Crop Epigenomics: Identifying, Unlocking, and Harnessing Cryptic Variation in Crop Genomes

Ji, Lexiang; Neumann, Drexel A.; Schmitz, Robert J.

doi:10.1016/j.molp.2015.01.021

Cited by 46 publications

(29 citation statements)

References 99 publications

(192 reference statements)

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“…Extensive experimental work has shown that changes in DNA methylation are associated with plant phenotypes [5–20], genome stability [21–25], polyploidization [26], recombination [27–31], and heterosis [32–40], and that such changes actively mediate environmental signaling [41–43], pathogen responses [44–46], and priming [47–49]. For these reasons, DNA methylation has emerged as a potentially important factor in plant evolution [50–53] and as a possible molecular target for the improvement of commercial crops [54, 55]. …”

Section: Introductionmentioning

confidence: 99%

Methylome evolution in plants

et al. 2016

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Despite major progress in dissecting the molecular pathways that control DNA methylation patterns in plants, little is known about the mechanisms that shape plant methylomes over evolutionary time. Drawing on recent intra- and interspecific epigenomic studies, we show that methylome evolution over long timescales is largely a byproduct of genomic changes. By contrast, methylome evolution over short timescales appears to be driven mainly by spontaneous epimutational events. We argue that novel methods based on analyses of the methylation site frequency spectrum (mSFS) of natural populations can provide deeper insights into the evolutionary forces that act at each timescale.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1127-5) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Methylome evolution in plants

et al. 2016

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“…As a consequence, the spontaneous formation of epialleles can be faithfully propagated between generations and there are multiple documented cases of epigenetic inheritance in plants [16–19]. This not only makes plants ideal for studying epigenetics, but also opens the possibility for utilizing or inducing epigenetic differences for purposes of plant breeding and improvement [20, 21]. Much of what we now know about DNA methylation in plants comes from the study of one species, Arabidopsis thaliana , but this is rapidly expanding to other species (23–30).…”

Section: Introductionmentioning

confidence: 99%

Putting DNA methylation in context: from genomes to gene expression in plants

Niederhuth

Schmitz

2017

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanism

138

114

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Plant DNA methylation is its own language, interpreted by the cell to maintain silencing of transposons, facilitate chromatin structure, and to ensure proper expression of some genes. Just as in any language, context is important. Rather than being a simple “on-off switch”, DNA methylation has a range of “meanings” dependent upon the underlying sequence and its location in the genome. Differences in the sequence context of individual sites are established, maintained, and interpreted by differing molecular pathways. Varying patterns of methylation within genes and surrounding sequences are associated with a continuous range of expression differences, from silencing to constitutive expression. These often-subtle differences have been pieced together from years of effort, but have taken off with the advent of methods for assessing methylation across entire genomes. Recognizing these patterns and identifying underlying causes is essential for understanding the function of DNA methylation and its systems-wide contribution to a range of processes in plant genomes.

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“…This notion has been extended to numerous considerations of the formation of plant stress memory, in which a state of altered stress responsivity is mitotically or meiotically transmissible (Bruce et al, 2007;Hauser et al, 2011b;Probst and Mittelsten Scheid, 2015;Crisp et al, 2016;van Loon, 2016). There is much interest in plant stress memory, including the underlying molecular mechanism(s) and its potential to impact crop yields, particularly in harsh and variable environments (Springer, 2013;Ji et al, 2015;Mickelbart et al, 2015).…”

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confidence: 99%

“…This potential has led to many investigations of transgenerational stress memory mediated by environmentally induced epi-alleles, which could open exciting possibilities for crop (epi)genomics (Hauser et al, 2011b;Springer, 2013;Ji et al, 2015). However, bona fide examples of transgenerational methylation changes leading to substantially altered plant behavior remain a rare observation (Pecinka et al, 2009;Becker et al, 2011;Jiang et al, 2014;Seymour et al, 2014;Crisp et al, 2016), with the majority of DNA methylome variation attributable to underlying genetic differences rather than being truly epigenetic (Eichten et al, 2013Schmitz et al, 2013;Li et al, 2014;Seymour et al, 2014;Dubin et al, 2015;Hagmann et al, 2015).…”

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confidence: 99%

The Arabidopsis DNA Methylome Is Stable under Transgenerational Drought Stress

et al. 2017

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Improving the responsiveness, acclimation, and memory of plants to abiotic stress holds substantive potential for improving agriculture. An unresolved question is the involvement of chromatin marks in the memory of agriculturally relevant stresses. Such potential has spurred numerous investigations yielding both promising and conflicting results. Consequently, it remains unclear to what extent robust stress-induced DNA methylation variation can underpin stress memory. Using a slow-onset water deprivation treatment in Arabidopsis (Arabidopsis thaliana), we investigated the malleability of the DNA methylome to drought stress within a generation and under repeated drought stress over five successive generations. While drought-associated epialleles in the methylome were detected within a generation, they did not correlate with drought-responsive gene expression. Six traits were analyzed for transgenerational stress memory, and the descendants of drought-stressed lineages showed one case of memory in the form of increased seed dormancy, and that persisted one generation removed from stress. With respect to transgenerational drought stress, there were negligible conserved differentially methylated regions in drought-exposed lineages compared with unstressed lineages. Instead, the majority of observed variation was tied to stochastic or preexisting differences in the epigenome occurring at repetitive regions of the Arabidopsis genome. Furthermore, the experience of repeated drought stress was not observed to influence transgenerational epi-allele accumulation. Our findings demonstrate that, while transgenerational memory is observed in one of six traits examined, they are not associated with causative changes in the DNA methylome, which appears relatively impervious to drought stress.

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Crop Epigenomics: Identifying, Unlocking, and Harnessing Cryptic Variation in Crop Genomes

Cited by 46 publications

References 99 publications

Methylome evolution in plants

Methylome evolution in plants

Putting DNA methylation in context: from genomes to gene expression in plants

The Arabidopsis DNA Methylome Is Stable under Transgenerational Drought Stress

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