ArticleBMC genomics2013
Genome-wide copy number variations in Oryza sativa L.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 43 citations in OpenAlex.
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- AthCNV: A Map of DNA Copy Number Variations in the Arabidopsis Genome.The Plant cell · 2020Article
- The Copy Number Variation ofFrontiers in plant science · 2020Article
- The Genomic Substrate for Adaptive Radiation: Copy Number Variation across 12 Tribes of African Cichlid Species.Genome biology and evolution · 2019Article
- A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism.BMC genomics · 2019Article
- Connecting genome structural variation with complex traits in crop plants.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Review
- Complex DNA structures trigger copy number variation across the Plasmodium falciparum genome.Nucleic acids research · 2019Article
- Modeling copy number variation in the genomic prediction of maize hybrids.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Article
- Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.Nature genetics · 2018Article
- Copy number variation and disease resistance in plants.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2017Review
- Copy number variation at the GL7 locus contributes to grain size diversity in rice.Nature genetics · 2015Article
- Genome-wide indel markers shared by diverse Asian rice cultivars compared to Japanese rice cultivar 'Koshihikari'.Breeding science · 2015Article
- Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber.The Plant cell · 2015Article
- Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection.PloS one · 2015Article
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCopy number variation (CNV) can lead to intra-specific genome variations. It is not only part of normal genetic variation, but also is the source of phenotypic differences. Rice (Oryza sativa L.) is a model organism with a well-annotated genome, but investigation of CNVs in rice lags behind its mammalian counterparts.
resultsWe comprehensively assayed CNVs using high-density array comparative genomic hybridization in a panel of 20 Asian cultivated rice comprising six indica, three aus, two rayada, two aromatic, three tropical japonica, and four temperate japonica varieties. We used a stringent criterion to identify a total of 2886 high-confidence copy number variable regions (CNVRs), which span 10.28 Mb (or 2.69%) of the rice genome, overlapping 1321 genes. These genes were significantly enriched for specific biological functions involved in cell death, protein phosphorylation, and defense response. Transposable elements (TEs) and other repetitive sequences were identified in the majority of CNVRs. Chromosome 11 showed the greatest enrichment for CNVs. Of subspecies-specific CNVRs, 55.75% and 61.96% were observed in only one cultivar of ssp. indica and ssp. japonica, respectively. Some CNVs with high frequency differences among groups resided in genes underlying rice adaptation.
conclusionsHigher recombination rates and the presence of homologous gene clusters are probably predispositions for generation of the higher number of CNVs on chromosome 11 by non-allelic homologous recombination events. The subspecies-specific variants are enriched for rare alleles, which suggests that CNVs are relatively recent events that have arisen within breeding populations. A number of the CNVs identified in this study are candidates for generation of group-specific phenotypes.
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