Growth and DNA Methylation Alteration in Rice (Oryza sativa L.) in Response to Ozone Stress

With the development of urban industrialization, the increasing ozone concentration (O(3)) at ground level stresses on the survival of plants. Plants have to adapt to ozone stress. DNA methylation is crucial for a rapid response to abiotic stress in plants. Little information is known regarding the epigenetic response of DNA methylation of plants to O(3) stress. This study is designed to explore the epigenetic mechanism and identify a possible core modification of DNA methylation or genes in the plant, in response to O(3) stress. We investigated the agronomic traits and genome-wide DNA methylation variations of the Japonica rice cultivar Nipponbare in response to O(3) stress at three high concentrations (80, 160, and 200 nmol·mol(−1)), simulated using open-top chambers (OTC). The flag leaf length, panicle length, and hundred-grain weight of rice showed beneficial effects at 80 nmol·mol(−1) O(3) and an inhibitory effect at both 160 and 200 nmol·mol(−1) O(3.) The methylation-sensitive amplified polymorphism results showed that the O(3)-induced genome-wide methylation alterations account for 14.72–15.18% at three different concentrations. Our results demonstrated that methylation and demethylation alteration sites were activated throughout the O(3) stress, mainly at CNG sites. By recovering and sequencing bands with methylation alteration, ten stress-related differentially amplified sequences, widely present on different chromosomes, were obtained. Our findings show that DNA methylation may be an active and rapid epigenetic response to ozone stress. These results can provide us with a theoretical basis and a reference to look for more hereditary information about the molecular mechanism of plant resistance to O(3) pollution.