A relative quantitative Methylation-Sensitive Amplified Polymorphism (MSAP) method for the analysis of abiotic stress

Bednarek, Piotr Tomasz; Orłowska, Renata; Niedziela, Agnieszka

doi:10.1186/s12870-017-1028-0

Cited by 42 publications

(48 citation statements)

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“…Methylation-sensitive amplified polymorphism (MSAP) (Baranek et al 2016) uses HpaII and MspI endonuclease to study methylation changes within DNA sequences at the restriction sites. This approach was recently extended, enabling quantification of only the site DNA methylation alterations (Bednarek et al 2017). Methylation amplified fragment length polymorphism (metAFLP) enables quantitative analysis of both sequence and DNA methylation changes affecting Acc65I-KpnI restriction sites (Bednarek et al 2007;Chwedorzewska and Bednarek 2012;Machczyńska et al 2014b;Wódkiewicz et al 2018).…”

Section: Introductionmentioning

confidence: 99%

Precise evaluation of tissue culture-induced variation during optimisation of in vitro regeneration regime in barley

Orłowska

Bednarek

2020

Plant Mol Biol

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Key message The Taguchi method and metAFLP analysis were used to optimise barley regenerants towards maximum andminimum levels of tissue culture-induced variation. The subtle effects of symmetric and asymmetric methylationchanges in regenerants were identified. Abstract Plant tissue cultures (PTCs) provide researchers with unique materials that accelerate the development of new breeding cultivars and facilitate studies on off-type regenerants. The emerging variability of regenerants derived from PTCs may have both genetic and epigenetic origins, and may be desirable or degrade the value of regenerated plants. Thus, it is crucial to determine how the PTC variation level can be controlled. The easiest way to manipulate total tissue cultureinduced variation (TTCIV) is to utilise appropriate stress factors and suitable medium components. This study describes the optimisation of in vitro tissue culture-induced variation in plant regenerants derived from barley anther culture, and maximizes and minimizes regenerant variation compared with the source explants. The approach relied on methylation amplified fragment length polymorphism (metAFLP)-derived TTCIV characteristics, which were evaluated in regenerants derived under distinct tissue culture conditions and analysed via Taguchi statistics. The factors that may trigger TTCIV included CuSO 4 , AgNO 3 and the total time spent on the induction medium. The donor plants prepared for regeneration purposes had 5.75% and 2.01% polymorphic metAFLP loci with methylation and sequence changes, respectively. The level of TTCIV (as the sum of all metAFLP characteristics analyzed) identified in optimisation and verification experiments reached 7.51 and 10.46%, respectively. In the trial designed to produce a minimum number of differences between donor and regenerant plants, CuSO 4 and AgNO 3 were more crucial than time, which was not a significant factor. In the trial designed to produce a maximum number of differences between donor and regenerant plants, all factors had comparable impact on variation. The Taguchi method reduced the time required for experimental trials compared with a grid method and suggested that medium modifications were required to control regenerant variation. Finally, the effects of symmetric and asymmetric methylation changes on regenerants were identified using novel aspects of the metAFLP method developed for this analysis.

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Section: Introductionmentioning

confidence: 99%

Precise evaluation of tissue culture-induced variation during optimisation of in vitro regeneration regime in barley

Orłowska

Bednarek

2020

Plant Mol Biol

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“…Under drought treatment, a decrease of DNA methylation was observed in leaf tissues of two faba bean genotypes (Abid et al, 2017). Moreover, Bednarek et al (2017) observed an elevated demethylation in both non-tolerant and tolerant plants, with de novo methylation occurring less frequently than demethylation under Aluminum stress in triticale lines.…”

Section: Introductionmentioning

confidence: 88%

“…The MSAP profiles showing reproducible results between replicates were transformed into a binary matrix, with 1 as a presence of band and 0 the absence of band from either EcoRI/MspI or EcoRI/HpaII digestion and analyzed according to the protocol developed by Bednarek et al (2017). In general, these fragments could be divided into four types representing four types of DNA methylation status of the restriction sites (5′-CCGG-3′):…”

Section: Data Scoring and Analysis Of Msap Profilesmentioning

confidence: 99%

“…The methylation-sensitive amplified polymorphism (MSAP) technique developed by Reyna-López et al (1997) is an adaptation of amplified fragment length polymorphism analysis and has proven to be a powerful tool for analyzing DNA methylation. The MSAP technique has been applied to study CpG methylation in the genome of plants, somaclonal epigenetic variation, cytosine methylation during various developmental stages and resistance to biotic and abiotic stresses (Ashikawa, 2001;Matthes et al, 2001;Portis et al, 2004;Sha et al, 2005, Ruiz-Garcia et al, 2005Tang et al, 2014;Zhang et al, 2015;Bednarek et al, 2017;Abid et al, 2017). Different approaches have been proposed to interpret MSAP outputs (Schulz et al, 2013;Fulneček and Kovařik, 2014), but none takes into account the multiple events reflecting various methylation patterns that must take place simultaneously to explain the differences in individual digestion patterns between control and stressed materials.…”

Section: Introductionmentioning

confidence: 99%

“…The arrangement of all possible events explaining the sixteen four-bit binary MSAP codes (adapted fromBednarek et al, 2017) …”

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The contrasting response to drought and waterlogging is underpinned by divergent DNA methylation programs associated with gene expression in sesame

Dossa

Zhou

et al. 2018

Preprint

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DNA methylation is a heritable epigenetic mechanism that participates in gene regulation under abiotic stresses in plants. Sesame (Sesamum indicum L.) is typically considered a drought-tolerant crop but highly susceptible to waterlogging, a property attributed to its presumed origin in Africa or India. Understanding DNA methylation patterns in sesame under drought and waterlogging conditions can provide insights into the regulatory mechanisms underlying its contrasting responses to these principal abiotic stresses. Here, we combined Methylation-Sensitive Amplified Polymorphism and transcriptome analyses to profile cytosine methylation patterns, gene expression alteration, and their interplay in droughttolerant and waterlogging-tolerant sesame genotypes under control, stress and recovery conditions. Our data showed that drought stress strongly induced de novo methylation (DNM) whereas most of the loci were demethylated (DM) during the recovery phase. In contrast, waterlogging decreased the level of methylation under stress but during the recovery phase, both DM and DNM were concomitantly deployed. In both stresses, the differentially expressed genes (DEGs) were highly correlated with the methylation patterns. We observed that DM was associated with the up-regulation of the DEGs while DNM was correlated with the down-regulation of the DEGs. In addition, we sequenced 44 differentially methylated regions of which 90% overlapped with the promoters and coding sequences of the DEGs. Altogether, we demonstrated that sesame has divergent epigenetic programs that respond to drought and waterlogging stresses. Our results also highlighted the possible interplay among DNA methylation and gene expression, which may modulate the contrasting responses to drought and waterlogging in sesame.

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Cross Talk Between Aluminum and Genetic Susceptibility and Epigenetic Modification in Alzheimer’s Disease

Liang

2018

Advances in Experimental Medicine and Biology

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A relative quantitative Methylation-Sensitive Amplified Polymorphism (MSAP) method for the analysis of abiotic stress

Cited by 42 publications

References 52 publications

Precise evaluation of tissue culture-induced variation during optimisation of in vitro regeneration regime in barley

Precise evaluation of tissue culture-induced variation during optimisation of in vitro regeneration regime in barley

The contrasting response to drought and waterlogging is underpinned by divergent DNA methylation programs associated with gene expression in sesame

Cross Talk Between Aluminum and Genetic Susceptibility and Epigenetic Modification in Alzheimer’s Disease

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