Genetic Implications of Somaclonal Variation in Plants

Clonal fidelity investigation of micropropagated hardened plants of jackfruit tree (Artocarpus heterophyllus L.) with RAPD markers

Background

Artocarpus heterophyllus is an important tropical agroforestry species that bears multiple applications. However, the population of this species is reduced due to various anthropogenic activities. For this reason, in vitro approach is needed to propagate or conserve this species as in vivo propagation methods face various obstacles. In this respect, the present investigation was undertaken to produce genetically stable jackfruit trees through in vitro technology. In vivo grew shoot tips were harvested on Murashige and Skoog (MS) medium containing several plant growth regulators to achieve this.

Results

The 6-benzylaminopurine (BAP) at the concentration of 1.5 mg L^-1, indole-3-butyric acid (IBA) at 0.5 mg L^-1, and α-naphthaleneacetic acid (NAA) at 0.1 mg L^-1 in combination on MS media yielded superior shoot response (94.44%), longest shoot length (4.02 cm), and the maximum number of shoots per explant (4.78). They were further multiplied by repeated subculturing on the same media composition and the third subculture resulted in a maximum number of shoots (5.92) with the largest shoot length (5.85 cm). Among the different media screened for rooting, the ¼ MS media yielded 94.44% rooting response, the longest root length (3.78 cm), and the maximum number of roots per shoot (8.44) with 0.1 mg L^-1 NAA, 0.5 mg L^-1 IBA and 0.1 mg L^-1 BAP in combination. Primary hardening showed 88.89% of plant survival under greenhouse conditions after 4 weeks of incubation having a sterilized mixture of garden soil and vermiculite mixture (1:1, w/w). It increased to 90.60% after the secondary hardening process in a vermiculite-soil mixture (2:1; w/w). No polymorphism was detected on random amplification of polymorphic DNA (RAPD) profiling between the mother plant and hardened plants, indicating high genetic stability among the clones.

Conclusions

This is the first report of the genetic fidelity study of in vitro grown regenerants of A. heterophyllus. This study established a micropropagation protocol for genetically uniform in vitro regeneration of this species to supply plant resources to various industries or conservation of elite germplasm.

Cultivar-specific markers, mutations, and chimerisim of Cavendish banana somaclonal variants resistant to Fusarium oxysporum f. sp. cubense tropical race 4

Background

The selection of tissue culture–derived somaclonal variants of Giant Cavendish banana (Musa spp., Cavendish sub-group AAA) by the Taiwan Banana Research Institute (TBRI) has resulted in several cultivars resistant to Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), a destructive fungus threatening global banana production. However, the mutations in these somaclonal variants have not yet been determined. We performed an RNA-sequencing (RNA-seq) analysis of three TBRI Foc TR4–resistant cultivars: ‘Tai-Chiao No. 5’ (TC5), ‘Tai-Chiao No. 7’ (TC7), and ‘Formosana’ (FM), as well as their susceptible progenitor ‘Pei-Chiao’ (PC), to investigate the sequence variations among them and develop cultivar-specific markers.

Results

A group of single-nucleotide variants (SNVs) specific to one cultivar were identified from the analysis of RNA-seq data and validated using Sanger sequencing from genomic DNA. Several SNVs were further converted into cleaved amplified polymorphic sequence (CAPS) markers or derived CAPS markers that could identify the three Foc TR4–resistant cultivars among 6 local and 5 international Cavendish cultivars. Compared with PC, the three resistant cultivars showed a loss or alteration of heterozygosity in some chromosomal regions, which appears to be a consequence of single-copy chromosomal deletions. Notably, TC7 and FM shared a common deletion region on chromosome 5; however, different TC7 tissues displayed varying degrees of allele ratios in this region, suggesting the presence of chimerism in TC7.

Conclusions

This work demonstrates that reliable SNV markers of tissue culture–derived and propagated banana cultivars with a triploid genome can be developed through RNA-seq data analysis. Moreover, the analysis of sequence heterozygosity can uncover chromosomal deletions and chimerism in banana somaclonal variants. The markers obtained from this study will assist with the identification of TBRI Cavendish somaclonal variants for the quality control of tissue culture propagation, and the protection of breeders’ rights.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08692-5.

