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Bardini, Mauro; Labra, Massimo; Winfield, Mark; Sala, F.

doi:10.1023/a:1022208302819

Cited by 38 publications

(7 citation statements)

References 33 publications

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“…Variation has often been attributed to differences in gene integration sites, the use of antibiotics for selection or gene copy number (Kim et al 2001; Zdzienicka et al 1985). Variation in plant cells, known as somaclonal variation, is predominantly attributed to stress factors, although epigenetic factors such as copy number variation, gene silencing and gene activation have been noted (Bardini et al 2003; Kaeppler et al 2000; Kidwell and Osborn 1993). …”

Section: Introductionmentioning

confidence: 99%

Insights into the prevalence and underlying causes of clonal variation through transcriptomic analysis in Pichia pastoris

Barton

Leak

2017

Appl Microbiol Biotechnol

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Clonal variation, wherein a range of specific productivities of secreted proteins are observed from supposedly identical transformants, is an accepted aspect of working with Pichia pastoris. It means that a significant number of transformants need to be tested to obtain a representative sample, and in commercial protein production, companies regularly screen thousands of transformants to select for the highest secretor. Here, we have undertaken a detailed investigation of this phenomenon by characterising clones transformed with the human serum albumin gene. The titers of nine clones, each containing a single copy of the human serum albumin gene (identified by qPCR), were measured and the clones grouped into three categories, namely, high-, mid- and low-level secretors. Transcriptomic analysis, using microarrays, showed that no regulatory patterns consistently correlated with titer, suggesting that the causes of clonal variation are varied. However, a number of physiological changes appeared to underlie the differences in titer, suggesting there is more than one biochemical signature for a high-secreting strain. An anomalous low-secreting strain displaying high transcript levels that appeared to be nutritionally starved further emphasises the complicated nature of clonal variation.Electronic supplementary materialThe online version of this article (doi:10.1007/s00253-017-8317-2) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Insights into the prevalence and underlying causes of clonal variation through transcriptomic analysis in Pichia pastoris

Barton

Leak

2017

Appl Microbiol Biotechnol

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“…SVs include morphological, cytological, biochemical, and genetic/epigenetic changes induced by tissue culture [25]; alterations in cytosine methylation were detected in all cases studied, thus suggesting that DNA methylation may play an important role in the mutation process [4,26,27,28,29]. Scherer et al found that DNA methylation level is associated with the density of newly formed shoot apical meristems [19].…”

Section: Discussionmentioning

confidence: 99%

“…DNA methylation is an epigenetic modification that plays a critical role in diverse biological processes, including regulation of gene expression [1], cellular differentiation [2], development [3], and stress responses [4]. In plants, DNA methylation is categorized in terms of site classes as CG, CHG, or CHH (H = A, C, or T) based on the sequence context accompanied by the methylated C (mC).…”

Section: Introductionmentioning

confidence: 99%

Whole-Genome Bisulfite Sequencing Reveals a Role for DNA Methylation in Variants from Callus Culture of Pineapple (Ananas comosus L.)

Lin

Xiou

Zhang

et al. 2019

Genes

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DNA methylation changes can occur in some loci during callus culture, resulting in somaclonal variations (SVs). In the present study, we applied whole genome bisulfite sequencing to analyze context-specific DNA methylation changes in the pineapple genome between the cutting seedings and 5 SV plants. In general, SV plants exhibited methylation patterns analogous to those of cutting seedlings (CK). A total of 27.98% of the genomic cytosines of CK were methylcytosines, which was higher than that of 5 SV plants. Moreover, mCG and mCHG was hypermethylated, whereas mCHH was hypomethylated among the 5 SV plants genomic when compared with the CK. Most of the variation of DNA methylation was distributed in gene bodies, thus suggesting that phenotypic differences are probably perturbed by genes methylated from callus culture. In addition, the methylated genes were highly enriched for the Gene Ontology (GO) categories of binding and catalytic activity, cell part and organelle, cellular process, abiotic stimulus, and DNA modification. These results suggest that methylation mediates these pathways in the callus culture of pineapple. The results also suggested that the callus culture induced DNA methylation may result in the SV.

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“…Aside from plant growth regulators, antibiotic application is also known to be associated with tissue culture-induced variations. In particular, Kanamycin has been reported to cause hypermethylation in tobacco plants (Schmitt et al 1997; Rakoczy-Trojanowska 2002; Bardini et al 2003). Kanamycin was hence used as a selection agent to generate transgenic plants in our study.…”

Section: Discussionmentioning

confidence: 99%

“…Phenotypic and genotypic variations, collectively called somaclonal variations, have long been known to be induced during dedifferentiation and regeneration of plants in tissue cultures (Larkin and Scowcroft 1981; Filipecki and Malepszy 2006). Several studies have reported the involvement of plant growth regulators used for regeneration of tissue culture and antibiotics used for transformant selection in somaclonal variations (LoSchiavo et al 1989; Bregitzer et al 1995; Schmitt et al 1997; Rakoczy-Trojanowska 2002; Bardini et al 2003). Factors such as explant genotypes and types of explants have also been known to play a role in somaclonal variations (Gaj 2004).…”

Section: Introductionmentioning

confidence: 99%

Tissue culture-induced somaclonal variation of decreased pollen viability in torenia (Torenia fournieri Lind.)

Sun

Zhong

et al. 2013

Bot Stud

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BackgroundPhenotypic and genotypic variations, collectively called somaclonal variations, are induced during tissue culture.ResultsWe studied the phenotypic variation in pollen viability of regenerants of torenia after subculturing for one to nine generations. We found that pollen viability of regenerants continuously decreased with increasing subculture time. High concentrations of plant growth regulators applied to the Murashige and Skoog (MS) medium also resulted in diminished pollen viability. Furthermore, antibiotic application during gene transformation also decreased pollen viability of the transformants. However, the process of long-term culture did not significantly change pollen viability. The mean methylation level of regenerants showed a 0.28% to 3.95% decrease in seedlings subcultured in vitro for nine generations. Moreover, when the ninth subcultured regenerants with reduced pollen vibility were recovered in soil to get seeds, the pollen viability of seed-derive plants was similar to that of the wild type.ConclusionsThe results show that plant growth regulators, antibiotics, and the number of subculture generations influence somaclonal variations in torenia. The somaclonal variations in torenia may results from epigenetic changes.Electronic supplementary materialThe online version of this article (doi:10.1186/1999-3110-54-36) contains supplementary material, which is available to authorized users.

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Untitled

Cited by 38 publications

References 33 publications

Insights into the prevalence and underlying causes of clonal variation through transcriptomic analysis in Pichia pastoris

Insights into the prevalence and underlying causes of clonal variation through transcriptomic analysis in Pichia pastoris

Whole-Genome Bisulfite Sequencing Reveals a Role for DNA Methylation in Variants from Callus Culture of Pineapple (Ananas comosus L.)

Tissue culture-induced somaclonal variation of decreased pollen viability in torenia (Torenia fournieri Lind.)

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