Epigenetics, Epigenomics and Crop Improvement

Abstract Epigenetics refers to heritable alterations in chromatin architecture that do not involve changes in the underlying DNA sequence but profoundly affect gene expression and impact cellular function. Epigenetic regulation is attained by specific mechanisms involving DNA methylation, histone posttranslational modifications and the action of noncoding (nc) RNAs which lead to open or closed chromatin states associated with gene activation or gene silencing, respectively. Over the past two decades extensive investigations have provided a wealth of information on epigenetic regulation at specific loci both in model and crop plants and the effect it may have on various aspects of plant development such as proper vegetative growth, successful reproduction and viability, effects on yield, and efficiency in coping with stress. In recent years, the rapid progress of high-throughput technologies has led to the unveiling of epigenetic landscapes at genome-wide scale (epigenomes) exemplified by the deciphering of the full methylomes, at single base resolution, of the model plant Arabidopsis and crop plants such as rice and tomato. An increasing number of epigenomes are now being investigated on crops of high economic value. Transgenerational natural or induced epigenetic variation can be a new source of phenotypic diversity especially for species with low genetic variation. The comparison of different epigenomes arising from different genotypes/tissues/cell types/environmental conditions can offer valuable information for the development of biomarkers paving the way to what is nowadays termed plant epibreeding. This review will attempt a comprehensive presentation of the progress in plant epigenetics both at small scale (single locus) and large scale (epigenome-wide) during development and in response to environmental stress, focusing on agronomically important crops and the impact that epigenetics, epigenomics and the new emerging field of epibreeding may have on crop improvement.