Rice responses to silicon addition at different Fe status and growth pH. Evaluation of ploidy changes

It has been described in rice that Si only plays a physical barrier that does not allow Fe to enter cell apoplast, causing Fe deficiency responses even under Fe sufficiency growth conditions. Most of the conclusions were attained at acidic pH, but rice is also grown at calcareous conditions, which especially induce Fe deficiency in the plants. In this study, we assay the effect of Si in rice suffering both Fe deficiency and sufficiency in hydroponics at two pHs (5.5 and 7.5). Plant biometric parameters, ROS concentration, enzymatic activities, and total phenolic compounds, as well as ploidy levels, have been determined. In general, both pHs promoted similar rice responses under Fe sufficiency and deficiency status, but at pH 7.5, stress was favored. Flow cytometry studies revealed that Fe deficiency increased the percentage of cells in higher ploidy levels. Moreover, under this Fe status, Si addition enhanced this effect. This increase contributed to maintaining chloroplast structure which may have preserved antioxidant activities, and fortified cell walls, diminishing Fe uptake. The first is considered a beneficial effect as plants presented acceptable SPAD values, well chloroplast structure, and qualitatively high fluorescence observed by confocal microscopy, even under Fe deficiency. But contributes to intensify the Fe shortage, by decreasing apoplast Fe pools. In summary, Si addition to rice plants may not only behave as an apoplastic barrier but may also protect plant chloroplast and alter the plant endoreplication cycle, giving a memory effect to cope with present and future stresses.

Tissue culture-induced DNA methylation in crop plants: a review

Plant tissue culture techniques have been extensively employed in commercial micropropagation to provide year-round production. Tissue culture regenerants are not always genotypically and phenotypically similar. Due to the changes in the tissue culture microenvironment, plant cells are exposed to additional stress which induces genetic and epigenetic instabilities in the regenerants. These changes lead to tissue culture-induced variations (TCIV) which are also known as somaclonal variations to categorically specify the inducing environment. TCIV includes molecular and phenotypic changes persuaded in the in vitro culture due to continuous sub-culturing and tissue culture-derived stress. Epigenetic variations such as altered DNA methylation pattern are induced due to the above-mentioned factors. Reportedly, alteration in DNA methylation pattern is much more frequent in the plant genome during the tissue culture process. DNA methylation plays an important role in gene expression and regulation of plant development. Variants originated in tissue culture process due to heritable methylation changes, can contribute to intra-species phenotypic variation. Several molecular techniques are available to detect DNA methylation at different stages of in vitro culture. Here, we review the aspects of TCIV with respect to DNA methylation and its effect on crop improvement programs. It is anticipated that a precise and comprehensive knowledge of molecular basis of in vitro-derived DNA methylation will help to design strategies to overcome the bottlenecks of micropropagation system and maintain the clonal fidelity of the regenerants.

Studies on growth dynamics of embryogenic cell suspension cultures of commercially important Indica rice cultivars ASD16 and Pusa basmati

Significant efforts are being directed towards the improvement of rice using genetic manipulations. A good and reproducible system for recovering fertile Indica rice plants is imperative. The aim of this study was to study the influence of initial cell density on growth dynamics of suspension cultures. The cultures were initiated from 3-week-old embryogenic calli derived from mature seeds of Indica rice cultivars ASD16 and Pusa basmati. Growth kinetics of the rice cell suspensions were measured and the obtained data reveal that viable cells at 3% PCV using 20 ml liquid (N6D) medium and sub-culturing at 7-day intervals resulted in rapid increase in fresh and dry weights and the embryogenic competency of the cells were found to be high. The growth kinetics analysis revealed that ASD16 showed better efficiency for high frequency and viable somatic embryo formation as compared to Pusa basmati. The technique was found to be suitable for developing somatic embryos for both cultivars ASD16 and Pusa basmati, which can be used for many important applications including micropropagation and secondary metabolites production.

