Somaclonal variation - a novel source of variability from cell cultures for plant improvement

DNA Methylation Level Changes in Transgenic Chinese Cabbage (Brassica rapa ssp. pekinensis) Plants and Their Effects on Corresponding Gene Expression Patterns

Plant tissue culture is an in vitro technique used to manipulate cells, tissues, or organs, and plays an important role in genetic transformation. However, plants cultured in vitro often exhibit unintended genetic and epigenetic variations. Since it is important to secure the stability of endogenous and exogenous gene expressions in transgenic plants, it is preferable to avoid the occurrence of such variations. In this study, we focused on epigenetic variations, exclusively on methylation level changes of DNA, in transgenic Chinese cabbage (Brassica rapa ssp. pekinensis) plants. To detect these methylation level changes of DNA, bisulfite sequencing was performed and the obtained sequences were compared with the ‘CT001’ reference genome. Differentially methylated regions (DMRs) of DNA between the non-transgenic and transgenic lines were detected by bisulfite sequencing, and ten DMRs located in exonic regions were identified. The regions with methylation variations that were inherited and consistently maintained in the next generation lines were selected and validated. We also analyzed the relationship between methylation status and expression levels of transformant-conserved DMR (TCD) genes by quantitative reverse transcription-PCR. These results suggested that the changes in methylation levels of these DMRs might have been related to the plant transformation process, affecting subsequent gene expression. Our findings can be used in fundamental research on methylation variations in transgenic plants and suggest that these variations affect the expression of the associated genes.

Comparative Phenotypic and Agronomic Assessment of Transgenic Potato with 3R-Gene Stack with Complete Resistance to Late Blight Disease

Transgenic potato event Vic.172, expressing three naturally occurring resistance genes (R genes) conferring complete protection against late blight disease, was evaluated for resistance to late blight, phenotypic characterization, and agronomic performance in field conditions at three locations during three seasons in Uganda. These trials were conducted by comparison to the variety Victoria from which Vic.172 derives, using identical fungicide treatment, except when evaluating disease resistance. During all seasons, the transgenic event Vic.172 was confirmed to have complete resistance to late blight disease, whereas Victoria plants were completely dead by 60-80 days after planting. Tubers from Vic.172 were completely resistant to LB after artificial inoculation. The phenotypic characterization included observations of the characteristics and development of the stems, leaves, flowers, and tubers. Differences in phenotypic parameters between Vic.172 and Victoria were not statistically significant across locations and seasons. The agronomic performance observations covered sprouting, emergence, vigor, foliage growth, and yield. Differences in agronomic performance were not statistically significant except for marketable yield in one location under high productivity conditions. However, yield variation across locations and seasons was not statistically significant, but was influenced by the environment. Hence, the results of the comparative assessment of the phenotype and agronomic performance revealed that transgenic event Vic.172 did not present biologically significant differences in comparison to the variety Victoria it derives from.

Chemical Composition and Cytotoxic Activity of the Essential Oil and Oleoresins of In Vitro Micropropagated Ansellia africana Lindl: A Vulnerable Medicinal Orchid of Africa

