From epigenetics to epigenomics and their implications in plant breeding

doi:10.1016/B978-0-12-381466-1.00014-6

Plant Biotechnology and Agriculture

Prospects for the 21st Century

2012, Pages 207-226

https://doi.org/10.1016/B978-0-12-381466-1.00014-6 Get rights and content

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Epigenetics involves the mitotically and meiotically heritable variation that does not entail a change in DNA. This chapter describes the transition from epigenetics to epigenomics, together with the genome-wide methods used and the data, resources, and tools available in exploring, integrating, and extracting useful information. It begins with a brief description of the different epigenetic mechanisms. Finally, the role of epigenomics in plant development, phenotypic variation, response to environmental cues and stresses, and the implication of different epigenetic phenomena in plant breeding are discussed. Work in epigenomics is reinforcing the view for the whole genome, providing significant outputs. The very recent sequence of the maize genome opens new avenues to this research. It is the largest plant genome to be fully sequenced and characterized. It contains a high percentage of transposable elements (TEs) of different types, providing an excellent opportunity to study and understand the role of different TEs in eukaryotic large genome organization and function, but essentially it provides an understanding of the function of epigenomic mechanisms as TE regulators at a genomic level.

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Citation Excerpt :
Dynamic transitions from open to closed chromatin forms and interactions among the epigenetic mechanisms are necessary to ensure proper cellular function at all stages of development and at different environmental conditions (Berger, 2007; Du, Johnson, Jacobsen, & Patel, 2015; Forderer, Zhou, & Turck, 2016; Jarillo, Piñeiro, Cubas, & Martínez-Zapater, 2009; Van Oosten, Bressan, Zhu, Bohnert, & Chinnusamy, 2014). Early and extensive investigations in Arabidopsis had provided a plethora of information concerning epigenetic mechanisms in plant growth and development that were then followed by intensive investigation in crop plants like rice, maize, barley, tomato, soybean, both at the locus-specific and genome-wide levels (in depth reviews: Gallusci, Hodgman, Teyssier, & Seymour, 2016; Kapazoglou, Papaefthimiou, & Tsaftaris, 2012; Kapazoglou & Tsaftaris, 2011; Niederhuth & Schmitz, 2017; Tsaftaris, Kapazoglou, & Darzentas, 2012; Van Oosten et al., 2014). DNA methylation is a well-conserved epigenetic mark in eukaryotes that involves the addition of a methyl group on the 5′carbon of the cytosine base to form 5-methylcytosine.
Epigenetics refers to heritable alterations in chromatin architecture that do not involve changes in the underlying DNA sequence but profoundly affect gene expression and impact cellular function. Epigenetic regulation is attained by specific mechanisms involving DNA methylation, histone posttranslational modifications and the action of noncoding (nc) RNAs which lead to open or closed chromatin states associated with gene activation or gene silencing, respectively. Over the past two decades extensive investigations have provided a wealth of information on epigenetic regulation at specific loci both in model and crop plants and the effect it may have on various aspects of plant development such as proper vegetative growth, successful reproduction and viability, effects on yield, and efficiency in coping with stress. In recent years, the rapid progress of high-throughput technologies has led to the unveiling of epigenetic landscapes at genome-wide scale (epigenomes) exemplified by the deciphering of the full methylomes, at single base resolution, of the model plant Arabidopsis and crop plants such as rice and tomato. An increasing number of epigenomes are now being investigated on crops of high economic value. Transgenerational natural or induced epigenetic variation can be a new source of phenotypic diversity especially for species with low genetic variation. The comparison of different epigenomes arising from different genotypes/tissues/cell types/environmental conditions can offer valuable information for the development of biomarkers paving the way to what is nowadays termed plant epibreeding. This review will attempt a comprehensive presentation of the progress in plant epigenetics both at small scale (single locus) and large scale (epigenome-wide) during development and in response to environmental stress, focusing on agronomically important crops and the impact that epigenetics, epigenomics and the new emerging field of epibreeding may have on crop improvement.
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