Detection of DNA methylation changes in micropropagated banana plants using methylation-sensitive amplification polymorphism (MSAP)

Peraza-Echeverría, Santy; Herrera-Valencia, Virginia Aurora; Kay, Andrew-James

doi:10.1016/s0168-9452(01)00421-6

Cited by 113 publications

(60 citation statements)

References 29 publications

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“…These results showed that methylation is present in V. planifolia genome, with 7.45% of the fragments revealed being methylated. This value is in accordance with methylation rates reported in banana (7,5%, (Noyer et al, 2005)), but less than what is revealed in other conventionally propagated plant species such as rice (16.3%, (Xiong et al, 1999)), other bananas (18.4%, (Peraza-Echeverria et al, 2001)), apple (25%, (Xu et al, 2000)) and cotton (32%, (Keyte et al, 2006)). A limited amount of methylation polymorphism (1%) was detected among 'Classique' and 'Mexique' accessions but the methylation patterns revealed were accession specific.…”

Section: Planifolia In Reunion Islandsupporting

confidence: 85%

Biodiversity and Evolution in the Vanilla Genus

Gigant¹,

Bory²,

Grisoni³

et al. 2011

The Dynamical Processes of Biodiversity - Case Studies of Evolution and Spatial Distribution

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Section: Planifolia In Reunion Islandsupporting

confidence: 85%

Biodiversity and Evolution in the Vanilla Genus

Gigant¹,

Bory²,

Grisoni³

et al. 2011

The Dynamical Processes of Biodiversity - Case Studies of Evolution and Spatial Distribution

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“…DNA hypomethylation can produce severe phenotypic assignment as noted in the progeny of ddm1 Arabidopsis mutants (Kakutani et al 1996). Tissue culture induces sequence-specific methylation variation that can be detected by DNA molecular markers such as Met-AFLP (Bednarek et al 2007;Fiuk et al 2010) or MSAP (Peraza-Echeverria et al 2001;Diaz-Martínez et al 2012).…”

Section: Introductionmentioning

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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“…These gradual methylation changes are most likely caused by unequal changes in the methylation state of the different cell types that make up the tissues of the harvested samples (Xiong et al, 1999;Peraza-Echeverria et al, 2001;Cervera et al, 2002). For our objectives, the most interesting loci were the CCGG sites that abruptly changed their methylation from one zone to the next.…”

Section: Maize Maintenance Methyltransferases Are Highly Expressed Inmentioning

confidence: 99%

Differential Methylation during Maize Leaf Growth Targets Developmentally Regulated Genes

et al. 2014

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DNA methylation is an important and widespread epigenetic modification in plant genomes, mediated by DNA methyltransferases (DMTs). DNA methylation is known to play a role in genome protection, regulation of gene expression, and splicing and was previously associated with major developmental reprogramming in plants, such as vernalization and transition to flowering. Here, we show that DNA methylation also controls the growth processes of cell division and cell expansion within a growing organ. The maize (Zea mays) leaf offers a great tool to study growth processes, as the cells progressively move through the spatial gradient encompassing the division zone, transition zone, elongation zone, and mature zone. Opposite to de novo DMTs, the maintenance DMTs were transcriptionally regulated throughout the growth zone of the maize leaf, concomitant with differential CCGG methylation levels in the four zones. Surprisingly, the majority of differentially methylated sequences mapped on or close to gene bodies and not to repeat-rich loci. Moreover, especially the 59 and 39 regions of genes, which show overall low methylation levels, underwent differential methylation in a developmental context. Genes involved in processes such as chromatin remodeling, cell cycle progression, and growth regulation, were differentially methylated. The presence of differential methylation located upstream of the gene anticorrelated with transcript expression, while gene body differential methylation was unrelated to the expression level. These data indicate that DNA methylation is correlated with the decision to exit mitotic cell division and to enter cell expansion, which adds a new epigenetic level to the regulation of growth processes.DNA methylation is the covalent modification of nucleotides in DNA by the addition of a methyl group. In the nuclear genome of higher eukaryotes, 5-methylcytosine is the most important DNA modification (Goll and Bestor, 2005). It is a phenomenon of ancient origin predating plant-animal diversification. However, some differences exist between plant and animal methylome patterning and function, and DNA methylation has been found to be evolutionarily lost in a few species (Feng et al., 2010;Zemach et al., 2010). Eukaryotic DNA methylation is established by DNA methyltransferase (DMT) enzymes that transfer a methyl group from S-adenosyl Met to the fifth carbon of cytosine. These enzymes can largely be subdivided in maintenance and de novo DMTs, depending on whether the recognition site is already methylated or not. Maintenance DMTs conserve the methylation status of symmetrical (palindromic) sites after DNA replication, by recognizing the hemimethylated locus and methylating the newly synthesized strand. In plants, there are two types of maintenance DMTs: DNA METHYLTRANSFERASE (MET) and CHROMOMETHYLASE (CMT). The former methylates CG sites during DNA replication, whereas the latter methylates CHG (H = A, C, or T) sites located in chromatin in which histone 3 is dimethylated on Lys-9 (Goll and Bestor, 2005). De no...

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Detection of DNA methylation changes in micropropagated banana plants using methylation-sensitive amplification polymorphism (MSAP)

Cited by 113 publications

References 29 publications

Biodiversity and Evolution in the Vanilla Genus

Biodiversity and Evolution in the Vanilla Genus

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

Differential Methylation during Maize Leaf Growth Targets Developmentally Regulated Genes

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