Molecular Mechanisms of Epigenetic Variation in Plants

Fujimoto, Ryo; Sasaki, Taku; Ishikawa, Ryo; Osabe, Kenji; Kawanabe, Takahiro; Dennis, Elizabeth S.

doi:10.3390/ijms13089900

Cited by 57 publications

(37 citation statements)

References 112 publications

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“…; Fujimoto et al . ). Together with changes of DNA‐associated molecules, such as modifications of DNA‐ and histone proteins or changes of chromatin structure and small noncoding RNAs (Chatterjee & Vinson ), DNA methylation is part of a complex interacting epigenetic network that, without changing the underlying genetic code, modulates and controls gene expression.…”

Section: Introductionmentioning

confidence: 97%

“…For model species, genome‐wide profiles of DNA methylation are available at high resolution using microarray technologies and next generation sequencing of bisulphite converted DNA (Bock ; Fujimoto et al . ). However, due to high costs and resource intensities, these methods usually are not suited for nonmodel species or for studies at the population level.…”

Section: Introductionmentioning

confidence: 97%

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Scoring and analysis of methylation‐sensitive amplification polymorphisms for epigenetic population studies

Schulz

Eckstein

Durka

2013

Molecular Ecology Resources

142

252

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DNA methylation is an important, heritable epigenetic modification in most eukaryotic organisms that is connected with numerous biological processes. To study the impact of natural epigenetic variation in an ecological or evolutionary context, epigenetic studies are increasingly using methylation-sensitive amplification polymorphism (MSAP) for surveys at the population or species level. However, no consensus exists on how to interpret and score the multistate information obtained from the MSAP banding patterns. Here, we review the previously used scoring approaches for population epigenetic studies and develop new alternatives. To assess effects of the different approaches on parameters of epigenetic diversity and differentiation, we applied eight scoring schemes to a case study of three populations of the plant species Viola elatior. For a total number of 168 detected polymorphic MSAP fragments, the number of ultimately scored polymorphic epiloci ranged between 78 and 286 depending on the particular scoring scheme. Both, estimates of epigenetic diversity and differentiation varied strongly between scoring approaches. However, linear regression and PCoA revealed qualitatively similar patterns, suggesting that the scoring approaches are largely consistent. For single-locus analyses of MSAP data, for example the search for loci under selection, we advocate a new scoring approach that separately takes into account different methylation types and thus seems appropriate for drawing more detailed conclusions in ecological or evolutionary contexts. An R script (MSAP_score.r) for scoring and basic data analysis is provided.

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Section: Introductionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 97%

Scoring and analysis of methylation‐sensitive amplification polymorphisms for epigenetic population studies

Schulz

Eckstein

Durka

2013

Molecular Ecology Resources

142

252

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“…However, it is becoming increasingly accepted that epigenetic polymorphism affects quantitative trait variation [9–11]. Epigenetic variation results from the same sequence allele possessing a different chromatin organization, modifying its propensity for expression or chromosomal interactions [12, 13]. Epigenetic variation has the potential to alter the magnitude of gene expression whereas genetic polymorphisms result from differences in the primary DNA sequence resulting in functional allelic variants.…”

Section: Introductionmentioning

confidence: 99%

Quantitative trait variation is revealed in a novel hypomethylated population of woodland strawberry (Fragaria vesca)

