Genome-Wide Analysis of a Radiation-Induced Lesion Mimic Mutant in Rice

Lesion mimic mutations (LMMs) are very useful genetic tools in plants, however, it is difficult to uncover genome-wide mutations using traditional technology, the development of whole genome sequencing (WGS) provides a means by which to identify genome-wide LMMs. In this study, WGS was performed to reveal the molecular mechanisms behind LMMs in rice. An LMM JA001 was derived from indica rice IR64 by treating with 60Co gamma-radiation. Solexa sequencing technology was applied to uncover the mutations. In the JA001 genome, 7.93% of the genome sequences were altered in the JA001 genome, among which were 351323 single nucleotide polymorphisms and 32,648 bp indel variations in 19,937 genes. Gene ontology clustering revealed that genes that are associated with binding, kinase activity, the oxoglutarate dehydrogenase complex, the beta-galactosidase complex, protein phosphorylation, and cell-pollen recognition had a high mutation rate. It was also predicted that five mutated genes were involved in the porphyrin and chlorophyll metabolism, carotenoid biosynthesis, and plant-pathogen interaction pathways. Genome-wide analysis of mutations provides new insights into the molecular mechanisms of LMMs mutagenesis.