ArticleBMC genomics2011
Detection of copy number variations in rice using array-based comparative genomic hybridization.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 73 citations in OpenAlex.
- Population-level gene copy number variations reveal distinct genetic properties of different Malus species.BMC genomics · 2025Article
- A Systematic Review of the Advances and New Insights into Copy Number Variations in Plant Genomes.Plants (Basel, Switzerland) · 2025Review
- Copy number variations at theFrontiers in plant science · 2024Article
- Identification of structural variations related to drought tolerance in wheat (Triticum aestivum L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Article
- Multiple Recurrent Copy Number Variations (CNVs) in Chromosome 22 Including 22q11.2 Associated with Autism Spectrum Disorder.Pharmacogenomics and personalized medicine · 2022Article
- In-Depth Sequence Analysis of Bread WheatInternational journal of molecular sciences · 2021Article
- A Reference Genome Sequence for Giant Sequoia.G3 (Bethesda, Md.) · 2020Article
- A genome-wide survey of copy number variations reveals an asymmetric evolution of duplicated genes in rice.BMC biology · 2020Article
- Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing.PLoS genetics · 2020Article
- Identification and characterization of a fast-neutron-induced mutant with elevated seed protein content in soybean.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Article
- A multiomics approach reveals the pivotal role of subcellular reallocation in determining rapeseed resistance to cadmium toxicity.Journal of experimental botany · 2019Article
- Connecting genome structural variation with complex traits in crop plants.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2019Review
- Transcriptomic and genomic structural variation analyses on grape cultivars reveal new insights into the genotype-dependent responses to water stress.Scientific reports · 2019Article
- Divergent evolution of rice blast resistance Pi54 locus in the genus Oryza.Rice (New York, N.Y.) · 2018Article
- Genomics-Assisted Identification and Characterization of the Genetic Variants Underlying Differential Nitrogen Use Efficiencies in Allotetraploid Rapeseed Genotypes.G3 (Bethesda, Md.) · 2018Article
- The Genome Sequence of the Wild TomatoFrontiers in plant science · 2018Article
- Copy number variation and disease resistance in plants.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2017Review
- Whole genome sequencing-based association study to unravel genetic architecture of cooked grain width and length traits in rice.Scientific reports · 2017Article
- Development of novel InDel markers and genetic diversity in Chenopodium quinoa through whole-genome re-sequencing.BMC genomics · 2017Article
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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 variations (CNVs) can create new genes, change gene dosage, reshape gene structures, and modify elements regulating gene expression. As with all types of genetic variation, CNVs may influence phenotypic variation and gene expression. CNVs are thus considered major sources of genetic variation. Little is known, however, about their contribution to genetic variation in rice.
resultsTo detect CNVs, we used a set of NimbleGen whole-genome comparative genomic hybridization arrays containing 718,256 oligonucleotide probes with a median probe spacing of 500 bp. We compiled a high-resolution map of CNVs in the rice genome, showing 641 CNVs between the genomes of the rice cultivars 'Nipponbare' (from O. sativa ssp. japonica) and 'Guang-lu-ai 4' (from O. sativa ssp. indica). The CNVs identified vary in size from 1.1 kb to 180.7 kb, and encompass approximately 7.6 Mb of the rice genome. The largest regions showing copy gain and loss are of 37.4 kb on chromosome 4, and 180.7 kb on chromosome 8. In addition, 85 DNA segments were identified, including some genic sequences. Contracted genes greatly outnumbered duplicated ones. Many of the contracted genes corresponded to either the same genes or genes involved in the same biological processes; this was also the case for genes involved in disease and defense.
conclusionWe detected CNVs in rice by array-based comparative genomic hybridization. These CNVs contain known genes. Further discussion of CNVs is important, as they are linked to variation among rice varieties, and are likely to contribute to subspecific characteristics.
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