Harnessing epigenome modifications for better crops.

Abstract

Chemical DNA modifications such as methylation influence translation of the DNA code to specific genetic outcomes. While such modifications can be heritable, others are transient, and their overall contribution to plant genetic diversity remains intriguing but uncertain. In this issue, Gouil and colleagues (pages 2655–2664) characterize the epigenome phenomenon termed ‘paramutation’ underlying a tomato photosynthesis-related gene defect, and in doing so expand our understanding of how epigenome modifications are conferred with exciting implications for crop improvement. It has long been recognized that DNA harbors information of richer texture and fidelity than the DNA sequence alone. Just as recorded texts contain information while volume, emphasis and accent contribute to the ultimate meaning conveyed by language, DNA sequence presents the genetic code while epigenome modifications influence specific conversion of this code into phenotypic traits. Epigenome contributions to genetic diversity and outcomes are gaining in appreciation as genomes and their modifications become ever more readily characterized and cataloged. As examples, whole genome sequencing and genomic DNA–protein interaction studies have revealed that many genomes, including those of important crops, include large repertoires of DNA- and RNA-derived mobile genetic elements rendered silent via chemical modifications, including cytosine methylation and methylation or acetylation of DNA-associated histone proteins (Cui and Cao, 2014). Also heritable epigenome reprogramming is critical in plant embryo development (Schmitz and Ecker, 2012), while developmental epigenome changes contribute to fruit maturation and ripening (Zhong et al., 2013), with additional modifications acquired in response to stress conditions. Recent evidence suggests the existence of molecular mechanisms in place to erase these induced modifications prior to meiotic transfer (Iwasaki and Paszkowski, 2014). A number of epi-alleles (stable genetic variants in DNA methylation patterns, but not DNA sequence) have been reported (Weigel and Colot, 2012), confirming that some heritable genetic diversity is anchored in the epigenome. The realization that a number of genetic diseases are traceable to the epigenome, including some cancers (Timp and Feinberg, 2013), has accelerated interest and inquiry into mechanisms of epigenome modification and resulting manifestations that can contribute to illness. Similarly, research in plants is spurred on by the knowledge that a clearer mechanistic picture of epigenome mechanisms will facilitate our understanding of their relative contributions to crop genetic diversity and open doors to their use for crop improvement.