Breakage-fusion-bridge cycles and de novo telomere formation on broken chromosomes in maize callus cultures

Breakpoints involved in chromosome alterations associated with heterochromatin have been detected in maize plants regenerated from callus culture. A cytogenetic analysis of plants regenerated from a maize callus was performed aiming to analyze the stability of a chromosome 7 bearing a deficiency-duplication (Df-Dp), which was interpreted as derived from a chromatid type breakage-fusion-bridge (BFB) cycle. The Df-Dp chromosome 7 was stable in mitotic and meiotic cells of the regenerated plants. Fluorescence in situ hybridization showed signals of telomeric sequences on the broken chromosome arm and provided evidence of de novo telomere formation. The stability of two types of altered chromosome 7 was investigated in C-banded metaphases from samples of the original callus that were collected during a period of 30-42 months after culture initiation. New alterations involving heterochromatic knobs of chromosomes 7 and 9 were observed. The aberrant chromosomes were stable in the subcultures, thus providing evidence of broken chromosome healing. The examination of anaphases showed the presence of bridges, which was consistent with the occurrence of BFB cycles. De novo telomere formation occurred in euchromatic and heterochromatic chromosome termini. The results point to events of chromosomal evolution that might occur in plants.

Leaf patterning of Clivia miniata var. variegata is associated with differential DNA methylation

Leaf patterns (yellow, green and striped) of Clivia miniata var. variegata might be caused by differential DNA methylation in CCGG sites in response to heterogeneous environmental pressure. Clivia miniata is an important ornamental plant.Clivia miniata var. variegata (Cmvv) is a variegated leaf mutant of C. miniata. Typical Cmvv has attractive green and yellow-stripped leaves. The study has revealed that an explant of Cmvv, even a full-green explant, could regenerate plants of three different types: yellow, green, ands triped; normal-appearing chloroplasts were found in guard cells but not in mesophyll cells of all the three types of Cmvv using confocal laser scanning microscopy (CLSM).Thus, we speculated that cells of the three types of Cmvv had an identical mutation and the mutation might disturb mesophyll cell chloroplast biogenesis after symplastic isolation of guard cells. Using CLSM and methylation sensitive amplification polymorphism (MSAP), we found that (a) striped leaves of Cmvv are due to sectorial decreases in chlorophyll levels and the decreases are associated with CG hypermethylation; (b) extent of epigenetic divergence among the three types of Cmvv leaves is positively correlated with intensity of leaf-color difference; and (c) green stripes of two plants are clustered in one group based on the MSAP profiles, but green and yellow stripes of a plant are not. Sequencing analysis indicated that CG hypermethylation in gene bodies of CPSAR1 and ycf2 might lead to gene silencing and yellow leaves/stripes of Cmvv. All together, it is possible that cytosine methylation involved regulating leaf color of Cmvv, also striped pattern of Cmvv might be caused by differential DNA methylation in response to heterogeneous environmental pressure. Furthermore, a novel leaf-color epigenetic hypothesis was proposed in this article.

Adjustments to In Vitro Culture Conditions and Associated Anomalies in Plants

Plant tissue culture techniques have become an integral part of progress in plant science research due to the opportunity offered for close study of detailed plant development with applications in food production through crop improvement, secondary metabolites production and conservation of species. Because the techniques involve growing plants under controlled conditions different from their natural outdoor environment, the plants need adjustments in physiology, anatomy and metabolism for successfulin vitropropagation. Therefore, the protocol has to be optimized for a given species or genotype due to the variability in physiological and growth requirement. Developing the protocol is hampered by several physiological and developmental aberrations in the anatomy and physiology of the plantlets, attributed toin vitroculture conditions of high humidity, low light levels and hetero- or mixotrophic conditions. Some of the culture-induced anomalies become genetic, and the phenotype is inherited by clonal progenies while others are temporary and can be corrected at a later stage of protocol development through changes in anatomy, physiology and metabolism. The success of protocols relies on the transfer of plantlets to field conditions which has been achieved with many species through stages of acclimatization, while with others it remains a challenging task. This review discusses various adjustments in nutrition, physiology and anatomy of micro-propagated plants and field grown ones, as well as anomalies induced by thein vitroculture conditions.

