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| Status |
Public on Jul 01, 2012 |
| Title |
Detection of copy number variations in rice using array-based comparative genomic hybridization |
| Organism |
Oryza sativa |
| Experiment type |
Genome variation profiling by genome tiling array
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| Summary |
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.
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| Overall design |
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.
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| Contributor(s) |
Yu P, Wei X |
| Citation missing |
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| Submission date |
Jul 11, 2011 |
| Last update date |
Jul 03, 2012 |
| Contact name |
Ping Yu |
| E-mail(s) |
pingping367@163.com
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| Phone |
86-571-63370583
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| Fax |
86-571-63370366
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| Organization name |
China National Rice Research Institute
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| Department |
Rice Germplasm Evaluation
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| Street address |
359 Tiyuchang Road
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| City |
Hangzhou |
| State/province |
Zhejiang Province |
| ZIP/Postal code |
310006 |
| Country |
China |
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| Platforms (1) |
| GPL13842 |
NimbleGen Rice CGH 3x720K Whole-Genome Tiling Arrays [100816_CB_Osat_NCBI_CGH] |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA144491 |
