title: Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome.
abstract: BACKGROUND
  There is growing evidence for the prevalence of copy number variation (CNV) and its role in phenotypic variation in many eukaryotic species. Here we use array comparative genomic hybridization to explore the extent of this type of structural variation in domesticated barley cultivars and wild barleys.
  
  
  RESULTS
  A collection of 14 barley genotypes including eight cultivars and six wild barleys were used for comparative genomic hybridization. CNV affects 14.9% of all the sequences that were assessed. Higher levels of CNV diversity are present in the wild accessions relative to cultivated barley. CNVs are enriched near the ends of all chromosomes except 4H, which exhibits the lowest frequency of CNVs. CNV affects 9.5% of the coding sequences represented on the array and the genes affected by CNV are enriched for sequences annotated as disease-resistance proteins and protein kinases. Sequence-based comparisons of CNV between cultivars Barke and Morex provided evidence that DNA repair mechanisms of double-strand breaks via single-stranded annealing and synthesis-dependent strand annealing play an important role in the origin of CNV in barley.
  
  
  CONCLUSIONS
  We present the first catalog of CNVs in a diploid Triticeae species, which opens the door for future genome diversity research in a tribe that comprises the economically important cereal species wheat, barley, and rye. Our findings constitute a valuable resource for the identification of CNV affecting genes of agronomic importance. We also identify potential mechanisms that can generate variation in copy number in plant genomes.
authors.forename: María
authors.initials: M
authors.lastname: Muñoz-Amatriaín
authors.forename: Steven R
authors.initials: SR
authors.lastname: Eichten
authors.forename: Thomas
authors.initials: T
authors.lastname: Wicker
authors.forename: Todd A
authors.initials: TA
authors.lastname: Richmond
authors.forename: Martin
authors.initials: M
authors.lastname: Mascher
authors.forename: Burkhard
authors.initials: B
authors.lastname: Steuernagel
authors.forename: Uwe
authors.initials: U
authors.lastname: Scholz
authors.forename: Ruvini
authors.initials: R
authors.lastname: Ariyadasa
authors.forename: Manuel
authors.initials: M
authors.lastname: Spannagl
authors.forename: Thomas
authors.initials: T
authors.lastname: Nussbaumer
authors.forename: Klaus F X
authors.initials: KF
authors.lastname: Mayer
authors.forename: Stefan
authors.initials: S
authors.lastname: Taudien
authors.forename: Matthias
authors.initials: M
authors.lastname: Platzer
authors.forename: Jeffrey A
authors.initials: JA
authors.lastname: Jeddeloh
authors.forename: Nathan M
authors.initials: NM
authors.lastname: Springer
authors.forename: Gary J
authors.initials: GJ
authors.lastname: Muehlbauer
authors.forename: Nils
authors.initials: N
authors.lastname: Stein
mesh_terms: D001483:Base Sequence; D001947:Breeding; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D055028:Comparative Genomic Hybridization; D056915:DNA Copy Number Variations; D018628:Gene Dosage; D018745:Genome, Plant; D005838:Genotype; D001467:Hordeum / Q000235:genetics*; D008969:Molecular Sequence Data; D016415:Sequence Alignment