title: Structural variation in the chicken genome identified by paired-end next-generation DNA sequencing of reduced representation libraries.
abstract: BACKGROUND
  Variation within individual genomes ranges from single nucleotide polymorphisms (SNPs) to kilobase, and even megabase, sized structural variants (SVs), such as deletions, insertions, inversions, and more complex rearrangements. Although much is known about the extent of SVs in humans and mice, species in which they exert significant effects on phenotypes, very little is known about the extent of SVs in the 2.5-times smaller and less repetitive genome of the chicken.
  
  
  RESULTS
  We identified hundreds of shared and divergent SVs in four commercial chicken lines relative to the reference chicken genome. The majority of SVs were found in intronic and intergenic regions, and we also found SVs in the coding regions. To identify the SVs, we combined high-throughput short read paired-end sequencing of genomic reduced representation libraries (RRLs) of pooled samples from 25 individuals and computational mapping of DNA sequences from a reference genome.
  
  
  CONCLUSIONS
  We provide a first glimpse of the high abundance of small structural genomic variations in the chicken. Extrapolating our results, we estimate that there are thousands of rearrangements in the chicken genome, the majority of which are located in non-coding regions. We observed that structural variation contributes to genetic differentiation among current domesticated chicken breeds and the Red Jungle Fowl. We expect that, because of their high abundance, SVs might explain phenotypic differences and play a role in the evolution of the chicken genome. Finally, our study exemplifies an efficient and cost-effective approach for identifying structural variation in sequenced genomes.
authors.affiliation: Animal Breeding and Genomics Center, Wageningen University, Marijkeweg 40, 6709 PG, Wageningen, the Netherlands.
authors.forename: Hindrik Hd
authors.initials: HH
authors.lastname: Kerstens
authors.forename: Richard Pma
authors.initials: RP
authors.lastname: Crooijmans
authors.forename: Bert W
authors.initials: BW
authors.lastname: Dibbits
authors.forename: Addie
authors.initials: A
authors.lastname: Vereijken
authors.forename: Ron
authors.initials: R
authors.lastname: Okimoto
authors.forename: Martien Am
authors.initials: MA
authors.lastname: Groenen
mesh_terms: D000818:Animals; D002645:Chickens; D016678:Genome / Q000235:genetics*; D056914:Genomic Structural Variation / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*