Trends in Plant Science
ReviewEpigenetics for Plant Improvement: Current Knowledge and Modeling Avenues
Section snippets
Epigenetics as a New Source to Broaden Plant Phenotypic Diversity
Over the past century, integration of desired traits into crops has mainly relied on the use of natural or induced genetic variability [1]. Intense breeding programs have narrowed the range of cultivars, resulting in a considerable loss of genetic diversity [2]. Indeed, the recent completion of many important crop genomes has increased the efficiency of breeding by providing new tools, such as genome-wide association studies (GWAS), that help capture a substantial proportion of sequence-based
Epigenetics: Stability and/or Heritability of Chromatin Marks
Epigenetic information is mediated by DNA methylation and histone PTMs, the so-called chromatin marks (Box 1) that together with chromatin remodeling, small RNAs, and histone variants (Box 2), determine the conformational state of chromatin and, thus, also its transcriptional state [29]. However, the stability and heritability of chromatin marks vary and not all chromatin regulations are associated with epigenetic memory (Box 1).
DNA methylation represents a highly stable and heritable
Chromatin Changes Are Involved in the Control of Plant Development and in Environmental Responses
As mentioned above, chromatin marks, including DNA methylation and histone PTMs, have crucial roles during plant development. They are involved in the control of flowering time [16], seed and endosperm development [50], parental imprinting [25], fruit ripening 28, 51, symbiotic nodule organogenesis [52], and cell fate maintenance and reprogramming 53, 54. Impairing DNA methylation control leads to pleiotropic phenotypes consistent with multiple functions of these epigenetic mechanisms in plants
Epialleles Generate Heritable Phenotypic Variation
Evidence that epigenetic processes act on the variability of plant traits was first provided by the characterization of plant epialleles [84]. These were used to show that methylation imprints could lead to gene misexpression and, thus, to new phenotypes that are stable across generations. The Colourless Non Ripening (CNR) locus provides one of the best-characterized examples of epiallelic variation that impacts important agronomical traits. In the Cnr background, fruit ripening is dramatically
Exploiting Epigenetic Variations for Crop Improvement
Exploiting epigenetic variations for breeding applications, whether they control developmental processes or contribute to adaptation to various environments, clearly relies on their transmission features and on the plant propagation strategies (sexual versus clonal) (Table 1) [92]. For example, because 5mC patterns can be transmitted after mitosis and meiosis, DNA methylation marks could be useful in all crops, irrespective of their propagation mode. By contrast, because histone PTMs are more
Recent Advances in Modeling Epigenetics
Plant modelers face manifold challenges to predict plant performance from epigenetic variations, including the identification of the epigenetic marks and/or epigenetic regulatory mechanisms, characterization of the transmission features (especially in support of breeding schemes), and the quantification of linkages between epigenetic and phenotypic variations. Due to the difficulty of tracking epigenetic variations and characterizing epigenetic features, modeling approaches for predictive
Concluding Remarks and Future Perspectives
Epigenetic marks are involved in a range of plant developmental processes shaping plant phenotypic plasticity, including adaptive responses to environmental stresses. Therefore, their variations are expected to broaden plant phenotypic space to improve plant adaptation under ever-changing environmental conditions and/or to ensure crop yield and production quality (Figure 2, Key Figure). We have demonstrated that epigenetic variations could be exploited in predictive models should their
Acknowledgments
We thank E. Personeni for critical reading and comments on the manuscript. We are also grateful to the three anonymous reviewers for their constructive suggestions. This work was supported by the INRA divisions Environment and Agronomy, and Plant Biology and Breeding, and the University of Bordeaux, and the INRA-EA ‘Fruit and seed quality’ network.
Glossary
- Chromatin marks
- covalent modifications of the chromatin that include the methylation of the fifth carbon of cytosine (5mC) on the DNA molecules and histone post-translational modifications (PTMs). Histone PTMs include methylation, acetylation, ubiquitination, phosphorylation, sumoylation, and poly (ADP) ribosylation. Genes, transposable elements, heterochromatin, and so on are marked by a particular combination of epigenetic marks that define their epigenetic state. When inherited, stable
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These authors contributed equally to this work.