High genetic and epigenetic stability in Coffea arabica plants derived from embryogenic suspensions and secondary embryogenesis as revealed by AFLP, MSAP and the phenotypic variation rate

Embryogenic suspensions that involve extensive cell division are risky in respect to genome and epigenome instability. Elevated frequencies of somaclonal variation in embryogenic suspension-derived plants were reported in many species, including coffee. This problem could be overcome by using culture conditions that allow moderate cell proliferation. In view of true-to-type large-scale propagation of C. arabica hybrids, suspension protocols based on low 2,4-D concentrations and short proliferation periods were developed. As mechanisms leading to somaclonal variation are often complex, the phenotypic, genetic and epigenetic changes were jointly assessed so as to accurately evaluate the conformity of suspension-derived plants. The effects of embryogenic suspensions and secondary embryogenesis, used as proliferation systems, on the genetic conformity of somatic embryogenesis-derived plants (emblings) were assessed in two hybrids. When applied over a 6 month period, both systems ensured very low somaclonal variation rates, as observed through massive phenotypic observations in field plots (0.74% from 200,000 plant). Molecular AFLP and MSAP analyses performed on 145 three year-old emblings showed that polymorphism between mother plants and emblings was extremely low, i.e. ranges of 0-0.003% and 0.07-0.18% respectively, with no significant difference between the proliferation systems for the two hybrids. No embling was found to cumulate more than three methylation polymorphisms. No relation was established between the variant phenotype (27 variants studied) and a particular MSAP pattern. Chromosome counting showed that 7 of the 11 variant emblings analyzed were characterized by the loss of 1-3 chromosomes. This work showed that both embryogenic suspensions and secondary embryogenesis are reliable for true-to-type propagation of elite material. Molecular analyses revealed that genetic and epigenetic alterations are particularly limited during coffee somatic embryogenesis. The main change in most of the rare phenotypic variants was aneuploidy, indicating that mitotic aberrations play a major role in somaclonal variation in coffee.

Molecular marker analysis of hypoploid regenerants from cultures of barley x Canada wild rye

Canada wild rye (CWR, Elymus canadensis L., 2n = 4x = 28) is a potential source of genes for disease resistance and environmental tolerance in barley (Hordeum vulgare L., 2n = 2x = 14). Tissue cultures were initiated from immature inflorescences of CWR x 'Betzes' barley hybrids to promote CWR introgression into barley through possible tissue culture induced chromosome breakage and exchange. Among the plants regenerated, some were missing one (2n = 20) or part of one (2n = 20 + telo) chromosome. The objective of this study was to identify the missing chromosome or chromosome arm in these regenerants through the analysis of molecular (RFLP) markers that previously had been mapped in barley. Forty-six hypoploid regenerants that traced to 30 separate explants obtained from 10 interspecific hybrid plants were evaluated. DNA was digested with the restriction enzyme HindIII, Southern blotted, and probed with 39 genomic and cDNA barley clones that identified sequences polymorphic between barley and CWR. Eight of these probes identified band loss patterns that separated the regenerants into two groups. One group, all with barley cytoplasm, were missing a CWR chromosome homoeologous to barley chromosome 3; a second group, all with CWR cytoplasm, were missing a CWR chromosome homoelogous to barley chromosome 7. These results indicated that chromosome elimination in culture was not random. The two cytoplasm groups were further differentiated by probes that identified band shifts. These band shifts were caused by differences in DNA methylation. Key words : Hordeum vulgare, aneuploidy, Elymus canadensis, tissue culture.

RFLP analysis of the progeny from Oryza alta Swallen x Oryza sativa L

RFLP analyses were carried out in the progeny from a cross of two phylogenetically distant rice species, wild rice Oryza alta Swallen (CCDD, 2n = 48) and cultivated rice O. sativa L. (AA, 2n = 24). The sterile plants gave heterozygous RFLP patterns at most of the loci detected. They looked more like their wild rice parent, with 36 chromosomes in their root-tip cells and pollen mother cells. In two partially fertile plants, however, most of the markers that were used showed RFLP patterns similar to the cultivated parent, O. sativa. By cytological study, it was found that nearly one-third of the chromosomes had been eliminated in the partially fertile plants. Their seeds have short awns, which is a characteristic of their wild parent, O. alta. An introgression occurred in one of the partially fertile plants, which led to the discussion about a nonconventional mechanism in wide hybridization for transference of wild rice chromosome segments to cultivated rice chromosomes.