Orchids are rich treasure troves of various important phytomolecules. Among the various medicinal orchids, Ansellia africana stands out prominently in the preparing of various herbal medicines due to its high therapeutic importance. The nodal explants of A. africana were sampled from asymbiotically germinated seedlings on basal Murashige and Skoog (MS) medium and were micropropagated in MS medium supplemented with 3% sucrose and 10 µM meta topolin (mT) + 5 µM naphthalene acetic acid (NAA) +15 µM indole butyric acid (IBA) + 30 µM phloroglucinol (PG). In the present study, the essential oil was extracted by hydrodistillation and the oleoresins by the solvent extraction method from the micropropagated A. africana. The essential oil and the oleoresins were analysed by Gas Chromatography (GC) and GC/MS (Mass spectrometry). A total of 84 compounds were identified. The most predominant components among them were linoleic acid (18.42%), l-ascorbyl 2,6-dipalmitate (11.50%), linolenic acid (10.98%) and p-cresol (9.99%) in the essential oil; and eicosane (26.34%), n-butyl acetate (21.13%), heptadecane (16.48%) and 2-pentanone, 4-hydroxy-4-methyl (11.13%) were detected in the acetone extract; heptadecane (9.40%), heneicosane (9.45%), eicosane (6.40%), n-butyl acetate (14.34%) and styrene (22.20%) were identified and quantified in the ethyl acetate extract. The cytotoxic activity of essential oil and oleoresins of micropropagated A. africana was evaluated by MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium Bromide) assay on Vero cells compared to the standard drug doxorubicin chloride. The present research contains primary information about the therapeutic utility of the essential oil and oleoresins of A. africana with a promising future research potential of qualitative and quantitative improvement through synchronised use of biotechnological techniques.

Understanding In Vitro Tissue Culture-Induced Variation Phenomenon in Microspore System

In vitro tissue culture plant regeneration is a complicated process that requires stressful conditions affecting the cell functioning at multiple levels, including signaling pathways, transcriptome functioning, the interaction between cellular organelles (retro-, anterograde), compounds methylation, biochemical cycles, and DNA mutations. Unfortunately, the network linking all these aspects is not well understood, and the available knowledge is not systemized. Moreover, some aspects of the phenomenon are poorly studied. The present review attempts to present a broad range of aspects involved in the tissue culture-induced variation and hopefully would stimulate further investigations allowing a better understanding of the phenomenon and the cell functioning.

Era-like GTP protein gene expression in rice

The mutations are genetic changes in the genome sequences and have a significant role in biotechnology, genetics, and molecular biology even to find out the genome sequences of a cell DNA along with the viral RNA sequencing. The mutations are the alterations in DNA that may be natural or spontaneous and induced due to biochemical reactions or radiations which damage cell DNA. There is another cause of mutations which is known as transposons or jumping genes which can change their position in the genome during meiosis or DNA replication. The transposable elements can induce by self in the genome due to cellular and molecular mechanisms including hypermutation which caused the localization of transposable elements to move within the genome. The use of induced mutations for studying the mutagenesis in crop plants is very common as well as a promising method for screening crop plants with new and enhanced traits for the improvement of yield and production. The utilization of insertional mutations through transposons or jumping genes usually generates stable mutant alleles which are mostly tagged for the presence or absence of jumping genes or transposable elements. The transposable elements may be used for the identification of mutated genes in crop plants and even for the stable insertion of transposable elements in mutated crop plants. The guanine nucleotide-binding (GTP) proteins have an important role in inducing tolerance in rice plants to combat abiotic stress conditions.

Androgenic-Induced Transposable Elements Dependent Sequence Variation in Barley

A plant genome usually encompasses different families of transposable elements (TEs) that may constitute up to 85% of nuclear DNA. Under stressful conditions, some of them may activate, leading to sequence variation. In vitro plant regeneration may induce either phenotypic or genetic and epigenetic changes. While DNA methylation alternations might be related, i.e., to the Yang cycle problems, DNA pattern changes, especially DNA demethylation, may activate TEs that could result in point mutations in DNA sequence changes. Thus, TEs have the highest input into sequence variation (SV). A set of barley regenerants were derived via in vitro anther culture. High Performance Liquid Chromatography (RP-HPLC), used to study the global DNA methylation of donor plants and their regenerants, showed that the level of DNA methylation increased in regenerants by 1.45% compared to the donors. The Methyl-Sensitive Transposon Display (MSTD) based on methylation-sensitive Amplified Fragment Length Polymorphism (metAFLP) approach demonstrated that, depending on the selected elements belonging to the TEs family analyzed, varying levels of sequence variation were evaluated. DNA sequence contexts may have a different impact on SV generated by distinct mobile elements belonged to various TE families. Based on the presented study, some of the selected mobile elements contribute differently to TE-related SV. The surrounding context of the TEs DNA sequence is possibly important here, and the study explained some part of SV related to those contexts.

