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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
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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).
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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
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Contributor(s) |
Bruce M, Leach J, Mauleon R |
Citation(s) |
19320995 |
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Submission date |
Mar 03, 2009 |
Last update date |
Dec 27, 2017 |
Contact name |
Ramil Paner Mauleon |
E-mail(s) |
r.mauleon@cgiar.org
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Organization name |
International Rice Research Institute
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Department |
Crop Research Informatics Laboratory
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Lab |
Bioinformatics team
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Street address |
IRRI Campus, Pili Drive
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City |
Los Banos |
State/province |
Laguna |
ZIP/Postal code |
4031 |
Country |
Philippines |
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Platforms (1) |
GPL2025 |
[Rice] Affymetrix Rice Genome Array |
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Samples (17)
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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 |
GSM377073 |
Genomic DNA - 45 day old leaf sample - mutant d2943 |
GSM377074 |
Genomic DNA - 45 day old leaf sample - mutant g282 |
GSM377075 |
Genomic DNA - 45 day old leaf sample - mutant g650 |
GSM377076 |
Genomic DNA - 45 day old leaf sample - mutant g6485 |
GSM377077 |
Genomic DNA - 45 day old leaf sample - mutant g6489 |
GSM377078 |
Genomic DNA - 45 day old leaf sample - mutant g6603 |
GSM377079 |
Genomic DNA - 45 day old leaf sample - mutant g6686 |
GSM377080 |
Genomic DNA - 45 day old leaf sample - mutant g6728 |
GSM377081 |
Genomic DNA - 45 day old leaf sample - mutant g7534 |
GSM377082 |
Genomic DNA - 45 day old leaf sample - mutant g9799 |
GSM377083 |
Genomic DNA - 45 day old leaf sample - mutant g6989 |
GSM377084 |
Genomic DNA - 45 day old leaf sample - mutant f1856 |
GSM377085 |
Genomic DNA - 45 day old leaf sample - mutant f2045 |
GSM377086 |
Genomic DNA - 45 day old leaf sample - IR64 wtcheck |
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Relations |
BioProject |
PRJNA114763 |