Abstract
BackgroundThere 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.ResultsA 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.ConclusionsWe 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.
Highlights
There is growing evidence for the prevalence of copy number variation (CNV) and its role in phenotypic variation in many eukaryotic species
We developed a high-density oligonucleotide microarray containing 2.1 million probes derived from low-copy sequences in 115,003 whole-genome shotgun (WGS) contigs of the barley reference genome Morex
For each 200 bp fragment the array included 10 long oligonucleotide probes of 56- to 100mers. This design strategy allowed for reliable detection of relatively small CNVs and coverage of the low-copy regions of the genome
Summary
There is growing evidence for the prevalence of copy number variation (CNV) and its role in phenotypic variation in many eukaryotic species. An increasing number of human studies have produced evidence for the association of CNV with complex diseases, environmental response, and population diversity (reviewed in [1]). There is evidence that prevalent CNV in maize plays an important role in contributing to phenotypic variation as it overlaps loci associated with important traits related to stress and stimulus responses [16]. Studies in other plant species including Arabidopsis [17,18], wheat [19], sorghum [20], rice [21,22], and soybean [23,24], demonstrated that CNV contributes to the genetic diversity of their genomes. CNV at the MATE1 transporter gene in maize is associated with increased aluminum tolerance [27]
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