Molding the Rice Methylome for Disease Resistance

In Arabidopsis thaliana, epigenetic changes in the DNA methylome can prime transcriptional responses to biotic and abiotic stress, resulting in enhanced resistance. Epigenetic recombinant inbred lines have further enabled the identification of trans-generationally stable epialleles controlling stress resistance without adverse effects on plant growth, highlighting their potential for crop improvement. Unfortunately, extending these approaches to crops has remained largely unsuccessful due to differences in genome architecture. The rice (Oryza sativa) genome consists for [~]40% of transposable elements and other epigenetically regulated repeat sequences. Therefore, perturbation of DNA methylation typically leads to severe developmental defects, sterility or lethality, which precludes the use of methylome engineering strategies for epiallele mapping and crop improvement. Here, we exploit an inducible system to introduce for the first time widespread epigenetic variation in rice without detrimental phenotypic consequences. We combined the A. thaliana DNA demethylase AtROS1 with the {beta}-estradiol-activated XVE cassette (XVE:AtROS1-YFP) to enable transient DNA demethylation during early development. Induction of the construct in transgenic Nipponbare seedlings yielded genome-wide changes in the DNA methylome which persisted for at least one generation. Strikingly, these methylome changes did not cause developmental defects or reduced seed yield, but instead correlated with enhanced resistance against Xanthomonas oryzae, the causal agent of bacterial leaf blight in rice. Our study demonstrates that controlled, transient DNA demethylation can uncouple epigenetic variation from deleterious phenotypes in rice. This approach provides a practical framework for generating epigenetic mapping populations and opens new avenues for harnessing epigenetic variation in crop improvement.