title: Insertion-deletion polymorphisms (indels) as genetic markers in natural populations.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden. ulo.vali@ebc.uu.se
authors.forename: Ulo
authors.initials: U
authors.lastname: Väli
authors.forename: Mikael
authors.initials: M
authors.lastname: Brandström
authors.forename: Malin
authors.initials: M
authors.lastname: Johansson
authors.forename: Hans
authors.initials: H
authors.lastname: Ellegren
mesh_terms: D000483:Alleles; D000818:Animals; D002874:Chromosome Mapping; D004285:Dogs / Q000235:genetics*; D005819:Genetic Markers; D005838:Genotype; D054643:INDEL Mutation; D011110:Polymorphism, Genetic; D013045:Species Specificity; D019596:Wolves / Q000235:genetics*
chemical_list: D005819:Genetic Markers