Autotetraploid Emergence via Somatic Embryogenesis in Vitis vinifera Induces Marked Morphological Changes in Shoots, Mature Leaves, and Stomata

Polyploidy plays an important role in plant adaptation to biotic and abiotic stresses. Alterations of the ploidy in grapevine plants regenerated via somatic embryogenesis (SE) may provide a source of genetic variability useful for the improvement of agronomic characteristics of crops. In the grapevine, the SE induction process may cause ploidy changes without alterations in DNA profile. In the present research, tetraploid plants were observed for 9.3% of ‘Frappato’ grapevine somatic embryos regenerated in medium supplemented with the growth regulators β-naphthoxyacetic acid (10 µM) and N⁶-benzylaminopurine (4.4 µM). Autotetraploid plants regenerated via SE without detectable changes in the DNA profiles were transferred in field conditions to analyze the effect of polyploidization. Different ploidy levels induced several anatomical and morphological changes of the shoots and mature leaves. Alterations have been also observed in stomata. The length and width of stomata of tetraploid leaves were 39.9 and 18.6% higher than diploids, respectively. The chloroplast number per guard cell pair was higher (5.2%) in tetraploid leaves. On the contrary, the stomatal index was markedly decreased (12%) in tetraploid leaves. The observed morphological alterations might be useful traits for breeding of grapevine varieties in a changing environment.

Solanum aethiopicum: The Nutrient-Rich Vegetable Crop with Great Economic, Genetic Biodiversity and Pharmaceutical Potential

Solanum aethiopicum is a very important vegetable for both rural and urban communities in Africa. The crop is rich in both macro- and micronutrients compared with other vegetables and is suitable for ensuring food and nutritional security. It also possesses several medicinal properties and is currently employed in the treatment of high blood pressure, diabetes, cholera, uterine complaints as well as skin infections in humans. The crop is predominantly cultivated by traditional farmers and plays an important role in the subsistence and economy of poor farmers and consumers throughout the developing world. It also holds potential for dietary diversification, greater genetic biodiversity and sustainable production in Africa. Despite the numerous benefits the crop presents, it remains neglected and underutilized due to the world’s over-dependence on a few plant species, as well as the little attention in research and development it has received over the years. This review highlights the importance of S. aethiopicum, its role in crop diversification, reducing hidden hunger, the potential for nutritive and medicinal benefits, agricultural sustainability and future thrusts for breeding and genetic improvement of the plant species.

Identification and Validation of Genetic Variations in Transgenic Chinese Cabbage Plants (Brassica rapa ssp. pekinensis) by Next-Generation Sequencing

Transgenic plants are usually produced through tissue culture, which is an essential step in Agrobacterium-mediated plant transformation. However, genomic variations, termed somaclonal variations, have been detected in transgenic plants cultured in vitro. The occurrence of these variations should be as low as possible to secure the stability of transgenic crops. Determining the cause and mechanism of somaclonal variations in tissue culture-derived plants will help reduce the rate of variation and promote the stable expression of genes in transgenic plants. In order to determine the genetic variability in transgenic Chinese cabbage plants, we performed whole-genome resequencing and compared the sequencing data with the ‘CT001’ reference genome. The variation candidates that were expected to consistently occur in the transgenic lines were selected and validated. The single nucleotide polymorphism (SNP) and insertion and deletion (InDel) candidates were identified using the resequencing data and validated by reverse transcription (RT)-PCR analysis. The deduced amino acid sequences were used to determine whether the variations caused changes in the resulting polypeptide, and the annotations of the mutated genes were analyzed to predict the possible effects of the SNPs on gene function. In conclusion, we selected and validated the genetic variations identified in transgenic Chinese cabbage plants. Their genomes were expected to be affected by the process of Agrobacterium-mediated transformation. The findings of our study will provide a genetic basis for transgenic plant research.

