We exome captured and sequenced 397 diverse barley accessions to carry out a genome-wide analysis copy number variants affecting coding sequences. The Roche Nimblegen exome capture array was used to enrich for exon sequences (http://sequencing.roche.com/products/nimblegen-seqcap-target-enrichment/seqcap-ez-system/seqcap-ez-designs.html). The enriched samples were then sequenced using an Illumina HiSeq 2000 sequencer. An average of 2 x 24.6 million paired end Illumina reads per sample were generated, which correspond to approximately 80x coverage of the 61.3 Mbp exome capture space.

Background: Copy number variants (CNVs) are pervasive in several animal and plant genomes and contribute to shape genetic diversity. In barley, there is evidence that changes in gene copy number underlie important agronomic traits. The recently released reference sequence of barley represents a valuable genomic resource for unveiling the incidence of CNVs that affect gene content and identifying sequence features associated with CNV formation.Results: Using exome sequencing and read count data, we detected 16,605 deletions and duplications that affect barley gene content surveying a panel of 397 diverse accessions. The quest of segmental duplications (SDs) in the reference sequence of barley, revealed plenty of these low-copy repeats, most of which overlap predicted coding sequences. Statistical analyses revealed that the incidence of CNVs increases significantly in SD-rich regions, pointing out that these sequence elements act as hot spots for the formation of CNVs.Conclusions: This study delivered a comprehensive genome-wide study of CNVs affecting barley gene content and suggested the implication of SDs in the molecular mechanisms that lead to the formation of this class of CNVs.