Genetic and epigenetic relationship in rye, Secale cereale L., somaclonal variation within somatic embryo-derived plants

Linacero, Rosario; Rueda, Julia; Esquivel, Estrella; Bellido, Alberto; Domingo, Angel; Vázquez, Ana María

doi:10.1007/s11627-011-9407-y

Cited by 26 publications

(14 citation statements)

References 52 publications

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“…Our results are consistent with previous studies that assessed specific genomic regions (Kaeppler and Phillips 1993;Zhang et al 2009;Linacero et al 2011;Gonzalez (Stroud et al 2013). The bulk of DNA methylation is not affected by tissue culture.…”

Section: Discussionsupporting

confidence: 92%

“…Instead, the more stochastic hypermethylation events may explain some of the somaclonal variation observed following tissue culture. Our results are consistent with previous studies that assessed specific genomic regions (Kaeppler and Phillips 1993;Zhang et al 2009;Linacero et al 2011;Gonzalez The bulk of DNA methylation is not affected by tissue culture. However, a subset of genomic regions exhibit altered DNA methylation levels.…”

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confidence: 92%

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Consistent and Heritable Alterations of DNA Methylation Are Induced by Tissue Culture in Maize

et al. 2014

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Plants regenerated from tissue culture and their progenies are expected to be identical clones, but often display heritable molecular and phenotypic variation. We characterized DNA methylation patterns in callus, primary regenerants, and regenerantderived progenies of maize using immunoprecipitation of methylated DNA (meDIP) to assess the genome-wide frequency, pattern, and heritability of DNA methylation changes. Although genome-wide DNA methylation levels remained similar following tissue culture, numerous regions exhibited altered DNA methylation levels. Hypomethylation events were observed more frequently than hypermethylation following tissue culture. Many of the hypomethylation events occur at the same genomic sites across independent regenerants and cell lines. The DNA methylation changes were often heritable in progenies produced from self-pollination of primary regenerants. Methylation changes were enriched in regions upstream of genes and loss of DNA methylation at promoters was associated with altered expression at a subset of loci. Differentially methylated regions (DMRs) found in tissue culture regenerants overlap with the position of naturally occurring DMRs more often than expected by chance with 8% of tissue culture hypomethylated DMRs overlapping with DMRs identified by profiling natural variation, consistent with the hypotheses that genomic stresses similar to those causing somaclonal variation may also occur in nature, and that certain loci are particularly susceptible to epigenetic change in response to these stresses. The consistency of methylation changes across regenerants from independent cultures suggests a mechanistic response to the culture environment as opposed to an overall loss of fidelity in the maintenance of epigenetic states. C LONAL propagation of plants and animals is expected to produce individuals identical to the donor. However, this is often not the case. Plant tissue culture involves dedifferentiation, or return to a "stem-cell-like" state, which involves dynamic reprogramming at the chromatin level to induce the formation of callus. Subsequently, proliferating cells start to redifferentiate when specific changes in the balance of growth regulators are introduced in the culture medium, ultimately leading to organogenesis or regeneration into whole plants (Grafi et al. 2011;Miguel and Marum 2011). This process represents a traumatic stress to plant cells and often provokes an array of genetic and epigenetic instabilities that are somatically and meiotically heritable (Phillips et al. 1994;Kaeppler et al. 2000). This suite of molecular and phenotypic phenomena is collectively termed somaclonal variation (Larkin and Scowcroft 1981).At the cellular and molecular levels, somaclonal variation is composed of chromosome rearrangements, polyploidy and aneuploidy, DNA sequence changes, activation of quiescent transposable elements (TEs), and epigenetic variation reflected by altered DNA methylation patterns (Karp and Maddock 1984;Brettell et al. 1986;Dennis et al. 1987;Pe...

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Section: Discussionsupporting

confidence: 92%

supporting

confidence: 92%

Consistent and Heritable Alterations of DNA Methylation Are Induced by Tissue Culture in Maize

et al. 2014

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“…Our data are congruent with the MSAP studies of genomic DNA methylation changes performed between rye donor plants and their regenerants where the level of demethylation was greater for the regenerants (González et al 2013). Similar results were obtained also in rye using HpaII and MspI digested DNA amplified with ISSR markers (Linacero et al 2011). It was demonstrated that the decrease in DNA methylation at the level of regenerants may be caused by the necessity of genes activation during cell reprogramming to facilitate plant regeneration (Kaeppler and Phillips 1993).…”

Section: Discussionsupporting

confidence: 90%

“…To study the extent of changes induced by tissue culture and inherited by the progeny different methods have been used (Hossain et al 2003;Peredo et al 2009;Linacero et al 2011;Díaz-Martínez et al 2012). Most of them involved isoschizomers differing in their sensitivity towards DNA methylation sites (Ochogavía et al 2009;Wang et al 2013;Machczyńska et al 2014).…”

