DNA methylation and tissue culture-induced variation in plants

Summary Plant cells growing in an artificial culture environment make numerous genetic mistakes. These alterations are manifested as increased frequencies of single-gene mutations, chromosome breakages, transposable element activations, quantitative trait variations, and modifications of normal DNA methylation patterns. Evidence is presented that indicates a high frequency of DNA hypomethylation as the result of the tissue culture process. Fifteen percent of the methylation changes appear to have been homozygous in the original regenerated plants. A hypothesis is advanced that relates DNA methylation to the variety of genetic alterations found among maize tissue culture regenerants and their progenies. The epigenetic nature of DNA methylation raises questions concerning the stability of tissue culture-induced changes in self-pollinations and crosses. Presented in the Session-in-Depth Exploitation of Plant Cell Culture Variants at the 1992 World Congress on Cell and Tissue Culture, Washington, DC, June 20–25, 1992.     

Insight into somaclonal variation

ABSTRACT

Somaclonal variation (S.V.) refers to mutational events occurring in tissue culture, although some permanent methylation processes should possibly also be included under this name. In this review, the possible causes as well as the mechanisms implicated in the induction of mutation in cultured cells are discussed. The needs for an easy assay to assess S.V. is pointed out.     

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

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 regenerant-derived 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.     

Heritable somaclonal variation in wheat

Summary Efficient tissue culture and regeneration methods were established using immature wheat embryos as expiants. Genotype differences in culturability were evident, and from the ten accessions most amenable to culture, a total of 2,846 plants were regenerated. Extensive somaclonal variation for morphological and biochemical traits was observed among 142 regenerants of a Mexican breeding line, Yaqui 50E, and their progeny. Variant characters included height, awns, tiller number, grain colour, heading date, waxiness, glume colour, gliadin proteins and -amylase regulation. The variant characters were heritable through two seed generations and included traits under both simple and quantitative genetic control. Segregation data suggested that mutations both from dominance to recessiveness, and from recessiveness to dominance, had occurred. Most mutations in the primary regenerants were in the heterozygous state but some were true-breeding and presumed to be homozygous. Chromosome loss or addition did not account for the variation and none of the variant phenotypes was observed in over 400 plants from the parental seed source. The distinctive parental gliadin pattern was maintained in the somaclones thus excluding seed contamination or cross-pollination as a source of the variation.Abbreviations 2,4-D 2,4-dichlorophenoxy acetic acid - 2,4,5-T 2,4,5-trichlorophenoxy acetic acid - IAA indole acetic acid - BAP 6-benzyl amino purine - ABA abscisic acid - GA₃ gibberellic acid - DAP days after planting     

T-DNA rearrangements due to tissue culture: somaclonal variation in crown gall tissues

After three years of apparent stability in tissue culture, the single cell derived shooty crown gall line sNT1.013 produced a revertant shoot which had switched from non-rooting (Rod⁺) and octopine synthesizing (Ocs⁺) to Rod^- Ocs^-, indicating that in this revertant TL-DNA genes 4 (causing the Rod⁺ trait) and gene 3 (causing the Ocs⁺ trait) had been inactivated. Southern blots revealed that the inactivation of these T-DNA genes was the result of a considerable rearrangement of DNA sequences, accompanied by deletions and possibly also by DNA amplifications. This study for the first time unambiguously proves that foreign genes which have been introduced via Agrobacterium tumefaciens can, at a low frequency, be inactivated after T-DNA integration because of reorganization of T-DNA sequences during tissue culture. This can be considered as an event of somaclonal variation.     

DNA fingerprinting of red clover (Trifolium pratense L.) with Jeffrey's probes: detection of somaclonal variation and other applications

Summary DNA fingerprints generated by the Jeffreys' probes, 33.6 and 33.15, indicated the presence of minisatellite-like sequences in the red clover genome. The fingerprints generated by probe 33.6 gave less background and fewer but better defined bands than those obtained with probe 33.15. Assay of a regenerative somaclonal variant (F49R) by DNA fingerprinting with probe 33.6 detected mutation that was unlinked to the regenerative trait. The fingerprints obtained under the applied conditions also demonstrated genetic stability of consecutive generations of the regenerants in tissue culture. DNA fingerprints of F₁ plants revealed that each polymorphic band was inherited from either one or the other parent. Both probes distinguished individual-specific genotypes in seven cultivars of red clover. Greater variability in DNA fingerprints was detected between (V=0.899) than within (0.417≤V≤0.548) cultivars.     