High Chromosomal Stability and Immortalized Totipotency Characterize Long-Term Tissue Cultures of Chinese Ginseng (Panax Ginseng)

Chinese ginseng (Panax ginseng C. A. Meyer) is a highly cherished traditional Chinese medicine, with several confirmed medical effects and many more asserted health-boosting functions. Somatic chromosomal instability (CIN) is a hallmark of many types of human cancers and also related to other pathogenic conditions such as miscarriages and intellectual disabilities, hence, the study of this phenomenon is of wide scientific and translational medical significance. CIN also ubiquitously occurs in cultured plant cells, and is implicated as a major cause of the rapid decline/loss of totipotency with culture duration, which represents a major hindrance to the application of transgenic technologies in crop improvement. Here, we report two salient features of long-term cultured callus cells of ginseng, i.e., high chromosomal stability and virtually immortalized totipotency. Specifically, we document that our callus of ginseng, which has been subcultured for 12 consecutive years, remained highly stable at the chromosomal level and showed little decline in totipotency. We show that these remarkable features of cultured ginseng cells are likely relevant to the robust homeostasis of the transcriptional expression of specific genes (i.e., genes related to tissue totipotency and chromosomal stability) implicated in the manifestation of these two complex phenotypes. To our knowledge, these two properties of ginseng have not been observed in any animals (with respect to somatic chromosomal stability) and other plants. We posit that further exploration of the molecular mechanisms underlying these unique properties of ginseng, especially somatic chromosomal stability in protracted culture duration, may provide novel clues to the mechanistic understanding of the occurrence of CIN in human disease.

Datura genome reveals duplications of psychoactive alkaloid biosynthetic genes and high mutation rate following tissue culture

BACKGROUND

Datura stramonium (Jimsonweed) is a medicinally and pharmaceutically important plant in the nightshade family (Solanaceae) known for its production of various toxic, hallucinogenic, and therapeutic tropane alkaloids. Recently, we published a tissue-culture based transformation protocol for D. stramonium that enables more thorough functional genomics studies of this plant. However, the tissue culture process can lead to undesirable phenotypic and genomic consequences independent of the transgene used. Here, we have assembled and annotated a draft genome of D. stramonium with a focus on tropane alkaloid biosynthetic genes. We then use mRNA sequencing and genome resequencing of transformants to characterize changes following tissue culture.

RESULTS

Our draft assembly conforms to the expected 2 gigabasepair haploid genome size of this plant and achieved a BUSCO score of 94.7% complete, single-copy genes. The repetitive content of the genome is 61%, with Gypsy-type retrotransposons accounting for half of this. Our gene annotation estimates the number of protein-coding genes at 52,149 and shows evidence of duplications in two key alkaloid biosynthetic genes, tropinone reductase I and hyoscyamine 6 β-hydroxylase. Following tissue culture, we detected only 186 differentially expressed genes, but were unable to correlate these changes in expression with either polymorphisms from resequencing or positional effects of transposons.

CONCLUSIONS

We have assembled, annotated, and characterized the first draft genome for this important model plant species. Using this resource, we show duplications of genes leading to the synthesis of the medicinally important alkaloid, scopolamine. Our results also demonstrate that following tissue culture, mutation rates of transformed plants are quite high (1.16 × 10- 3 mutations per site), but do not have a drastic impact on gene expression.

Somatic Embryogenesis in Olive

The olive is a fruit tree species economically very important in countries of the Mediterranean basin. Somatic embryogenesis is a powerful in vitro technique with multiple uses in different fields, including breeding programs performed by both classical and innovative procedures. Thus, somatic embryogenesis enables the application of biotechnological methods such as genetic transformation, somaclonal variation, somatic hybridization, germplasm cryopreservation, in vitro mutagenesis or in vitro selection. This editorial paper presents a special issue focused on “Somatic embryogenesis in olive”. In this manuscript, the conceptual framework of the special issue is established and the contributions are summarized and put into context. Finally, the main bottlenecks limiting the practical applicability of somatic embryogenesis in this species are identified and the future research prospects are discussed.

