Detection of Deletion Mutants in Rice Via Overgo Hybridization Onto Membrane Spotted Arrays

Overlapping nucleotides or overgos were designed and used to detect deletions in rice mutants that had been generated by treatment with a chemical (diepoxybutane, DB) or irradiation (gamma ray, GR). As a proof of concept, DNA of three spotted leaf 11 (spl11) deletion mutants, GR5612, GR5717 and DB2487, and the wild-type DNA (IR64) were spotted onto nylon membranes in different concentrations and probed with radiolabeled overgos designed from different regions within the Spl11 gene. At least 3 μg per spot of DNA was required to show unambiguous and visible signals. Overgos designed from regions putatively deleted in GR5612 consistently did not hybridize to the GR5612 genomic DNA, whereas DNA from wild-type IR64 and from mutants in other regions consistently hybridized to the overgos. DNA of mutant DB2487 hybridized to all the overgos tested, suggesting the deletion is small and undetectable by the overgos. Overall, this study demonstrates that overgos can be employed to detect, verify, and characterize deletions, particularly in single copy genes, in mutant genomes. However, the technique requires careful adjustment of DNA concentration before spotting and the spotting of relatively high DNA concentrations onto the membranes.