Effects of different combinations of benzyl adenine and indole acetic acid concentrations on in vitro plant regeneration in hexaploid wheat

Development of a reliable in vitro plant regeneration procedure for hexaploid bread wheat (Triticum aestivum L.) is a prerequisite for its improvement by genetic transformation. Here, we report the effects of two growth regulators, benzyl adenine (BA) and indole acetic acid (IAA) on callus induction and plant regeneration from scutellum cultures of two commercial bread wheat cultivars: Giza 164 and Sakha 69. Callus induction was obtained from isolated embryos cultured on modified Murashige and Skoog (MS) basal medium. After four weeks of callus induction, all calli were plated on MS basal medium for regeneration. Wheat genotype and callus induction medium played a dominant role in plantlet regeneration. 2.0 mg/L BA and 0.2 mg/L IAA were the best combinations for inducing callus and let to highest regeneration frequency (81.67%) across the cultivars. Overall, based on our medium conditions, Giza 164 displayed higher regeneration frequency (81.11%) than Sakha 69. These results will facilitate genetic transformation for the economic varieties Giza 164 and Sakha 69.

Assessment of genetic and epigenetic changes following cryopreservation in papaya

A vitrification based cryopreservation technique for storage of in vitro shoot tips of papaya has been tested to ensure applicability across a range of genotypes and to assess the stability of both genotype and phenotype of such clonal material following cryopreservation. Shoot tips of 12 genotypes were cryopreserved, recovery rates were determined and resultant plants were screened for genetic and epigenetic changes. Genomic DNA structure was explored using polymerase chain reaction (PCR) based randomly amplified DNA fingerprinting (RAF), and methylation patterns were monitored using the amplified DNA methylation polymorphism (AMP) PCR technique. Plantlets were recovered following cryopreservation in all but one genotype and recovery rates of 61-73% were obtained from six genotypes. The regenerated plantlets showed varying levels of genomic DNA modifications (0-10.07%), and methylation modifications (0.52-6.62%) of detected markers. These findings have not been reported previously for papaya, and indicate some genotype dependent variability in DNA modifications occur following cryopreservation which may result in somaclonal variation.

The negative influence of N-mediated TMV resistance on yield in tobacco: linkage drag versus pleiotropy

Resistance to tobacco mosaic virus (TMV) is controlled by the single dominant gene N in Nicotiana glutinosa L. This gene has been transferred to cultivated tobacco (N. tabacum L.) by interspecific hybridization and backcrossing, but has historically been associated with reduced yields and/or quality in flue-cured tobacco breeding materials. Past researchers have suggested the role of pleiotropy and/or linkage drag effects in this unfavorable relationship. Introduction of the cloned N gene into a TMV-susceptible tobacco genotype (cultivar 'K326') via plant transformation permitted investigation of the relative importance of these possibilities. On average, yield and cash return ($ ha(-1)) of 14 transgenic NN lines of K326 were significantly higher relative to an isoline of K326 carrying N introduced via interspecific hybridization and backcrossing. The negative effects of tissue culture-induced genetic variation confounded comparisons with the TMV-susceptible cultivar, K326, however. Backcrossing the original transgenic lines to non-tissue cultured K326 removed many of these unfavorable effects, and significantly improved their performance for yield and cash return. Comparisons of the 14 corresponding transgenic NN backcross-derived lines with K326 indicated that linkage drag is the main factor contributing to reduced yields in TMV-resistant flue-cured tobacco germplasm. On average, these transgenic lines outyielded the conventionally-developed TMV-resistant K326 isoline by 427 kg ha(-1) (P < 0.05) and generated $1,365 ha(-1) more (P < 0.05). Although transgenic tobacco cultivars are currently not commercially acceptable, breeding strategies designed to reduce the amount of N. glutinosa chromatin linked to N may increase the likelihood of developing high-yielding TMV-resistant flue-cured tobacco cultivars.

Chromosome endoreduplication as a factor of salt adaptation in Sorghum bicolor

Nuclear DNA amounts were measured by Feulgen cytophotometry in Sorghum bicolor cv. 610 plants early exposed to 150 mM NaCl, a treatment known to induce an increased tolerance to salinity in plants carrying this genotype. In salt-treated plants, the percentages of 8C, 16C, and 32C nuclei in roots in the primary state of growth were 21.9%, 13.3%, and 4.3%, respectively. By contrast, in nonsalinized plants, only 3.5% of the nuclei had an 8C content and no higher DNA contents were observed. The salt treatment induced chromosome endoreduplication during the differentiation of cells in the root cortex, where 41.2% of the cells displayed a DNA content higher than 4C (versus 1.3% in control plants). No enhancement of endopolyploidy was observed in cells of the root vascular cylinder or the leaves of the salt-treated plants. In another S. bicolor genotype (DK 34-Alabama), noncompetent for salt adaptation, the same NaCl treatment did not induce chromosome endoreduplication in root cortex cells. Endopolyploidy may be considered as a part of the adaptive response of S. bicolor competent genotypes to salinity.

