Genomic methylation in plant cell cultures: A barrier to the development of commercial long‐term biofactories

Sanchez-Muñoz, Raúl; Moyano, Encarnación; Khojasteh, Abbas; Bonfill, Mercedes; Cusidó, Rosa M.; Palazón, Javier

doi:10.1002/elsc.201900024

Cited by 29 publications

(25 citation statements)

References 47 publications

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“…A specific DNA methylation state reflects the outcome of the dynamic regulation of establishment, maintenance and removal activities: de novo methylation, maintenance of DNA methylation, active DNA methylation and passive DNA methylation [ 113 , 114 ]. These activities are catalyzed by several enzymes that act in a coordinate fashion and are activated by different mechanisms, making the level of DNA methylation in the cells dynamic and variable, and therefore affecting MSAP results analyses.…”

Section: Statistical Methods For Msap Analysis In Plant Conservatimentioning

confidence: 99%

Application of the MSAP Technique to Evaluate Epigenetic Changes in Plant Conservation

González‐Benito

Ibáñez

Pirredda

et al. 2020

IJMS

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Epigenetic variation, and particularly DNA methylation, is involved in plasticity and responses to changes in the environment. Conservation biology studies have focused on the measurement of this variation to establish demographic parameters, diversity levels and population structure to design the appropriate conservation strategies. However, in ex situ conservation approaches, the main objective is to guarantee the characteristics of the conserved material (phenotype and epi-genetic). We review the use of the Methylation Sensitive Amplified Polymorphism (MSAP) technique to detect changes in the DNA methylation patterns of plant material conserved by the main ex situ plant conservation methods: seed banks, in vitro slow growth and cryopreservation. Comparison of DNA methylation patterns before and after conservation is a useful tool to check the fidelity of the regenerated plants, and, at the same time, may be related with other genetic variations that might appear during the conservation process (i.e., somaclonal variation). Analyses of MSAP profiles can be useful in the management of ex situ plant conservation but differs in the approach used in the in situ conservation. Likewise, an easy-to-use methodology is necessary for a rapid interpretation of data, in order to be readily implemented by conservation managers.

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Section: Statistical Methods For Msap Analysis In Plant Conservatimentioning

confidence: 99%

Application of the MSAP Technique to Evaluate Epigenetic Changes in Plant Conservation

González‐Benito

Ibáñez

Pirredda

et al. 2020

IJMS

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“…Local hypo- and hypermethylation were reported before as the result of a tissue culture and appeared at the same genomic location across independent lines [64,65]. Generally increased methylation levels have been reported to render in vitro cultures unsuitable for long term production of secondary metabolites [66]. In the light of these reports and our genomic alteration findings, substantial methylation differences between At7 cells in a suspension culture and hypocotyl cells in a Col-0 plant can be expected.…”

Section: Resultsmentioning

confidence: 97%

“…In-depth investigation of genomic changes under cell cultures conditions including methylation differences could benefit applications like the development of stable transgenic lines from in vitro cell cultures [67]. Using regenerable protoplasts for non-transgenic genome editing could advance crop improvements [56] and plant cells could even be used as efficient biofactories once epigenetic challenges are overcome [66].…”

Section: Resultsmentioning

confidence: 99%

Twenty-Five Years of Propagation in Suspension Cell Culture Results in Substantial Alterations of the Arabidopsis Thaliana Genome

Pucker

Rückert

Stracke

et al. 2019

Genes

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Arabidopsis thaliana is one of the best studied plant model organisms. Besides cultivation in greenhouses, cells of this plant can also be propagated in suspension cell culture. At7 is one such cell line that was established about 25 years ago. Here, we report the sequencing and the analysis of the At7 genome. Large scale duplications and deletions compared to the Columbia-0 (Col-0) reference sequence were detected. The number of deletions exceeds the number of insertions, thus indicating that a haploid genome size reduction is ongoing. Patterns of small sequence variants differ from the ones observed between A. thaliana accessions, e.g., the number of single nucleotide variants matches the number of insertions/deletions. RNA-Seq analysis reveals that disrupted alleles are less frequent in the transcriptome than the native ones.