Wheat omics: Classical breeding to new breeding technologies

Wheat is an important cereal crop, and its significance is more due to compete for dietary products in the world. Many constraints facing by the wheat crop due to environmental hazardous, biotic, abiotic stress and heavy matters factors, as a result, decrease the yield. Understanding the molecular mechanism related to these factors is significant to figure out genes regulate under specific conditions. Classical breeding using hybridization has been used to increase the yield but not prospered at the desired level. With the development of newly emerging technologies in biological sciences i.e., marker assisted breeding (MAB), QTLs mapping, mutation breeding, proteomics, metabolomics, next-generation sequencing (NGS), RNA_sequencing, transcriptomics, differential expression genes (DEGs), computational resources and genome editing techniques i.e. (CRISPR cas9; Cas13) advances in the field of omics. Application of new breeding technologies develops huge data; considerable development is needed in bioinformatics science to interpret the data. However, combined omics application to address physiological questions linked with genetics is still a challenge. Moreover, viroid discovery opens the new direction for research, economics, and target specification. Comparative genomics important to figure gene of interest processes are further discussed about considering the identification of genes, genomic loci, and biochemical pathways linked with stress resilience in wheat. Furthermore, this review extensively discussed the omics approaches and their effective use. Integrated plant omics technologies have been used viroid genomes associated with CRISPR and CRISPR-associated Cas13a proteins system used for engineering of viroid interference along with high-performance multidimensional phenotyping as a significant limiting factor for increasing stress resistance in wheat.

A Rapid Method for Stably Transforming Rice Seeds

Plant transformation technology offers ample opportunities for basic scientific and translational research. Several Agrobacterium-mediated plant transformation protocols are available, for transforming rice, through callus initiation and regeneration. The regularly used transformation procedures require time and skilled labor and are limited by the regeneration capabilities of the tissue. Here we describe a simple, robust and tissue culture-independent method for transformation of rice seeds using pCAMBIA-amiR820 as model construct. Plants obtained from the transformed seeds were selected on antibiotic media and tested for transgene integration and expression by molecular techniques. The transgenic seedlings thus produced include a mix of stable transformants and chimeras; however the first generation seeds contained stably integrated transgene.

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.

Approaching the genetic dissection of indirect adventitious organogenesis process in tomato explants

The screening of 862 T-DNA lines was carried out to approach the genetic dissection of indirect adventitious organogenesis in tomato. Several mutants defective in different phases of adventitious organogenesis, namely callus growth (tdc-1), bud differentiation (tdb-1, -2, -3) and shoot-bud development (tds-1) were identified and characterized. The alteration of the TDC-1 gene blocked callus proliferation depending on the composition of growth regulators in the culture medium. Calli from tds-1 explants differentiated buds but did not develop normal shoots. Histological analysis showed that their abnormal development is due to failure in the organization of normal adventitious shoot meristems. Interestingly, tdc-1 and tds-1 mutant plants were indistinguishable from WT ones, indicating that the respective altered genes play specific roles in cell proliferation from explant cut zones (TDC-1 gene) or in the organization of adventitious shoot meristems (TDS-1 gene). Unlike the previous, plants of the three mutants defective in the differentiation of adventitious shoot-buds (tdb-1, -2, -3) showed multiple changes in vegetative and reproductive traits. Cosegregation analyses revealed the existence of an association between the phenotype of the tdb-3 mutant and a T-DNA insert, which led to the discovery that the SlMAPKKK17 gene is involved in the shoot-bud differentiation process.

