Analysis of genome-wide copy number variations in Oryza sativa L.
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PROVIDER: PRJNA183091 | ENA |
REPOSITORIES: ENA
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Project description:Copy 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. To detect CNVs, we used a set of NimbleGen whole-genome comparative genomic hybridization arrays containing 715,851 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). These CNVs contain some known genes. They are linked to variation among rice varieties, and are likely to contribute to subspecific characteristics.
2012-07-01 | GSE30542 | GEO
Project description:De novo copy number variations in cloned dogs from the same nuclear donor In this study, we aimed to identify de novo post-cloning CNV events and estimated the rate of CNV mosaicism in cloned dogs with the identical genetic background.
2013-12-17 | GSE49092 | GEO
Project description:BACKGROUND: Copy 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. RESULTS: We 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. CONCLUSIONS: Higher 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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Project description:De novo copy number variations in cloned dogs from the same nuclear donor In this study, we aimed to identify de novo post-cloning CNV events and estimated the rate of CNV mosaicism in cloned dogs with the identical genetic background.
2013-12-17 | GSE49123 | GEO
Project description:Detection of genomic copy number variations induced by multiple DNA breaks
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Project description:Copy number variations of Ph+ ALL, Ph+ MPAL and Ph+ AML
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Project description:Copy 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. To detect CNVs, we used a set of NimbleGen whole-genome comparative genomic hybridization arrays containing 715,851 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 M-bM-^@M-^XNipponbareM-bM-^@M-^Y (from O. sativa ssp. japonica) and M-bM-^@M-^XGuang-lu-ai 4M-bM-^@M-^Y (from O. sativa ssp. indica). These CNVs contain some known genes. They are linked to variation among rice varieties, and are likely to contribute to subspecific characteristics. Genomic DNA isolated from Nipponbare and Guang-lu-ai 4. Cy5 labeled DNA from Nipponbare used as reference and Cy3 labeled DNA from Guang-lu-ai 4 was hybridized to the 720K rice tiling array including three replicates. Fluorescence intensity data were normalized with qspline algorithm and ratio data were analyzed with the circular binary segmentation algorithm. Copy number variation calls were made if the averaged Log2 ratio of a segment was shifted by 1.0 from the baseline.
2012-06-30 | E-GEOD-30542 | biostudies-arrayexpress