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

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.

Genome Structures and Transcriptomes Signify Niche Adaptation for the Multiple-Ion-Tolerant Extremophyte Schrenkiella parvula

“…Structural variation can lead to CNV of genes, which, in turn, affects gene dosage and transcription strength (Stranger et al, 2007;Schlattl et al, 2011;Massouras et al, 2012;Haraksingh and Snyder, 2013). In plants, many examples exist for the copy number of a gene or genome segment associated with phenotype changes (Cook et al, 2012;Li et al, 2012;Maron et al, 2013;Nitcher et al, 2013), and genome-wide CNVs appear to predict phenotypes to some extent Muñoz-Amatriaín et al, 2013). The S. parvula genome is characterized by a higher copy number of genes associated with transporter activity (Dassanayake et al, 2011a).…”

Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber

“…In plants, SVs are related to numerous phenotypic variations such as leaf size (Horiguchi et al, 2009), fruit shape (Xiao et al, 2008), and aluminum tolerance (Maron et al, 2013). Initially, for different species such as human (Homo sapiens) (Iafrate et al, 2004), rice (Oryza sativa) (Yu et al, 2013), soybean (Glycine max) (McHale et al, 2012), and barley (Hordeum vulgare) (Muñoz-Amatriaín et al, 2013), the majority of SVs were detected by microarray-based comparative genomic hybridization. However, array-based technology can only detect SVs with sequences that are homologous to probes and cannot determine the exact copy number or breakpoint.…”

Discovery of genes affecting resistance of barley to adapted and non-adapted powdery mildew fungi

“…Morex [43]. For CNV assessment the expectation maximization algorithm was used to estimate the mixing proportion, mean, and variance associated with two predicted signal sub-distributions found within the tested genotype vs. Morex fragments.…”