Establishment of CRISPR/Cas9 Genome Editing in Witloof (Cichorium intybus var. foliosum)

Cichorium intybus var. foliosum (witloof) is an economically important crop with a high nutritional value thanks to many specialized metabolites, such as polyphenols and terpenoids. However, witloof plants are rich in sesquiterpene lactones (SL) which are important for plant defense but also impart a bitter taste, thus limiting industrial applications. Inactivating specific genes in the SL biosynthesis pathway could lead to changes in the SL metabolite content and result in altered bitterness. In this study, a CRISPR/Cas9 genome editing workflow was implemented for witloof, starting with polyethylene glycol (PEG) mediated protoplast transfection for CRISPR/Cas9 vector delivery, followed by whole plant regeneration and mutation analysis. Protoplast transfection efficiencies ranged from 20 to 26 %. A CRISPR/Cas9 vector targeting the first exon of the phytoene desaturase (CiPDS) gene was transfected into witloof protoplasts and resulted in the knockout of CiPDS, giving rise to an albino phenotype in 23% of the regenerated plants. Further implementing our protocol, the SL biosynthesis pathway genes germacrene A synthase (GAS), germacrene A oxidase (GAO), and costunolide synthase (COS) were targeted in independent experiments. Highly multiplex (HiPlex) amplicon sequencing of the genomic target loci revealed plant mutation frequencies of 27.3, 42.7, and 98.3% in regenerated plants transfected with a CRISPR/Cas9 vector targeting CiGAS, CiGAO, and CiCOS, respectively. We observed different mutation spectra across the loci, ranging from consistently the same +1 nucleotide insertion in CiCOS across independent mutated lines, to a complex set of 20 mutation types in CiGAO across independent mutated lines. These results demonstrate a straightforward workflow for genome editing based on transfection and regeneration of witloof protoplasts and subsequent HiPlex amplicon sequencing. Our CRISPR/Cas9 workflow can enable gene functional research and faster incorporation of novel traits in elite witloof lines in the future, thus facilitating the development of novel industrial applications for witloof.

Somaclonal Variation in Chrysanthemum × morifolium Protoplast Regenerants

Chrysanthemum × morifolium protoplasts were isolated and regenerated to assess possible protoclonal variation in the regenerants. After a preliminary screening of the potential of different regeneration systems for protoplast regeneration, we produced a series of cut chrysanthemum 'Arjuna' leaf protoplast regenerants through liquid culture. Regenerants (54) were vegetatively propagated and grown under a commercial production system in 2 different seasons. All screened regenerants were significantly affected with regard to either flower number, flower size, flower weight, leaf weight, stalk weight, or plant size. A significant plant size reduction in 43/52 and 48/49 regenerants for both seasons was the most recorded effect. Also a reduction in flowering induction time up to 10 days, altered flower types and colors were observed. Differences between growing seasons were notable. Possible molecular backgrounds including genome size variation and commercial applications in breeding of chrysanthemum are discussed.

Development of an In Vitro Method of Propagation for Artemisia tridentata subsp. tridentata to Support Genome Sequencing and Genotype-by-Environment Research

Basin big sagebrush (Artemisia tridentata subsp. tridentata) is a keystone species of the sagebrush steppe, a widespread ecosystem of western North America threatened by climate change. The study’s goal was to develop an in vitro method of propagation for this taxon to support genome sequencing and genotype-by-environment research on drought tolerance. Such research may ultimately facilitate the reintroduction of big sagebrush in degraded habitats. Seedlings were generated from two diploid mother plants (2n = 2x = 18) collected in environments with contrasting precipitation regimes. The effects of IBA and NAA on rooting of shoot tips were tested on 45 individuals and 15 shoot tips per individual. Growth regulator and individual-seedling effects on percent rooting and roots per shoot tip were evaluated using statistical and clustering analyses. Furthermore, rooted shoot tips were transferred into new media to ascertain their continued growth in vitro. The results suggest that A. tridentata is an outbred species, as shown by individuals’ effect on rooting and growth. IBA addition was the most effective method for promoting adventitious rooting, especially in top-performing individuals. These individuals also have high survival and growth rates upon transferring to new media, making them suitable candidates for generating biomass for genome sequencing and producing clones for genotype-by-environment research.

