Genetic and DNA Methylation Changes in Cotton (Gossypium) Genotypes and Tissues

Osabe, Kenji; Clement, J.D.; Bedon, Frank; Pettolino, Filomena; Ziolkowski, Lisa; Llewellyn, Danny; Finnegan, E. Jean; Wilson, Iain W.

doi:10.1371/journal.pone.0086049

Cited by 60 publications

(48 citation statements)

References 84 publications

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“…More recently, Whole Genome Bisulfite Sequencing in three Brassicaceae species found lower methylation levels in roots than shoots, with changes between the two tissues being more frequent at repetitive sites and transposons, although across-species variation in cytosine methylation patterns was larger [3]. Here, we found that, in E. cicutarium, methylation was also lower in roots than in above ground leaves (see [47,50] for similar results in chicory and cotton, respectively). Scarcity of studies, disparity of the analytical methods that were used to quantify cytosine methylation, and some contrasting results between the few species analyzed in more detail (see e.g., [51]) precludes us to ascertain whether, apart from a reduced methylation level in endosperm, methylation varies among plant tissues in some definite way [52].…”

Section: Discussionsupporting

confidence: 75%

“…Scarcity of studies, disparity of the analytical methods that were used to quantify cytosine methylation, and some contrasting results between the few species analyzed in more detail (see e.g., [51]) precludes us to ascertain whether, apart from a reduced methylation level in endosperm, methylation varies among plant tissues in some definite way [52]. The high-performance liquid chromatography (HPLC) method applied here could help to provide precise and genome reference-free global measure of DNA cytosine methylation, useful as a molecular phenotype for tissue-specific comparisons among and within species (see e.g., [47,50]) that could improve our current understanding of epigenetic regulation during plant development in a broader range of plant species.…”

Section: Discussionmentioning

confidence: 99%

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Tissue-Specific Response to Experimental Demethylation at Seed Germination in the Non-Model Herb Erodium cicutarium

et al. 2017

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Experimental alteration of DNA methylation is a suitable tool to infer the relationship between phenotypic and epigenetic variation in plants. A detailed analysis of the genome-wide effect of demethylating agents, such as 5-azacytidine (5azaC), and zebularine is only available for the model species Arabidopsis thaliana, which suggests that 5azaC may have a slightly larger effect. In this study, global methylation estimates obtained by high-performance liquid chromatography (HPLC) analyses were conducted to investigate the impact of 5azaC treatment on leaf and root tissue in Erodium cicutarium (Geraniaceae), which is an annual herb native to Mediterranean Europe that is currently naturalized in all continents, sometimes becoming invasive. We used seeds collected from two natural populations in SE Spain. Root tissue of the second generation (F2) greenhouse-grown seedlings had a significantly lower global cytosine methylation content than leaf tissue (13.0 vs. 17.7% of all cytosines). Leaf tissue consistently decreased methylation after treatment, but the response of root tissue varied according to seed provenance, suggesting that genetic background can mediate the response to experimental demethylation. We also found that both leaf number and leaf length were reduced in treated seedlings supporting a consistent phenotypic effect of the treatment regardless of seedling provenance. These findings suggest that, although the consequences of experimental demethylation may be tissue-and background-specific, this method is effective in altering early seedling development, and can thus be useful in ecological epigenetic studies that are aiming to investigate the links between epigenetic and phenotypic variation in non-model plant species.

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Section: Discussionsupporting

confidence: 75%

Section: Discussionmentioning

confidence: 99%

Tissue-Specific Response to Experimental Demethylation at Seed Germination in the Non-Model Herb Erodium cicutarium

et al. 2017

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“…Including a third schizomer ( Bsi SI) with the same cleavage site but insensible to any methylation and/or the addition of the combined digestion of the two isoschizomers ( Hpa II + Msp I) may help to reduce uncertainty of some ambiguous results and improve reliability of MSAP interpretations if subsequent increased costs are affordable (Fulneček & Kovařík ; Osabe et al . ).…”

Section: Discussionmentioning

confidence: 97%

MSAP markers and global cytosine methylation in plants: a literature survey and comparative analysis for a wild‐growing species