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“…DNA methylation is an epigenetic mechanism that living organisms use for adaptations. It plays a role in diverse plant physiological processes, such as transcriptional regulation, vernalization, or long-term adaptation to the environment [31]. The exposure to acidy or alkaline substratum very likely determines a cascade of reactions in the hydrangea plants to face these new growth conditions.…”

Section: Discussionmentioning

confidence: 99%

“…Quantitative differences in amplification indicate variation in the global DNA methylation pattern of individuals. MSAPs help to identify the differences in methylated genomic regions within and between populations with different genetic backgrounds, as well as in plants that were grown under different environmental conditions [30,31]. The advantages of this technique are that it is not necessary to previously know the nucleotide sequence, it has a high level of reliability, and it is easily reproducible and highly polymorphic [32].…”

mentioning

confidence: 99%

Hydrangea DNA Methylation Caused by pH Substrate Changes to Modify Sepal Colour is Detected by MSAP and ISSR Markers

et al. 2019

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The hydrangea (Hydrangea macrophylla (Thunb). Ser.) is an ornamental species with great market potential. It is known for its ability to change the colour of its inflorescence, according to the pH of the culture substrate. The molecular mechanisms that underlie these changes are still unclear. It is known that epigenetic mechanisms, such as DNA methylation, play an important role in genetic expression, so they could be responsible for this phenomenon in hydrangea. In the present study, the molecular markers ISSR (Inter Simple Sequence Repeat) and MSAP (Methyl-Sensitive Amplification Polymorphism) were used to detect molecular changes in the genome of hydrangea plants that were cultivated under different pH levels to modify the colour of the sepals. The results showed a correspondence between the methylation signal measured with MSAP and amplification ISSR patterns when compared before and after the modification of pH culture substrates. These results suggest that DNA methylation might be involved as a molecular mechanism underlying the colour change of hydrangea sepals in response to a differential pH in the substrate. In addition, the results pave the way to study the relationship between DNA methylation and ISSR marker profiles.Agronomy 2019, 9, 871 2 of 11 largely known in the flower field, although the molecular mechanisms that underlie these changes are still not clear [9].Most of the flowering plants accumulate pigments in the vacuole, which are predominantly secondary metabolites of the flavonoids pathway. The most widely distributed floral pigment are the anthocyanins, which are big polar molecules that are transported to the vacuole for proper biological functioning [10][11][12]. Biosynthetic and regulatory genes mediate the biosynthesis of the almost 20 different types of anthocyanin [10,[13][14][15]. The variety of colours from blue to purple and red in hydrangea sepals are just due to the anthocyanin delphinidin 3-glucoside in combination with other co-pigments quinic acid esters, such as: chlorogenic acid, neochlorogenic acid, and 5-O-p-coumaroyl quinic acid, and ion Al 3+ . The composition analysis of protoplast extracts that were derived from blue and red sepals showed that the molar ratios of neochlorogenic acid, 5-O-p-coumaroylquinic, and Al 3+ to delphinidin 3-Oglucoside were much higher in the blue cells than in the red cells [12,[16][17][18][19][20]. Aluminum (Al) is soluble in acid soil (below pH 5.0) as a toxic form, Al3+, considered to be a limiting factor for many crops production. The primary symptom is the inhibition of root growth. The plants have developed different strategies for developing Al tolerance, like the secretion of organic anions from root tips or Al protein transporters [21]. Different Al transporter have already been identified and characterized in hydrangea: HmVALT and HmPALT1, both member of the aquaporin family (only the last only expressed in the sepals) or HmPALT2, an anion permease, whose transcript was expressed in all tissues of hydrangea plants [22,23]. In additi...

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Genomic methylation in plant cell cultures: A barrier to the development of commercial long‐term biofactories

Cited by 29 publications

References 47 publications

Application of the MSAP Technique to Evaluate Epigenetic Changes in Plant Conservation

Application of the MSAP Technique to Evaluate Epigenetic Changes in Plant Conservation

Twenty-Five Years of Propagation in Suspension Cell Culture Results in Substantial Alterations of the Arabidopsis Thaliana Genome

Hydrangea DNA Methylation Caused by pH Substrate Changes to Modify Sepal Colour is Detected by MSAP and ISSR Markers

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