Epi-fingerprinting and epi-interventions for improved crop production and food quality

Abstract

Increasing crop production at a time of rapid climate change represents the greatest challenge facing contemporary agricultural research. Our understanding of the genetic control of yield derives from controlled field experiments designed to minimize environmental variance. In spite of these efforts there is substantial residual variability among plants attributable to Genotype × Environment interactions. Recent advances in the field of epigenetics have revealed a plethora of gene control mechanisms that could account for much of this unassigned variation. These systems act as a regulatory interface between the perception of the environment and associated alterations in gene expression. Direct intervention of epigenetic control systems hold the enticing promise of creating new sources of variability that could enhance crop performance. Equally, understanding the relationship between various epigenetic states and responses of the crop to specific aspects of the growing environment (epigenetic fingerprinting) could allow for a more tailored approach to plant agronomy. In this review, we explore the many ways in which epigenetic interventions and epigenetic fingerprinting can be deployed for the improvement of crop production and quality.

Botrytis cinerea loss and restoration of virulence during in vitro culture follows flux in global DNA methylation

“…This observed accumulation of somaclonal variation as culture progressed, showed a positive linear correlation with the observed changes in virulence. This correlation is consistent with previous reports of accumulative genetic/methylome change for other species when similarly exposed to prolonged periods of culture (15,29). Our observations also accord with the high levels of somaclonal variability arising during in vitro growth of phytopathogenic fungi, which seemingly depresses the level of virulence of the culture isolates (30).…”

“…This observed accumulation of somaclonal variation as culture progressed showed a positive linear correlation with the observed changes in virulence (R 2 =0.5, P=0.002 and R 2 =0.5 P=0.007, for epigenetic distances calculated using HpaII and MspI respectively). Such correlation between time in culture and genetic/epigenetic somaclonal variation is consistent with accumulation of sequence and/or DNA methylation changes with time in culture as previously reported for other species when cultivated in vitro (15,29). Moreover, these results are consistent with previous reports of high levels of somaclonal variability appearing during in vitro culture of phytopathogenic fungi, which affect the level of virulence of the culture isolates (30).…”

“…These include DNA methylation, histone modifications, and mRNA editing and degradation by noncoding RNAs. Such processes are intimately entwined and often work in a synergistic way to ultimately achieve changes in phenotype (15). DNA methylation, and more specifically cytosine methylation (i.e.…”

Environmental conditions and agronomic practices induce consistent global changes in DNA methylation patterns in grapevine (Vitis viniferacv Shiraz)

“…Epigenetic priming is an adaptive strategy by which plants use their memory of the environment to modify their phenotypes to adapt to subsequent conditions (Kelly et al, 2012; Tricker et al, 2013a; 2013b, Vogt, 2015). It is now also widely accepted that epigenetic mechanisms have been the source of useful variability during crop varietal selection (Amoah et al, 2012; Bloomfield et al, 2014; Rodríguez López and Wilkinson, 2015). Of the known epigenetic mechanisms, cytosine methylation (5mC) is arguably the best understood (Goldberg et al, 2007).…”

“…The contribution of DNA methylation to plant performance has been extensively studied in model organisms and some annual crops (Rodríguez López and Wilkinson, 2015). However, we are only beginning to understand how long-living plants, such as grapevines, use epigenetic mechanisms to adapt to changing environments (Fortes and Gallusci, 2017).…”