IBIP seminar

Thursday, May 31, 2018
Rom 108 (School Heart)

Exploring and modelling epigenetic regulations:
A new key lever for crop adaptation to on-going agricultural challenges?

Sophie Brunel-Muguet
EVA, Normandie Univ, UNICAEN, INRA, Caen, France

Epigenetic variations are involved in the control of plant developmental processes (e.g. control of flowering time, parental imprinting, fruit ripening, symbiotic nodule organogenesis) and in adaptive responses to environmental (a)biotic stresses [1–3]. Because intense breeding programs have eroded genetic diversity since the Green Revolution [4–7], epigenetic variations now emerge as a new source of phenotypic variations which offer a new lever for crop improvement, especially in the context of climate change that will force rapid adaptation to ever-changing conditions.
Their potential use in crop improvement raises the question of their stability and transmission features which will impact on the memory acquisition of the environmental or development cues [8–11]. Epigenetic changes can be reset between generations or transmitted to the progeny through several cycles of mitoses and meioses. The transmission features were shown to be tightly related to the types of epigenetic marks e.g. DNA methylation, post translational histone modifications [12]. According to the crop-specific reproductive strategies i.e. clonal vs. sexual reproduction [13], different transmission features of epigenetic marks used for breeding schemes should be targeted. For instance, for species that reproduce through clonal spread, the transmission of the epigenetic marks associated to adaptive traits through mitosis only is adequate.
Finally, a challenging step is how to predict the impacts of epigenetic marks on plant phenotypes according to developmental and/or environmental constraints. Only a few studies have already tackled the issue of modeling epigenetic modifications [14–17]. As a proof of concept to illustrate the added value of modeling epigenetic variations in breeding strategies, we present a model that was implemented to allow the prediction of lycopene production during tomato fruit ripening, a process recently shown to be under epigenetic control [18].
Overall, epigenetic variations could offer innovative options for breeding applications. Crop modellers are urged to take epigenetic modifications into account to develop model-driven breeding strategies. This will open new avenues for improving crop adaptation to the on-going agricultural challenges.

References:
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2 Baulcombe, D.C. and Dean, C. (2014) Epigenetic regulation in plant responses to the environment. Cold Spring Harb. Perspect. Biol. 6, a019471
3 Pikaard, C.S. and Scheid, O.M. Epigenetic Regulation in Plants. DOI: 10.1101/cshperspect.a019315
4 Zhang, Y.-Y. et al. (2013) Epigenetic variation creates potential for evolution of plant phenotypic plasticity. New Phytol. 197, 314–22
5 King, G.J. (2015) Crop epigenetics and the molecular hardware of genotype × environment interactions. Front. Plant Sci. 6, 968
6 Esquinas-Alcázar, J. (2005) Science and society: protecting crop genetic diversity for food security: political, ethical and technical challenges. Nat. Rev. Genet. 6, 946–53
7 Giovannoni, J. (2016) Harnessing epigenome modifications for better crops. J. Exp. Bot. 67, 2535–2537
8 Iwasaki, M. and Paszkowski, J. (2014) Epigenetic memory in plants. EMBO J. 33, 1–12
9 Eichten, S.R. et al. (2014) Epigenetics: Beyond Chromatin Modifications and Complex Genetic Regulation. Plant Physiol. 165, 933–947
10 Vriet, C. et al. (2015) Stress-induced chromatin changes in plants: of memories, metabolites and crop improvement. Cell. Mol. Life Sci. 72, 1261–73
11 Paszkowski, J. and Grossniklaus, U. (2011) Selected aspects of transgenerational epigenetic inheritance and resetting in plants. Curr. Opin. Plant Biol. 14, 195–203
12 Lämke, J. and Bäurle, I. (2017) Epigenetic and chromatin-based mechanisms in environmental stress adaptation and stress memory in plants. Genome Biol. 18, 124
13 Douhovnikoff, V. and Dodd, R.S. (2014) Epigenetics: a potential mechanism for clonal plant success. Plant Ecol. 216, 227–233
14 Colicchio, J.M. et al. (2015) DNA methylation and gene expression in Mimulus guttatus. BMC Genomics 16, 507
15 Hu, Y. et al. (2015) Prediction of plant height in arabidopsis thaliana using DNA methylation data. Genetics 201, 779–793
16 Richards, D. et al. (2012) Illustrations of mathematical modeling in biology: epigenetics, meiosis, and an outlook. Cold Spring Harb. Symp. Quant. Biol. 77, 175–81
17 Song, J. et al. (2012) Vernalization – a cold-induced epigenetic switch. J. Cell Sci. 125,
18 Liu, R. et al. (2015) A DEMETER-like DNA demethylase governs tomato fruit ripening. Proc. Natl. Acad. Sci. U. S. A. 112, 10804–9

Contact : Denis Vile

Contacts IBIP :
Sabine Zimmermann
Alexandre Martinière
Florent Pantin
Chantal Baracco
Véronique Rafin