Variation in DNA methylation patterns of grapevine somaclones (Vitis vinifera L.)

Schellenbaum, Paul; Mohler, Volker; Wenzel, G.; Walter, Bernard

doi:10.1186/1471-2229-8-78

Cited by 109 publications

(85 citation statements)

References 37 publications

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“…Similarly, low levels of methylation variation were found in freesia somatic seedlings derived from short-term cultures (Gao et al 2010) and pea long-term multiple shoot cultures (Smýkal et al 2007). Many studies with methylation-sensitive molecular markers that reported a high level of epigenetic variation reported no effect on phenotype or morpho-agronomic traits (Bednarek et al 2007;Li et al 2007;Schellenbaum et al 2008;Fiuk et al 2010). Methylation changes contribute poorly to global estimations when they do not occur at high frequencies (Smulders and Klerk 2011).…”

Section: Discussionmentioning

confidence: 99%

Assessment of genetic and epigenetic changes during cell culture ageing and relations with somaclonal variation in Coffea arabica

Landey

Cenci²,

Guyot

et al. 2015

Plant Cell Tiss Organ Cult

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Long-term cell cultures were used in coffee to study the cytological, genetic and epigenetic changes occurring during cell culture ageing. The objective was to identify the mechanisms associated with somaclonal variation (SV). Three embryogenic cell lines were established in Coffea arabica (2n = 4x = 44) and somatic seedlings were regenerated after 4, 11 and 27 months. Phenotyping and AFLP, MSAP, SSAP molecular markers were performed on 199 and 124 plants, respectively. SV were only observed from the 11 and 27-month-old cultures, affecting 30 and 94 % of regenerated plants, respectively. Chromosome counts performed on 15 plants showed that normal plants systematically displayed normal chromosome numbers and that, conversely, aneuploidy (monosomy) was systematically found in variants. The allopolyploid structure of C. arabica allowed aneuploid cells to survive and regenerate viable plants. No polymorphic fragments were observed between the AFLP and SSAP electrophoretic profiles of mother plants and those of the in vitro progeny. Methylation polymorphism was low and ranged between 0.087 and 0.149 % irrespective of the culture age. The number of methylation changes per plant-normal or variant-was limited and ranged from 0 (55-80 % of the plants) to 4. The three cell lines showed similar SV rate increases during cell culture ageing and produced plants with similar molecular patterns indicating a non random process. The results showed that cell culture ageing is highly mutagenic in coffee and chromosomal rearrangements are directly linked to SV. Conversely, the analysis of methylation and transposable elements changes did not reveal any relation between the epigenetic patterns and SV.

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Section: Discussionmentioning

confidence: 99%

Assessment of genetic and epigenetic changes during cell culture ageing and relations with somaclonal variation in Coffea arabica

Landey

Cenci²,

Guyot

et al. 2015

Plant Cell Tiss Organ Cult

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“…Somaclonal variations arise from multiple genetic causes, including chromosome number changes (polyploidy and aneuploidy), chromosomal structural rearrangements, gene mutations, gene copy number changes, and activation and transposition of transposable elements (Lee and Phillips 1987;Lee 1988;Bairu et al 2011). Somatic variation could also result from epigenetic changes or pre-existing mutations in the explants used in cell and tissue culture (Alatzas and Foundouli 2006;Schellenbaum et al 2008;Bairu et al 2011).…”

Section: Electronic Supplementary Materialsmentioning

confidence: 99%

Somaclonal variation in ‘Red Flash’ caladium: morphological, cytological and molecular characterization

