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

María Muñoz-Amatriaín1, Steven R Eichten2, Thomas Wicker3, Todd A Richmond4, Martin Mascher5, Burkhard Steuernagel56, Uwe Scholz5, Ruvini Ariyadasa5, Manuel Spannagl7, Thomas Nussbaumer7, Klaus FX Mayer7, Stefan Taudien8, Matthias Platzer8, Jeffrey A Jeddeloh4, Nathan M Springer2, Gary J Muehlbauer12* and Nils Stein5*

Author Affiliations

1 Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA

2 Department of Plant Biology, University of Minnesota, St. Paul, MN 55108, USA

3 Institute of Plant Biology, University of Zurich, CH-8008 Zurich, Switzerland

4 Roche NimbleGen, Inc, Madison, WI 53719, USA

5 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, D-06466, Germany

6 Current address: The Sainsbury Laboratory, Norwich, NR47UH, UK

7 Helmholtz Center Munich, German Research Centre for Environmental Health (GmbH), MIPS/IBIS, Institute for Bioinformatics and Systems Biology, 85764 Neuherberg, Germany

8 Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena D-07745, Germany

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Genome Biology 2013, 14:R58 doi:10.1186/gb-2013-14-6-r58

Published: 12 June 2013

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.

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