Expression and DNA methylation of SERK, BBM, LEC2 and WUS genes in in vitro cultures of Boesenbergia rotunda (L.) Mansf.

Karim, Rezaul; Tan, Yew Seong; Singh, Pooja; Khalid, Norzulaani; Harikrishna, Jennifer Ann

doi:10.1007/s12298-018-0566-8

Cited by 25 publications

(31 citation statements)

References 70 publications

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“…A decreased 5mC level has been found in the promotors of LEAFY COTYLEDON1 (LEC1) and WUS, respectively, in an embryogenic culture of D. carota [142] and during shoot organogenesis in Arabidopsis [131,143]. Similarly, a decreased methylation level has been reported in the SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE (SERK), LEC2, and WUS genes in the embryogenic calli of Boesenbergia rotunda [144]. Hypomethylation at the CHH sites in a promoter has been associated with the activation of some hormone related and WOX genes in G. hirsutum SE [126].…”

Section: Dna Methylationmentioning

confidence: 84%

Epigenetic Regulation of Auxin-Induced Somatic Embryogenesis in Plants

Wójcikowska

Wójcik

Gaj

2020

IJMS

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Somatic embryogenesis (SE) that is induced in plant explants in response to auxin treatment is closely associated with an extensive genetic reprogramming of the cell transcriptome. The significant modulation of the gene transcription profiles during SE induction results from the epigenetic factors that fine-tune the gene expression towards embryogenic development. Among these factors, microRNA molecules (miRNAs) contribute to the post-transcriptional regulation of gene expression. In the past few years, several miRNAs that regulate the SE-involved transcription factors (TFs) have been identified, and most of them were involved in the auxin-related processes, including auxin metabolism and signaling. In addition to miRNAs, chemical modifications of DNA and chromatin, in particular the methylation of DNA and histones and histone acetylation, have been shown to shape the SE transcriptomes. In response to auxin, these epigenetic modifications regulate the chromatin structure, and hence essentially contribute to the control of gene expression during SE induction. In this paper, we describe the current state of knowledge with regard to the SE epigenome. The complex interactions within and between the epigenetic factors, the key SE TFs that have been revealed, and the relationships between the SE epigenome and auxin-related processes such as auxin perception, metabolism, and signaling are highlighted.

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Section: Dna Methylationmentioning

confidence: 84%

Epigenetic Regulation of Auxin-Induced Somatic Embryogenesis in Plants

Wójcikowska

Wójcik

Gaj

2020

IJMS

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“…Reversed phase-high performance liquid chromatography (RP-HPLC) provides robust data on DNA methylation changes affecting the whole genome, but the method may not detect many subtle phenomena (Machczyńska et al 2014a). Bisulfite sequencing was tested recently, and provided promising results on tissue culture-induced variation in Boesenbergia rotunda (Karim et al 2018) and sugar beet (Zakrzewski et al 2017). Diversity arrays technology sequencing methylation analysis (DArTseqMet, developed by Diversity Arrays Technology, https ://www.diver sitya rrays .com/techn ology -and-resou rces/darts eq/) is a promising technology for methylation analysis, although it is relatively costly for routine analysis.…”

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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“…DNA methylation plays a vital role in cell dedifferentiation, redifferentiation and the growth and development of plants [ 56 ]. In SE, DNA methylation regulates and maintains the gene expression programs of several genes; however, due to the previously reported critical implications for the embryogenic process in plants, a group of genes has been especially studied ( Figure 1 ): Leafy Cotyledon 1 ( LEC1 ), Wuschel ( WUS), Somatic Embryogenesis Receptor Kinase ( SERK ), Pickle ( PKL ) and Baby Boom ( BBM ) [ 20 , 23 , 57 ]. For instance, the manipulation of methylation in specific genes, such as LEC1 [ 58 ] and Wuschel ( WUS ) [ 59 ], drastically affects the regulation of the differentiation of plant explants.…”

Section: Dna Methylation: a Key Player During Somatic Embryogenesimentioning

confidence: 99%

“…In Boesenbergia rotunda (L.) Mansf., the expression of the SERK , BBM , LEC2 and WUS genes was studied, and also the gene-specific methylation by bisulfite sequencing data of these genes. Based on these results, it was suggested that relatively higher expression and lower level of DNA methylation of SERK , BBM , LEC2 , and WUS are associated with somatic embryogenesis and plant regeneration [ 23 ]. Recently it was reported in cotton that the inhibition of methylation by the use of zebularine activated the transcription of hormone-related genes ( IAA14 , CKX6 , LBD1/3 , LOX1 , CRF4.1 ) and may promote SE [ 33 ].…”

Section: Dna Methylation: a Key Player During Somatic Embryogenesimentioning

confidence: 99%

“…Currently, it is known that DNA methylation plays an essential role in the regulation of gene expression during development. Methylation states in the DNA, resulting from in vitro cultures, are often related to the control of SE and the regeneration process through the modulation of gene expression [ 19 , 23 ]. By changing the methylation profile, it is possible to alter gene expression, and this can be applied to produce a large number of high-quality plants or to improve the agronomic characteristics leading to the improvement of a crop [ 24 ].…”

Section: Introductionmentioning

confidence: 99%

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5-Azacytidine: A Promoter of Epigenetic Changes in the Quest to Improve Plant Somatic Embryogenesis

Osorio-Montalvo

Sáenz

De‐la‐Peña

2018

IJMS

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Somatic embryogenesis (SE) is a widely studied process due to its biotechnological potential to generate large quantities of plants in short time frames and from different sources of explants. The success of SE depends on many factors, such as the nature of the explant, the microenvironment generated by in vitro culture conditions, and the regulation of gene expression, among others. Epigenetics has recently been identified as an important factor influencing SE outcome. DNA methylation is one of the most studied epigenetic mechanisms due to its essential role in gene expression, and its participation in SE is crucial. DNA methylation levels can be modified through the use of drugs such as 5-Azacytidine (5-AzaC), an inhibitor of DNA methylation, which has been used during SE protocols. The balance between hypomethylation and hypermethylation seems to be the key to SE success. Here, we discuss the most prominent recent research on the role of 5-AzaC in the regulation of DNA methylation, highlighting its importance during the SE process. Also, the molecular implications that this inhibitor might have for the increase or decrease in the embryogenic potential of various explants are reviewed.

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Expression and DNA methylation of SERK, BBM, LEC2 and WUS genes in in vitro cultures of Boesenbergia rotunda (L.) Mansf.

Cited by 25 publications

References 70 publications

Epigenetic Regulation of Auxin-Induced Somatic Embryogenesis in Plants

Epigenetic Regulation of Auxin-Induced Somatic Embryogenesis in Plants

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

5-Azacytidine: A Promoter of Epigenetic Changes in the Quest to Improve Plant Somatic Embryogenesis

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