Tanino

Horner

et al. 2016

BMC Plant Biol

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BackgroundPhenotypic variation is determined by a combination of genotype, environment and their interactions. The realization that allelic diversity can be both genetic and epigenetic allows the environmental component to be further separated. Partitioning phenotypic variation observed among inbred lines with an altered epigenome can allow the epigenetic component controlling quantitative traits to be estimated. To assess the contribution of epialleles on phenotypic variation and determine the fidelity with which epialleles are inherited, we have developed a novel hypomethylated population of strawberry (2n = 2x = 14) using 5-azacytidine from which individuals with altered phenotypes can be identified, selected and characterized.ResultsThe hypomethylated population was generated using an inbred strawberry population in the F. vesca ssp. vesca accession Hawaii 4. Analysis of whole genome sequence data from control and hypomethylated lines indicate that 5-azacytidine exposure does not increase SNP above background levels. The populations contained only Hawaii 4 alleles, removing introgression of alternate F. vesca alleles as a potential source of variation. Although genome sequencing and genetic marker data are unable to rule out 5-azacytidine induced chromosomal rearrangements as a potential source of the trait variation observed, none were detected in our survey. Quantitative trait variation focusing on flowering time and rosette diameter was scored in control and treated populations where expanded levels of variation were observed among the hypomethylated lines. Methylation sensitive molecular markers indicated that 5-azacytidine induced alterations in DNA methylation patterns and inheritance of methylation patterns were confirmed by bisulfite sequencing of targeted regions. It is possible that methylation polymorphisms might underlie or have induced genetic changes underlying the observable differences in quantitative phenotypes.ConclusionsThis population developed in a uniform genetic background provides a resource for the discovery of new variation controlling quantitative traits. Genome sequence analysis indicates that 5-azacytidine did not induce point mutations and the induced variation is largely restricted to DNA methylation. Using this resource, we have identified new variation and demonstrated the inheritance of both variant trait and methylation patterns. Although direct associations remain to be determined, these data suggest epigenetic variation might be subject to selection.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0936-8) contains supplementary material, which is available to authorized users.

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“…Epigenetic regulation is defined as changes in gene activities that are inherited through cell divisions without alteration in the DNA sequence. Epigenetic regulation is crucial for the development and adaptation of plants to the changing environment [30,31]. DNA methylation and histone modification are the best examples of epigenetic modifications.…”

Section: Epigenetic Regulation Of Flc Genementioning

confidence: 99%

“…Histone lysine residues can be mono-, di-, or tri-methylated, and each methylation state is associated with different functions [32]. In plants, histone deacetylation, H3K9me2, and H3K27me3 are associated with gene repression, and histone acetylation, H3K4me3, and H3K36me3 are associated with gene activation [22,31,33,34].…”

Section: Epigenetic Regulation Of Flc Genementioning

confidence: 99%

Genetic and Epigenetic Regulation of Vernalization in Brassicaceae

Akter¹,

Nishida²,

Takada³

et al. 2018

Brassica Germplasm - Characterization, Breeding and Utilization

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A wide variation of morphological traits exists in Brassica rapa L. and Brassica oleracea L., and cultivated vegetable varieties of these species are consumed worldwide. Flowering time is an important agronomic trait in these species and varies among varieties or cultivars. Especially, leafy vegetable species need a high bolting resistance. Isolation of FLOWERING LOCUS C (FLC), one of the key genes involved in vernalization, has now provided an insight into the molecular mechanism involved in the regulation of flowering time, including the role of histone modification. In the model plant Arabidopsis thaliana, FLC plays an important role in modulating flowering time. The response to vernalization causes an increase in histone H3 lysine 27 tri-methylation (H3K27me3) that leads to reduced expression of the FLC gene. B. rapa and B. oleracea both contain several paralogs of FLC at syntenic regions identified as major flowering time and vernalization response quantitative trait loci (QTL). We introduce the recent research, not only in A. thaliana, but also in the genus Brassica from a genetic and epigenetic view point.

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Molecular Mechanisms of Epigenetic Variation in Plants

Cited by 57 publications

References 112 publications

Scoring and analysis of methylation‐sensitive amplification polymorphisms for epigenetic population studies

Scoring and analysis of methylation‐sensitive amplification polymorphisms for epigenetic population studies

Quantitative trait variation is revealed in a novel hypomethylated population of woodland strawberry (Fragaria vesca)

Genetic and Epigenetic Regulation of Vernalization in Brassicaceae

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