Cao

Sui

Cai

et al. 2016

Plant Cell Tiss Organ Cult

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Somaclonal variation is a major concern to many applications of plant cell and tissue culture techniques, yet it could be a useful source of variation for plant genetic improvement. High frequencies of somaclonal variants were reported in caladium, but little was known about changes in caladium somaclonal variants at the cellular and molecular levels. Twenty-four somaclonal variants were identified among 'Red Flash' caladium plants regenerated from two types of leaf explants and on two media containing different auxins. Results showed that the type of leaf explants and auxin affected the occurrence of somaclonal variants in 'Red Flash'. The highest percentage of variants (25.0 %) was observed among plants regenerated from mature leaf explants cultured on the media containing 2,4-dichlorophenoxyacetic acid. These somaclonal variants exhibited considerable changes in leaf shape, coloring of the main veins, spots, margins, and leaf size, and could be separated into 10 somaclonal variant groups. Twelve variants contained 1.1-5.4 % less nuclear DNA and appeared to have lost one chromosome. Two variants contained 5.4-9.2 % less nuclear DNA and appeared to have lost two chromosomes. One variant contained 95.0 % more nuclear DNA and 2n = 58 chromosomes. Two SSR markers (CaM1 and CaM103) revealed DNA banding pattern changes in nine variants, including allele loss in eight variants and allele size change in one variant. These results suggested that several cytological and/or molecular causes were involved in the somaclonal variation in 'Red Flash' and chromosome number change was a frequent cause leading to a high frequency of aneuploids and marker allele loss. The CaM1-carrying chromosome seemed to be unstable and prone to loss during tissue culture.

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“…The variation in gene expression is believed to be mediated by epigenetic mechanisms involving methylation of DNA and chromatin modifications. Shifts from parental methylation states have been observed in many cell cultures and regenerated plants at both global and local levels (Kaeppler and Phillips, 1993;Smulders et al, 1995;Olhoft and Philips, 1999;Jaligot et al, 2000;Kubis et al, 2003;Schellenbaum et al, 2008). Alleviation of silencing of ribosomal genes (Komarova et al, 2004;Koukalova et al, 2005), increased transposon activity (Hirochika, 1993;Grandbastien, 1998), and activation of cell cycle-controlling genes (Williams et al, 2003) were reported in studies linking changes in DNA methylation with changes in expression patterns.…”

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confidence: 99%

Cell Culture-Induced Gradual and Frequent Epigenetic Reprogramming of Invertedly Repeated Tobacco Transgene Epialleles

et al. 2009

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Using a two-component transgene system involving two epiallelic variants of the invertedly repeated transgenes in locus 1 (Lo1) and a homologous single-copy transgene locus 2 (Lo2), we have studied the stability of the methylation patterns and trans-silencing interactions in cell culture and regenerated tobacco (Nicotiana tabacum) plants. The posttranscriptionally silenced (PTGS) epiallele of the Lo1 trans-silences and trans-methylates the target Lo2 in a hybrid (Lo1/Lo2 line), while its transcriptionally silenced variant (Lo1E) does not. This pattern was stable over several generations in plants. However, in early Lo1E/Lo2 callus, decreased transgene expression and partial loss of Lo1E promoter methylation compared with leaf tissue in the parental plant were observed. Analysis of small RNA species and coding region methylation suggested that the transgenes were silenced by a PTGS mechanism. The Lo1/Lo2 line remained silenced, but the nonmethylated Lo1 promoter acquired partial methylation in later callus stages. These data indicate that a cell culture process has brought both epialleles to a similar epigenetic ground. Bisulfite sequencing of the 35S promoter within the Lo1 silencer revealed molecules with no, intermediate, and high levels of methylation, demonstrating, to our knowledge for the first time, cell-to-cell methylation diversity of callus. Regenerated plants showed high interindividual but low intraindividual epigenetic variability, indicating that the callusinduced epiallelic variants were transmitted to plants and became fixed. We propose that epigenetic changes associated with dedifferentiation might influence regulatory pathways mediated by trans-PTGS processes.

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Variation in DNA methylation patterns of grapevine somaclones (Vitis vinifera L.)

Cited by 109 publications

References 37 publications

Assessment of genetic and epigenetic changes during cell culture ageing and relations with somaclonal variation in Coffea arabica

Assessment of genetic and epigenetic changes during cell culture ageing and relations with somaclonal variation in Coffea arabica

Somaclonal variation in ‘Red Flash’ caladium: morphological, cytological and molecular characterization

Cell Culture-Induced Gradual and Frequent Epigenetic Reprogramming of Invertedly Repeated Tobacco Transgene Epialleles

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