Section: Introductionmentioning

confidence: 99%

DNA methylation changes in triticale due to in vitro culture plant regeneration and consecutive reproduction

Machczyńska

Orłowska

Mańkowski

et al. 2014

Plant Cell Tiss Organ Cult

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Doubled haploids of triticale are of interest for plant breeders due to hybrid breeding programs based on cytoplasmic male sterility Tt phenomenon. However, (epi)mutations appearing during in vitro culture regeneration may lead to a phenotypic variation that makes the uniformity of plant materials questionable. Using RP-HPLC genomic DNA methylation of donor doubled haploid plants utilized as a source of tissues for the in vitro regeneration (via androgenesis and somatic embryogenesis) of triticale cv. Bogo and their consecutive generative progeny was evaluated. It was demonstrated that in vitro cultures induced a decrease of the DNA methylation of the regenerants independently of the approach used for plant regeneration. The decrease in DNA methylation of genomic DNA proceeded up to the first/second successive generations followed by the beginning of its reestablishment. Moreover, somatic embryogenesis resulted in a higher level of genomic DNA demethylation in regenerants than androgenesis and the process of methylation seems to be affected by donor plant. It is being speculated that long term changes in genomic DNA methylation may be a source of off-type individuals that may spontaneously arise during plant breeding.

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“…Several bases for somaclonal variation have been proposed, which include changes in chromosome number (Mujib et al 2007; Leva et al 2012), point mutations (D’Amato 1985; Ngezahayo et al 2007), somatic crossing over and sister chromatid exchange (Duncan 1997; Bairu et al 2011), chromosome breakage and rearrangement (Czene and Harms-Ringdahl 1995; Alvarez et al 2010), somatic gene rearrangement, DNA amplification (Karp 1995; Tiwari et al 2013), changes in organelle DNA (Cassells and Curry 2001; Bartoszewski et al 2007), DNA methylation (Guo et al 2007; Linacero et al 2011), epigenetic variation (Kaeppler et al 2000; Guo et al 2006; Smulders and de Klerk 2011), histone modifications and RNA interference (Miguel and Marum 2011), segregation of pre-existing chimeral tissue (Brar and Jain 1998; Vázquez 2001; Ravindra et al 2012; Nwauzoma and Jaja 2013) and insertion or excision of transposable elements (Gupta 1998; Sato et al 2011b). In particular, transposable elements are one of the causes of genetic rearrangements in in vitro culture (Hirochika et al 1996; Sato et al 2011a).…”

Section: Molecular Basis Of Somaclonal Variationmentioning

confidence: 99%

Somaclonal variations and their applications in horticultural crops improvement

Krishna¹,

Alizadeh

Singh³

et al. 2016

3 Biotech

343

216

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The advancements made in tissue culture techniques has made it possible to regenerate various horticultural species in vitro as micropropagation protocols for commercial scale multiplication are available for a wide range of crops. Clonal propagation and preservation of elite genotypes, selected for their superior characteristics, require high degree of genetic uniformity amongst the regenerated plants. However, plant tissue culture may generate genetic variability, i.e., somaclonal variations as a result of gene mutation or changes in epigenetic marks. The occurrence of subtle somaclonal variation is a drawback for both in vitro cloning as well as germplasm preservation. Therefore, it is of immense significance to assure the genetic uniformity of in vitro raised plants at an early stage. Several strategies have been followed to ascertain the genetic fidelity of the in vitro raised progenies comprising morpho-physiological, biochemical, cytological and DNA-based molecular markers approaches. Somaclonal variation can pose a serious problem in any micropropagation program, where it is highly desirable to produce true-to-type plant material. On the other hand, somaclonal variation has provided a new and alternative tool to the breeders for obtaining genetic variability relatively rapidly and without sophisticated technology in horticultural crops, which are either difficult to breed or have narrow genetic base. In the present paper, sources of variations induced during tissue culture cycle and strategies to ascertain and confirm genetic fidelity in a variety of in vitro raised plantlets and potential application of variants in horticultural crop improvement are reviewed.

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Genetic and epigenetic relationship in rye, Secale cereale L., somaclonal variation within somatic embryo-derived plants

Cited by 26 publications

References 52 publications

Consistent and Heritable Alterations of DNA Methylation Are Induced by Tissue Culture in Maize

Consistent and Heritable Alterations of DNA Methylation Are Induced by Tissue Culture in Maize

DNA methylation changes in triticale due to in vitro culture plant regeneration and consecutive reproduction

Somaclonal variations and their applications in horticultural crops improvement

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