Identification of DNA variation in callus derived from Zingiber officinale and anticoagulation activities of ginger rhizome and callus

Background

The medicinal plants have been used as alternative treatments for many diseases in many countries. Thus, the possibility of the alteration of some naturally relatively cheap sources into highly valuable products for pharmaceutical and biological importance via tissue culture is investigated in this study. Special attention is needed to estimate the molecular genetic variation between the studied plant and the callus.

Results

Ginger (Zingiber officinale Roscoe) rhizome was affected by various concentrations of cytokinin and auxin for the induction of callus. The highest percentage of callus induction and maximal callus fresh weight was achieved when Murashige and Skoog (MS) medium was supplemented with 2 mg/l 2, 4-D + 1mg/l BA. The genetic variations accompanied with in vitro conditions of callus induction was evaluated by four primers of inter-simple sequence repeat (ISSR) that amplified 36 bands. The highest readings for clotting times were found by using the sulfated neutral extract of ginger rhizome at a concentration of 400 μg/ml, and the extract of sulfated alkaline plant callus had an anticoagulation activity at (200 μg/ml) comparable to that of a standard preparation of heparin sodium.

Conclusion

These results showed that ginger (Zingiber officinale Roscoe) rhizome was affected by various concentrations of cytokinin and auxin for induction of callus especially when MS was supplemented with 2 mg/l 2, 4-D + 1 mg/l BA. Also, the results of ISSR markers confirmed the occurrence of genetic variations during callus induction process. The results indicated that the sulfated alkaline of ginger rhizome and sulfated aqueous extracts of ginger rhizome and callus exhibited anticoagulant activity. So, it was clear that the addition of sulfate group into the investigated extracts enhances the anticoagulation activities.

Analysis of a radiation-induced dwarf mutant of a warm-season turf grass reveals potential mechanisms involved in the dwarfing mutant

Zoysia matrella [L.] Merr. is a widely cultivated warm-season turf grass in subtropical and tropical areas. Dwarf varieties of Z. matrella are attractive to growers because they often reduce lawn mowing frequencies. In this study, we describe a dwarf mutant of Z. matrella induced from the 60Co-γ-irradiated calluses. We conducted morphological test and physiological, biochemical and transcriptional analyses to reveal the dwarfing mechanism in the mutant. Phenotypically, the dwarf mutant showed shorter stems, wider leaves, lower canopy height, and a darker green color than the wild type (WT) control under the greenhouse conditions. Physiologically, we found that the phenotypic changes of the dwarf mutant were associated with the physiological responses in catalase, guaiacol peroxidase, superoxide dismutase, soluble protein, lignin, chlorophyll, and electric conductivity. Of the four endogenous hormones measured in leaves, both indole-3-acetic acid and abscisic acid contents were decreased in the mutant, whereas the contents of gibberellin and brassinosteroid showed no difference between the mutant and the WT control. A transcriptomic comparison between the dwarf mutant and the WT leaves revealed 360 differentially-expressed genes (DEGs), including 62 up-regulated and 298 down-regulated unigenes. The major DEGs related to auxin transportation (e.g., PIN-FORMED1) and cell wall development (i.e., CELLULOSE SYNTHASE1) and expansin homologous genes were all down-regulated, indicating their potential contribution to the phenotypic changes observed in the dwarf mutant. Overall, the results provide information to facilitate a better understanding of the dwarfing mechanism in grasses at physiological and transcript levels. In addition, the results suggest that manipulation of auxin biosynthetic pathway genes can be an effective approach for dwarfing breeding of turf grasses.