Alonso

Pérez

Bazaga

et al. 2015

Molecular Ecology Resources

105

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Methylation of DNA cytosines affects whether transposons are silenced and genes are expressed, and is a major epigenetic mechanism whereby plants respond to environmental change. Analyses of methylation-sensitive amplification polymorphism (MS-AFLP or MSAP) have been often used to assess methyl-cytosine changes in response to stress treatments and, more recently, in ecological studies of wild plant populations. MSAP technique does not require a sequenced reference genome and provides many anonymous loci randomly distributed over the genome for which the methylation status can be ascertained. Scoring of MSAP data, however, is not straightforward, and efforts are still required to standardize this step to make use of the potential to distinguish between methylation at different nucleotide contexts. Furthermore, it is not known how accurately MSAP infers genome-wide cytosine methylation levels in plants. Here, we analyse the relationship between MSAP results and the percentage of global cytosine methylation in genomic DNA obtained by HPLC analysis. A screening of literature revealed that methylation of cytosines at cleavage sites assayed by MSAP was greater than genome-wide estimates obtained by HPLC, and percentages of methylation at different nucleotide contexts varied within and across species. Concurrent HPLC and MSAP analyses of DNA from 200 individuals of the perennial herb Helleborus foetidus confirmed that methyl-cytosine was more frequent in CCGG contexts than in the genome as a whole. In this species, global methylation was unrelated to methylation at the inner CG site. We suggest that global HPLC and context-specific MSAP methylation estimates provide complementary information whose combination can improve our current understanding of methylation-based epigenetic processes in nonmodel plants.

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“…2008; Vanyushin and Ashapkin 2011; Osabe et al. 2014). Irrespective of mechanisms, our results emphasize the importance of adopting scoring approaches in future MSAP‐based ecological epigenetics studies that allow to differentiate spatial structure, variability levels, transgenerational constancy and phenotypic correlates of cytosine methylation marks in different genomic contexts.…”

Section: Discussionmentioning

confidence: 99%

Genetic and epigenetic divergence between disturbed and undisturbed subpopulations of a Mediterranean shrub: a 20‐year field experiment

Herrera

Bazaga

2016

Ecology and Evolution

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Little is known on the potential of ecological disturbance to cause genetic and epigenetic changes in plant populations. We take advantage of a long‐term field experiment initiated in 1986 to study the demography of the shrub Lavandula latifolia, and compare genetic and epigenetic characteristics of plants in two adjacent subplots, one experimentally disturbed and one left undisturbed, 20 years after disturbance. Experimental setup was comparable to an unreplicated ‘Before‐After‐Control‐Impact’ (BACI) design where a single pair of perturbed and control areas were compared. When sampled in 2005, plants in the two subplots had roughly similar ages, but they had established in contrasting environments: dense conspecific population (‘Undisturbed’ subpopulation) versus open area with all conspecifics removed (‘Disturbed’ subpopulation). Plants were characterized genetically and epigenetically using amplified fragment length polymorphism (AFLP) and two classes of methylation‐sensitive AFLP (MSAP) markers. Subpopulations were similar in genetic diversity but differed in epigenetic diversity and multilocus genetic and epigenetic characteristics. Epigenetic divergence between subpopulations was statistically unrelated to genetic divergence. Bayesian clustering revealed an abrupt linear boundary between subpopulations closely coincident with the arbitrary demarcation line between subplots drawn 20 years back, which supports that genetic and epigenetic divergence between subpopulations was caused by artificial disturbance. There was significant fine‐scale spatial structuring of MSAP markers in both subpopulations, which in the Undisturbed one was indistinguishable from that of AFLP markers. Genetic differences between subpopulations could be explained by divergent selection alone, while the concerted action of divergent selection and disturbance‐driven appearance of new methylation variants in the Disturbed subpopulation is proposed to explain epigenetic differences. This study provides the first empirical evidence to date suggesting that relatively mild disturbances could leave genetic and epigenetic signatures on the next adult generation of long‐lived plants.

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Genetic and DNA Methylation Changes in Cotton (Gossypium) Genotypes and Tissues

Cited by 60 publications

References 84 publications

Tissue-Specific Response to Experimental Demethylation at Seed Germination in the Non-Model Herb Erodium cicutarium

Tissue-Specific Response to Experimental Demethylation at Seed Germination in the Non-Model Herb Erodium cicutarium

MSAP markers and global cytosine methylation in plants: a literature survey and comparative analysis for a wild‐growing species

Genetic and epigenetic divergence between disturbed and undisturbed subpopulations of a Mediterranean shrub: a 20‐year field experiment

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