Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome

María Muñoz-Amatriaín, Steven R. Eichten, Thomas Wicker, Todd A. Richmond, Martin Mascher, Burkhard Steuernagel, Uwe Scholz, Ruvini Ariyadasa, Manuel Spannagl, Thomas Nussbaumer, Klaus F.X. Mayer, Stefan Taudien, Matthias Platzer, Jeffrey A. Jeddeloh, Nathan M. Springer, Gary J. Muehlbauer, Nils Stein

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85 Scopus citations


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.

Original languageEnglish (US)
Article numberR58
JournalGenome biology
Issue number6
StatePublished - Jun 12 2013

Bibliographical note

Funding Information:
Authors kindly acknowledge Manuela Knauft and Peter Hermanson for their excellent technical help in array hybridization, Amy Landreman for her initial help in processing images, Jelena Perovic and Axel Himmelbach for semiquantitative PCR and qPCR, Benjamin Kilian for providing the H. vulgare ssp. spontaneum accessions, Doreen Stengel for the submission of the sequence to EMBL/ENA, and Robert M Stupar, Ron J. Okagaki and Peter L. Morrell for their helpful suggestions. The authors would also like to thank the anonymous reviewers for their valuable comments to improve the manuscript. This work was financially supported by the following grants: project GABI-BARLEX, German Federal Ministry of Education and Research (BMBF), #0314000 to MP, US, KFXM and NS; Triticeae Coordinated Agricultural Project, USDA-NIFA #2011-68002-30029 to GJM; and Agriculture and Food Research Initiative Plant Genome, Genetics and Breeding Program of USDA’s Cooperative State Research and Extension Service, #2009-65300-05645 to GJM.


  • Barley, Copy number variation
  • Comparative genomic hybridization
  • Disease-resistance genes
  • Double-strand break repair mechanisms


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