Chromatin remodeling in plant cell culture: patterns of DNA methylation and histone H3 and H4 acetylation vary during growth of asynchronous potato cell suspensions

Changes in DNA cytosine methylation and core histone multi-acetylation were determined in cell suspension cultures of potato (Solanum tuberosum L. cv. Russet Burbank) during 15 days of in vitro culture. Cell subculture induced a transient 33% decrease in genome-wide 5-methylcytosine (5mC) content and a transient threefold increase in transcription rates that were most evident at 6 and 9 days after subculture, respectively. In contrast to the global reduction in 5mC content, subculture resulted in a transient twofold increase in 5mC levels within 5'-CCGG-3' sequences and no detectable change in 5'-CG-3' methylation. Multi-acetylation of histones H3.1, H3.2 and H4 rose 2-, 1.5- and 3-fold by 9, 9 and 12 days after subculture, respectively. All observed epigenetic changes were reset during aging of cell cultures. Inclusion of the histone deacetylase inhibitor trichostatin A (TSA) and/or the cytosine methylation inhibitor 5-azacytidine (5AC) in culture sequentially decreased genome-wide 5mC levels by approximately 25% at day 9, then decreased 5'-mCmCGG-3' by 30-50% and increased H3 and H4 multi-acetylation by 30-60% at day 15, compared to controls. Treatment with 5AC or TSA alone or in combination had no effect on RNA synthesis at day 9. At day 15, 5AC treatment remained ineffective, while de novo RNA synthesis was approximately twofold higher in cells grown in both inhibitors or in TSA alone. Collectively, these results demonstrate that in potato suspension cultures, rapid, reversible changes in 5mC levels precede regulatory post-translational acetylation of core histones, and suggest that interactions between these epigenetic processes appear to be necessary to power transcription and growth induction in potato cells.

Stable maintenance and expression of a foreign gene in transgenic pear shoots retrieved from in vitro conservation

Shoot-tips of transgenic pear were successfully conserved in vitro by slow-growth and cryopreservation methods. After 1 year of storage in slow growth conditions, all shoot-tips survived showing shoot re-growth. Similarly, shoot-tips showed high survival and regeneration rates after cryopreservation. The genetic stability of the transgenic GUS construct in shoots recovered from slow-growth and cryopreservation was assessed. The results from polymerase chain reaction and Southern blotting showed the stable maintenance of the GUS gene in genome, and the Single-Strand Conformation Polymorphism assay did not detect single base variation. X-Gluc staining suggested a normal expression of the GUS gene in shoots retrieved from these storage methods.

Transfer of resistance to potato virus Y (PVY) from Nicotiana africana to Nicotiana tabacum: possible influence of tissue culture on the rate of introgression

A disomic chromosome addition line of tobacco, Nicotiana tabacum L., was established previously that possesses a single chromosome pair from N. africana [Merxm. and Buttler]. This addition chromosome carries a gene that confers increased resistance to severe strains of potato virus Y (PVY). Methods to increase the probability of gene transfer from alien chromosomes to tobacco (2n=48) are desired. In the research described here, the PVY resistance gene was transferred to a tobacco chromosome from the N. africana addition chromosome in seven independent cases. One introgression event was obtained using conventional backcrossing of the disomic addition line to N. tabacum cv. Petite Havana, while the remaining six events were obtained using a scheme that involved exposure of explants of the addition line to tissue culture. Twenty-six derived 2n=48 individuals heterozygous for PVY resistance were found to exhibit 24 bivalents or 23 bivalents + 2 univalents at metaphase I. Ovular transmission rates for the PVY resistance factor ranged from 25% to 52%, while pollen transmission rates were much lower, ranging from 0 to 39%. Fifty-one random amplified polymorphic DNA (RAPD) markers specific for the intact addition chromosome were identified and used to characterize derived 2n=48/PVY-resistant genotypes. Variability was observed among these plants with respect to the total number of N. africana RAPD markers that were present, which is an indication that crossing over was occurring within each of the seven introgressed chromosome segments. A limited molecular marker-assisted backcrossing experiment allowed for selection of a 2n=48/PVY-resistant individual that possessed only 6 of the 51 original N. africana RAPD markers. In vitro culture is potentially a valuable system for increasing the rate of alien gene transfer in tobacco, and the successful transfer of PVY resistance from N. africana may allow for an increased level and range of resistance to this virus in tobacco.

