Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays

ABSTRACT: 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).

ORGANISM(S): Oryza sativa Oryza sativa Indica Group

PROVIDER: GSE15071 | GEO | 2009/03/06

SECONDARY ACCESSION(S): PRJNA114763

REPOSITORIES: GEO