Heritable somaclonal variation in wild barley (Hordeum spontaneum)

Summary Progenies of H. spontaneum plants regenerated from immature embryo derived calli were analysed for somaclonal variation on the following traits: (1) organization of the intergenic spacer of the rRNA genes; (2) B and C hordein pattern on SDS-PAGE; (3) genomic organization of the B and C hordein coding sequences; (4) mitochondrial DNA organization assayed by hybridization of Southern blots of total DNA with mitochondrial coding genes; (5) cytology. One out of twelve progeny plants was characterized as variant for two traits: (a) a loss of 1.8 and 2.5 kb Taq I intergenic rDNA spacer fragments and (b) a variant pattern of hordeins on 1-D SDS-PAGE. No numerical or structural chromosome variation was detected among the control plants therefore it is assumed that the variation was caused by the in vitro culture and transmitted, through sexual reproduction, to the analysed progeny.     

植物DNA甲基化及胁迫诱导的变异

DNA中碱基的化学修饰近年来一直是生命科学领域研究的热点之一。DNA甲基化是一种常见的表观遗传现象,它能在不改变DNA序列的前提下改变遗传表型。各种胁迫因素能诱导植物DNA甲基化产生变异,但其应答胁迫机制仍然未知。本文对植物DNA甲基化研究进展进行了综述,结合本课题组的研究结果,对7Li离子束注入、~(60)CO-γ射线诱变诱导产生的DNA甲基化变异进行了报道,以期为DNA甲基化可能参与涉及植物的表型可塑性提供一定的依据。     

Exploiting wild population diversity and somaclonal variation in the salt marsh grass Distichlis spicata (Poaceae) for marsh creation and restoration

The salt marsh grass Distichlis spicata was regenerated from tissue culture and propagated in a greenhouse. Selected regenerants, along with selections from six wild populations, were grown for two years in a common garden flood-irrigated thrice weekly with tidal creek water. Selected wild and regenerated plants were also planted in a created salt marsh. Significant differences among regenerant and wild population selections were found in several functionally important salt marsh plant characteristics, including potential detritus production, belowground organic matter production, canopy structure, and decomposition rate. A combination of characteristics not found in the wild populations was evident in a regenerated line that exhibited both a high detritus production potential and a high decomposition rate. The amount of variation that occurred among regenerants from one parental line via somaclonal variation was similar to that which occurred among the wild population selections. Results of this study suggest that tissue culture may provide a means of producing marsh grasses with specific characteristics for directing the functional development of newly created salt marshes.     

Studies on somaclonal variation in Phalaenopsis

The morphological and genetic variations in somaclones of Phalaenopsis True Lady “B79-19” derived from tissue culture were evaluated. In 1360 flowering somaclones, no apparent difference was found in the shape of the leaves, whereas flowers in some somaclones were deformed. We have demonstrated that 38 selected random primers can be used to generate amplified segments of genomic DNA and to differentiate polymorphisms of somaclonal variations in Phalaenopsis. The random amplified polymorphic DNA (RAPD) data indicated that normal and variant somaclones are not genetically identical. We also studied the banding patterns of aspartate aminotransferase (AAT) and phosphoglucomutase (PGM) in young leaves of variant and normal somaclones of Phalaenopsis. With respect to AAT, three distinct banding patterns were found in normal somaclones and only two-banded phenotypes were detected in variant somaclones. In a comparison of the banding patterns of PGM isozymes, three to four bands were detected in normal somaclones and two to three bands in variant ones. Received: 15 August 1997 / Revision received: 16 February 1998 / Accepted: 1 May 1998     

Variants of carnation (Dianthus caryophyllus L.) obtained by organogenesis from irradiated petals

To obtain carnation variants differing from those produced by organogenesis alone, in vitro petal cultures were subjected to gamma irradiation. Histological analysis revealed the surface origin of buds and the different steps in meristem formation. A dose of 40 Gy administered on the fourth day of culture produced variants of horticultural interest in Niky. This period corresponded to dedifferentiation of cells that subsequently developed into bubs.Abbreviations BA benzyladenine - NAA naphthaleneacetic acid     

SAMPL: A technique for somaclonal variation fingerprinting inMusa

SAMPL primers designed for genomic profiling in chickpea (Cicer arietinum L.) were tested for their applicability to fingerprinting of DNA of banana cultivars and soma-clonal variants. Most of the chickpea primers allowed amplification of genomic DNA of banana and detection of sequence polymorphisms within theMusa acuminata genome (A). Our results demonstrate that the highly resolving SAMPL technique is useful in banana genomics, especially for the distinction and characterization of commercially important cultivars and promising somaclonal variants containing the A genome.     

Genetic analysis of variation in micropropagated plants of Melia azedarach L.

Summary Plants were regenerated by shoot multiplication from four clones of Melia azedarach L. during 12 mo. of subculturing. One hundred and one of these plants were examined by randomly amplified polymorphic DNA analysis. All regenerated plants showed at least one polymorphism. However, no chromosome number alterations were observed. The pattern of variation obtained by principal coordinated analysis showed a random distribution of variation among regenerated plants and their controls, indicating that genetic alterations were not cumulative during in vitro culture. Similar results were found using Shannon's index, which revealed that 50% of the observed diversity resided among plants coming from the same subculture generation. This high intraclonal variation does not provide a clear scenario for predicting the amount of culture time required to preserve genetic fidelity in commercially micropropagated M. azedarach plants. Our work suggests that other mechanisms, such as chimerism, contribute to intraclonal heterogeneity in vitro.     