Genetic and epigenetic evaluations of citrus calluses recovered from slow-growth culture

The embryogenic callus of "Red Marsh" grapefruit was stored in vitro by slow growth culture method for one year, and survived with a significant weight increment over that period. The survivers regenerated somatic embryos more easily than the controls. Eight callus lines were used for genetic analyses. Although chromosome number variations were verified by cytological examination both in the controls and the stored samples, the ploidy level remained relatively stable during the storage period. Randomly amplified polymorphic DNA (RAPD) analysis was performed to detect DNA sequence variation. No difference in RAPD pattern was found with the 102 primers used. However, a methylation sensitive amplified polymorphism (MSAP) assay showed DNA methylation changes in the stored samples compared with the controls.

Feasibility of antibody production in plants for human therapeutic use

From the description above, the diversity of antibodies as a class of potential therapeutic agents is weighed against the constraints of developing any therapeutic molecule. Although much of this limit is specific to the antibody design, plant-based production systems have a potential to impact commercialization by making larger volume products manageable, with lower up-front capital requirements. Due to their novel glycosylation pattern (Faye et al. 1989), plants at present may not create antibodies with all the functions of mammalian-glycosylated antibodies (Wright and Morrison 1994). This is not a limit for all current products. Success is dependent on fusing the efficient agriculture infrastructure with the narrow tolerances required for a drug production system. Further validation of plants as a production system will come as more therapeutics from plants follow the corn-produced material through human clinical trials.

Probing the morphological developmental path of plant embryos by image tracking

An image analysis and pattern recognition system was applied to track the morphological changes of individual plant somatic embryos during the course of their development into mature embryos. A Fourier descriptor was used to transform the morphological information into quantitative features (Fourier features), which are amenable to mathematical and statistical analysis. At a given time point, the status of each developing embryo is represented by a point in the multidimension feature space spanned by these Fourier features. Connecting each point representing the individual embryos over time gives a trajectory which depicts the embryos' developmental "path" or history. Large variations in embryo development were observed, which is consistent with the population heterogeneity seen in batch embryo cultures. The rate at which each embryo progresses in the feature space was measured by a developmental vector. For embryos in a given class or developmental stage, the magnitude of the developmental vector exhibited a wide distribution. The results revealed that embryos with a higher developmental rate during the early stage of development had a higher chance of reaching the mature stage in a relatively short time. This single embryo tracking method is potentially a valuable tool in developing a correlation between the embryo's morphological features during the early stage of development and its eventual developmental fate. Copyright 1998 John Wiley & Sons, Inc.

Strategies for "minimal growth maintenance" of cell cultures: a perspective on management for extended duration experimentation in the microgravity environment of a Space station

How cells manage without gravity and how they change in the absence of gravity are basic questions that only prolonged life on a Space station will enable us to answer. We know from investigations carried out on various kinds of Space vehicles and stations that profound physiological effects can and often to occur. We need to know more of the basic biochemistry and biophysics both of cells and of whole organisms in conditions of reduced gravity. The unique environment of Space affords plant scientists an unusual opportunity to carry out experiments in microgravity, but some major challenges must be faced before this can be done with confidence. Various laboratory activities that are routine on Earth take on special significance and offer problems that need imaginative resolution before even a relatively simple experiment can be reliably executed on a Space station. For example, scientists might wish to investigate whether adaptive or other changes that have occurred in the environment of Space are retained after return to Earth-normal conditions. Investigators seeking to carry out experiments in the low-gravity environment of Space using cultured cells will need to solve the problem of keeping cultures quiescent for protracted periods before an experiment is initiated, after periodic sampling is carried out, and after the experiment is completed. This review gives an evaluation of a range of strategies that can enable one to manipulate cell physiology and curtail growth dramatically toward this end. These strategies include cryopreservation, chilling, reduced oxygen, gel entrapment strategies, osmotic adjustment, nutrient starvation, pH manipulation, and the use of mitotic inhibitors and growth-retarding chemicals. Cells not only need to be rendered quiescent for protracted periods but they also must be recoverable and further grown if it is so desired. Elaboration of satisfactory procedures for management of cells and tissues at "near zero or minimal growth" will have great value and practical consequences for experimentation on Earth as well as in Space. All of the parameters and conditions and procedural details needed to meet all the specific objectives will be the basis of the design and fabrication of cell culture units for use in the Space environment. It is expected that this will be an evolutionary process.

