Specific-Locus Amplified Fragment Sequencing Reveals Spontaneous Single-Nucleotide Mutations in Rice Mutants.

Genomic stability depends in part on an efficient DNA lesion recognition and correction by the DNA mismatch repair (MMR) system. We investigated mutations arising spontaneously in rice mutants by specific-locus amplified fragment sequencing. Totally 994 single-nucleotide mutations were identified in three mutants and on average the mutation density is about 1/136.72 Kb per mutant line. These mutations were relatively randomly distributed in genome and might be accumulated in generation-dependent manner. All possible base transitions and base transversions could be seen and the ratio of transitions to transversions was about 3.12. We also observed the nearest-neighbor bias around the mutated base. Our data suggests that is important in ensuring genome stability by recognizing mismatches that arise spontaneously and provides useful information for investigating the function of the gene in DNA repair and exploiting MMR mutants in rice induced mutation breeding.