Epigenetic memory transmission through mitosis and meiosis in plants

Gene activities can be regulated by epigenetic modifications of nucleotides and chromatin that are stably propagated through somatic cell divisions and, in some cases, across generations. The mechanisms that control epigenetic marks have recently been uncovered using model organisms, such as the flowering plant Arabidopsis thaliana. In Arabidopsis, perturbation of epigenetic gene activity often results in heritable developmental phenotypes. Stable, but potentially reversible, changes in epigenetic status can also be sources for phenotypic variations in natural plant populations.     

Transgenic plants: performance,release and containment

This review focuses on transgenic plants, from the initial stages of the genetic modification process in the laboratory to their release stage in the field and indicates possible areas of concern and strategies for dealing with them. The classes of marker genes and issues about their safety, the gene flow and strategies that are used to isolate transgenic plants genetically are specifically examined. In addition, an assessment is provided of the phenomena which affect the performance of transgenic plants, such as gene disruption, the pleiotropic effect on plant phenotype and genetic variation. Finally, strategies are suggested for preventing unexpected consequences of transgenic plant production.The author is with the Department of Genetics, University of Leeds, Leeds LS2 9JT, UK     

Somaclonal variation in embryogenic cultures of silver fir (Abies alba Mill.)

Abstract

The somaclonal variation analysis was conducted on callus of 57 lines obtained by the method of somatic embryogenesis from six zygotic embryos (with different genotypes) of silver fir (Abies alba Mill.) located in two mountain regions in the south of Poland. The somaclonal variation at the DNA level was estimated using RAPD markers and the data produced were used to estimate the level of similarity using Jaccard’s coefficient. For RAPD analysis, 24 ten‐nucleotide primers from the groups OPA, OPB and OPG were used. Two genotypes deriving from Krynica and My?lenice showed high genetic similarity (Jaccard’s coefficient 0.74 and 0.83), which provides a substantial chance for producing firs with the parental genotype. The remaining four genotypes showed somaclonal variation (average Jaccard’s coefficient approx. 0.5). The significance in variation of the research sites was ascertained by the ANOVA statistical test, which showed the impact of genotype, type of medium and phytohormones included in it on the variation among the fir lines bred in vitro. The somaclonal variation data in silver fir could be useful for its propagation through in vitro culture, and in generating detailed genetic maps of this species.     

Somatic embryogenesis in peach palm using the thin cell layer technique: induction, morpho-histological aspects and AFLP analysis of somaclonal variation

BACKGROUND AND AIMS: The thin cell layer (TCL) technique is based on the use of very small explants and has allowed enhanced in vitro morphogenesis in several plant species. The present study evaluated the TCL technique as a procedure for somatic embryo production and plantlet regeneration of peach palm. METHODS: TCL explants from different positions in the shoot apex and leaf sheath of peach palm were cultivated in MS culture medium supplemented with 0-600 microM Picloram in the presence of activated charcoal. The production of primary calli and embryogenic calli was evaluated in these different conditions. Histological and amplified fragment length polymorphism (AFLP) analyses were conducted to study in vitro morphogenetic responses and genetic stability, respectively, of the regenerated plantlets. KEY RESULTS: Abundant primary callus induction was observed from TCLs of the shoot meristem in culture media supplemented with 150-600 microM Picloram (83-97%, respectively). The production of embryogenic calli depends on Picloram concentration and explant position. The best response observed was 43% embryogenic callus production from shoot meristem TCL on 300 microM Picloram. In maturation conditions, 34+/-4 somatic embryos per embryogenic callus were obtained, and 45.0+/-3.4% of these fully developed somatic embryos were converted, resulting in plantlets ready for acclimatization, of which 80% survived. Histological studies revealed that the first cellular division events occurred in cells adjacent to vascular tissue, resulting in primary calli, whose growth was ensured by a meristematic zone. A multicellular origin of the resulting somatic embryos arising from the meristematic zone is suggested. During maturation, histological analyses revealed bipolarization of the somatic embryos, as well as the development of new somatic embryos. AFLP analyses revealed that 92% of the regenerated plantlets were true to type. The use of TCL explants considerably improves the number of calli and somatic embryos produced in comparison with previously described protocols for in vitro regeneration of peach palm. CONCLUSIONS: The present study suggests that the TCL somatic embryogenesis protocol developed is feasible, although it still requires further optimization for in vitro multiplication of peach palm, especially the use of similar explants obtained from adult palm trees.