Physiological aspects of genome variability in tissue culture. II. Growth phase-dependent quantitative variability of repetitive BstNI fragments of primary cultures of Daucus carota L

Systematic investigations on the occurrence of differential DNA replication in carrot cultures, expressed at the total genome level, were performed. The genome of Daucus carota L. could be characterized by a pattern of repetitive BstNI fragments that was independent of tissue specificity or cultivar differences. Characterization of the genomic DNA of the secondary phloem of carrot roots, in comparison to the DNA of the induced primary cultures at different growth phases, revealed dramatic differences in the copy number of the repetitive fragments. Highly proliferative tissue showed extensive reduction in the proportion of repetitive sequences in the genome in all of the 37 investigated variants. In contrast, during subsequent transition to stationary growth the repetitive fragments re-amplified. The results suggest that the quantitative genome organisation was involved in the regulation of the growth potential of cells. A hypothesis is discussed suggesting a determining influence of the observed differential DNA replication on cell-cycle rates and the cell program of proliferative tissue by structural and positioning effects on DNA loops. To study the causality of somaclonal variation, research on the relationship between physiological genome variability and the induction of heritable changes is recommended.

Treatment with propionic and butyric acid enhances expression variegation and promoter methylation in plant transgenes

Two phenotypic marker genes (A1 and GUS) were employed to monitor the influence of small chain fatty acids on transgene expression in petunia and tobacco. In plants homozygous with respect to the A1 transgene, which normally carry red flowers due to A1 expression, fatty acid treatment induced a range of variegated and white pigmentation patterns which persisted for several months after terminating the treatment. The inhibitory effect was clearly less pronounced for heterozygous plants of the same transgenic line. In all cases the reduction of transgene activities correlated with an increase in transgene promoter methylation. Contrary to evidence reported for mammals and Drosophila, we do not observe an increase in gene expression, but an enhancement of DNA methylation and epigenetic variegation. The inhibition of transgene activity was also observed in several tobacco transformants cultured on fatty acid containing media. Some tobacco transformants carrying Gus-coding regions driven by either 35S or 1'2' promoters responded with a significant reduction in GUS activity. This study suggests that, rather than exerting a general response on all chromatin regions, fatty acids appear to affect genes in a labile epigenetic surrounding or all genes in a susceptible chromatin configuration. Thus, application of these agents may be useful to screen and monitor transgenes prone to epigenetic instabilities.

Structural changes in the plastid DNA of rice (Oryza sativa L.) during tissue culture

To investigate the rearrangement of the plastid genome during tissue culture, DNA from rice callus lines, which had been derived individually from single protoplasts isolated from seed or pollen callus (protoclones), was analyzed by Southern hybridization with rice chloroplast DNA (ctDNA) clones as probes. Among 44 long-term cultured protoclones, maintained for 4, 8 or 11 years, 28 contained plastid DNA (ptDNA) from which portions had been deleted. The ptDNA of all protoclones that had been maintained for 11 years had a deletion that covered a large region of the plastid genome. The deletions could be classified into 15 types from their respective sizes and positions. By contrast, no deletions were found in the ptDNA of 38 protoclones that had been maintained for only 1 month. These results indicate that long-term culture causes deletions in the plastid genome. Detailed hybridization experiments revealed that plastid genomes with deletions in several protoclones were organized as head-to-head or tail-to-tail structures. Furthermore, ptDNAs retained during long-term culture all had a common terminus at one end, where extensive rearrangement is known to have occurred during the speciation of rice and tobacco. Morphological analysis revealed the accumulation of starch granules in plastids and amyloplasts in protoclones in which the plastid genome had undergone deletion. Our observations indicated that novel structural changes in the plastid genome and morphological changes in the plastid had occurred in rice cells during long-term tissue culture. Moreover, the morphological changes in plastids were associated with deletions in the plastid genome.