Advances and Promises of Epigenetics for Forest Trees

Abstract

The importance of tree genetic variability in the ability of forests to respond and adapt to environmental changes is crucial in forest management and conservation. Along with genetics, recent advances have highlighted “epigenetics” as an emerging and promising field of research for the understanding of tree phenotypic plasticity and adaptive responses. In this paper, we review recent advances in this emerging field and their potential applications for tree researchers and breeders, as well as for forest managers. First, we present the basics of epigenetics in plants before discussing its potential for trees. We then propose a bibliometric and overview of the literature on epigenetics in trees, including recent advances on tree priming. Lastly, we outline the promises of epigenetics for forest research and management, along with current gaps and future challenges. Research in epigenetics could use highly diverse paths to help forests adapt to global change by eliciting different innovative silvicultural approaches for natural- and artificial-based forest management.

Induction of Radiata Pine Somatic Embryogenesis at High Temperatures Provokes a Long-Term Decrease in DNA Methylation/Hydroxymethylation and Differential Expression of Stress-Related Genes

“…During the annual cycle, for example, different developmental transitions like bud set in autumn and bud burst in spring are governed by changes in DNA methylation patterns [ 29 ]. Moreover, these epigenetic alterations and the establishment of epigenetic marks strongly contribute to the development of phenotypic plasticity and environmental stress memory through the differential expression of specific genes and the regulation of transposable elements mobility [ 5 ]. Despite this fact, only limited studies have been implemented with trees and we still lack information about the multiple regulatory layers connecting epigenetic variations, gene expression, and phenotypic traits in trees.…”

“…DNA methylation is the most studied epigenetic mark due to its occurrence in plants and mammals, its stability, and its role in gene regulation and genome structure maintenance through transposon silencing [ 5 ]. Methylation is site specific and usually occurs in the fifth carbon position of cytosines in the following sequences: CG, CHG, and CHH (where H = A, T or C) [ 6 ].…”

Epigenetics for Crop Improvement in Times of Global Change

“…For trans-generational memory the repetition of the stress in successive generations is key for keeping the transcriptional state associated with the primed response [ 46 , 190 , 191 ] and a stress recovery phase of the mother plants may be crucial [ 191 ]. Although priming has been well-studied in annual plants, such as Arabidopsis [ 179 ] or the model crops maize and rice [ 172 , 192 , 193 ], the molecular memory induced by stress may indeed be particularly relevant for perennial species, among them economically important crops such as poplar [ 65 , 66 , 194 ], and clonally propagated plants, for instance grapevine [ 195 ]. In addition, maintaining the primed state required to surpass the energetic costs, otherwise resetting the memory, may be more advantageous for the plant [ 181 , 187 , 191 ].…”

“…The authors proposed (i) “concurrent analysis of epigenetic variation and phenotypic trait variation, including plant fitness between individuals exposed to contrasted biotic interactions” and (ii) “analysis of specific loci and physiological pathways to clarify the epigenetic contribution to the stabilisation of environmentally induced phenotypes (priming) or across generations’’ to gain insights into functional relationships. In addition to these recommendations, Amaral [ 194 ] proposed a complementary methodological plan for tree breeding that can be easily extended to crops, including (i) use of both forward and reverse (epi)genetic approaches and development of population epigenomics; (ii) assessment of the effects of multiple, potentially interacting, stressful conditions (intensity, duration, frequency, interaction); (iii) favour of field experimental designs; (iv) use of kinetics approaches by sampling biological material along a developmental gradient for a better understanding of the molecular chain acting from short to long term during development and environment interactions; (v) taking into account crop features (species, genotype or variety, physiological and chronological ages, organs, tissues), but also the geographic origin, clone or seed history, clonal propagation vs. sexual reproduction, and all features of breeding, management of genetic resources and culture; and (vi) development of trans-omics approach to overcome the lack of comprehensive understanding and the information gap regarding interaction across multiple -omic layers to move from correlative to causal inference and predictions.…”

“…Increasing evidence indicates that together with hormones, epigenetic mechanisms play an important role in somatic embryogenesis induction and progression [ 275 , 279 , 280 ]. This data opens the door for targeting epigenetics as a potential biotech strategy to improve and accelerate crop plant regeneration and breeding [ 66 , 194 ]. For these studies, methodologies to monitor changes in global DNA methylation levels and nuclear patterns have been very useful [ 281 , 282 ].…”