysis, single strand conformation polymorphism (SSCP) analysis, random amplified polymorphism detection (RAPD) and amplified fragment length polymorphism (AFLP) analysis [4]
We surveyed 200,000 of these trace reads for the occurrence of short insertion and deletion polymorphisms, as detected by alignment against the reference sequence of one female boxer [18]
Summary
We introduce the use of short insertion-deletion polymorphisms (indels) for genetic analysis of natural populations. Seen in long time perspective, genetic marker methodology has evolved from focusing on phenotypes, via immunological parameters and proteins, to genotypes. Following their introduction to the study of natural populations about 15 years ago [1,2,3], microsatellites or short simple tandem repeats have been the genotype-based marker approach of choice for many applications where the relatedness between individuals, populations or species is sought. Single nucleotide polymorphisms (SNPs) are increasingly (page number not for citation purposes) finding their application in studies of natural populations [5,6].
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