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Series GSE15071 Query DataSets for GSE15071
Status Public on Mar 06, 2009
Title Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays
Platform organism Oryza sativa
Sample organism Oryza sativa Indica Group
Experiment type Genome variation profiling by array
Summary Rice deletion mutants have not been widely used in functional genomics, because the mutated genes are not tagged and therefore, difficult to identify
We present a microarray-based approach to identify deleted genomic regions in rice mutants selected from a large collection generated by gamma ray or fast neutron treatment.
Our study focuses not only on the utility of this method for forward genetics, but also its potential as a reverse genetics tool through accumulation of hybridization data for a collection of deletion mutants harboring multiple genetic lesions.
We demonstrate that hybridization of labeled genomic DNA directly onto the Affymetrix Rice GeneChip® allows rapid localization of deleted regions in rice mutants. Deletions ranged in size from one gene model to ~500 kb and were predicted on all 12 rice chromosomes. The utility of the technique as a tool in forward genetics was demonstrated in combination with an allelic series of mutants to rapidly narrow the genomic region, and eventually identify a candidate gene responsible for a lesion mimic phenotype.
We demonstrate the utility of oligonucleotide arrays to discover deleted genes in rice. The density and distribution of deletions suggests the feasibility of a database saturated with deletions across the rice genome. This community resource can continue to grow with further hybridizations, allowing researchers to quickly identify mutants that harbor deletions in candidate genomic regions, for example, regions containing QTL of interest.
MS Accepted at BMC Genomics, MS ID : 2798701382204393

Note: 14 of the 16 mutants deposited are reported in the published manuscript (mutants d1137 & g6989 are not discussed).
Overall design Genomic DNA from 16 rice deletion mutants (induced by treatment of the indica variety IR64 with DEB-treatment, Fast Neutron or gamma ray (GR) exposure) and wildtypes were hybridized to affymetrix-rice oligonucleotide array
Contributor(s) Bruce M, Leach J, Mauleon R
Citation(s) 19320995
Submission date Mar 03, 2009
Last update date Dec 27, 2017
Contact name Ramil Paner Mauleon
Organization name International Rice Research Institute
Department Crop Research Informatics Laboratory
Lab Bioinformatics team
Street address IRRI Campus, Pili Drive
City Los Banos
State/province Laguna
ZIP/Postal code 4031
Country Philippines
Platforms (1)
GPL2025 [Rice] Affymetrix Rice Genome Array
Samples (17)
GSM377070 Genomic DNA - 45 day old leaf sample - mutant d1
GSM377071 Genomic DNA - 45 day old leaf sample - mutant d256
GSM377072 Genomic DNA - 45 day old leaf sample - mutant d1137
BioProject PRJNA114763

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Supplementary file Size Download File type/resource
GSE15071_RAW.tar 105.8 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table

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