Short‐Term High Light Stress Analysis Through Differential Methylation Identifies Root Architecture and Cell Size Responses

DNA methylation repatterning is an epigenomic component of plant stress response, but the extent that methylome data can elucidate changes in plant growth following stress onset is not known. We applied high-resolution DNA methylation analysis to decode plant responses to short- and long-term high light stress and, integrating with gene expression data, attempted to predict components of plant growth response. We identified 105 differentially methylated genes (DMGs) following 1 h of high light treatment and 193 DMGs following 1 week of intermittent high light treatment. Two distinct methylome-predicted plant growth responses to high light treatment could be confirmed by linking methylome changes in auxin response pathways to observed changes in root architecture and methylome changes in cell cycle pathway components to endoreduplication and palisade cell enlargement. We observed methylome changes in a cyclic GMP-dependent protein kinase in association with high light stress signalling. The ability to associate intragenic methylation repatterning with predictable plant phenotypic outcomes after a limited period of high light treatment allows for data-based early prediction of plant growth responses. The approach also permits the dissection of gene networks underpinning plant growth adjustments during environmental change to uncover dynamic phenotype determinants.