Comparative efficacy of gypsy moth (Lepidoptera: Erebidae) entomopathogens on transgenic blight-tolerant and wild-type American, Chinese, and hybrid chestnuts (Fagales: Fagaceae)

American chestnut (Castanea dentata [Marsh.] Borkh.) was once the dominant hardwood species in Eastern North America before an exotic fungal pathogen, Cryphonectria parasitica (Murrill) Barr, functionally eliminated it across its range. One promising approach toward restoring American chestnut to natural forests is development of blight-tolerant trees using genetic transformation. However, transformation and related processes can result in unexpected and unintended phenotypic changes, potentially altering ecological interactions. To assess unintended tritrophic impacts of transgenic American chestnut on plant-herbivore interactions, gypsy moth (Lymantria dispar L.) caterpillars were fed leaf disks excised from two transgenic events, Darling 54 and Darling 58, and four control American chestnut lines. Leaf disks were previously treated with an LD₅₀ dose of either the species-specific Lymantria dispar multiple nucleopolyhedrovirus (LdMNPV) or the generalist pathogen Bacillus thuringiensis subsp. kurstaki (Btk). Mortality was quantified and compared to water blank controls. Tree genotype had a strong effect on the efficacies of both pathogens. Larval mortality from Btk-treated foliage from only one transgenic event, Darling 54, differed from its isogenic progenitor, Ellis 1, but was similar to an unrelated wild-type American chestnut control. LdMNPV efficacy was unaffected by genetic transformation. Results suggest that although genetic modification of trees may affect interactions with other nontarget organisms, this may be due to insertion effects, and variation among different genotypes (whether transgenic or wild-type) imparts a greater change in response than transgene presence.

High frequency direct shoot regeneration from Kazakh commercial potato cultivars

Potato (Solanum tuberosum L.) is the third most economically important crop in the world and has a high nutritional value. In this study, the in vitro culture response of four widely grown in Kazakhstan potato cultivars, Astanalyk, Monument Kunaev, Tokhtar, and Aksor, was investigated using stem and leaf explants. Published protocols were evaluated and optimized to develop a more efficient protocol for the regeneration of plants from local potato cultivars in tissue culture, which is a prerequisite to facilitate potato genome modification. The explants were cultured on solid Murashige and Skoog medium supplemented with different concentrations and combinations of zeatin, 6-benzylaminopurine (BAP), gibberellic acid (GA₃), 1-naphthaleneacetic acid (NAA) and indole-3-acetic acid (IAA). The maximum regeneration was induced from the stem internodal explants. A significant effect of the explant source on direct regeneration was confirmed with statistical analysis. The number of shoots obtained from the internode was 10.0 from cv. Aksor followed by cvs. Tokhtar and Astanalyk. The medium DRM-VIII with 1 mg/l zeatin, 0.1 mg/l IAA and 7.0 mg/l GA₃ was considered the best for direct shoot regeneration and multiple shoot formation from all cultivars. To conclude, we outline a protocol for direct plant regeneration from four potato cultivars. Our findings suggest commercial cultivars Astanalyk and Aksor are good candidates for developing the genome-edited plants through direct shoot regeneration.

Cellular, Molecular, and Physiological Aspects of In Vitro Plant Regeneration

Plants generally have the highest regenerative ability because they show a high degree of developmental plasticity. Although the basic principles of plant regeneration date back many years, understanding the cellular, molecular, and physiological mechanisms based on these principles is currently in progress. In addition to the significant effects of some factors such as medium components, phytohormones, explant type, and light on the regeneration ability of an explant, recent reports evidence the involvement of molecular signals in organogenesis and embryogenesis responses to explant wounding, induced plant cell death, and phytohormones interaction. However, some cellular behaviors such as the occurrence of somaclonal variations and abnormalities during the in vitro plant regeneration process may be associated with adverse effects on the efficacy of plant regeneration. A review of past studies suggests that, in some cases, regeneration in plants involves the reprogramming of distinct somatic cells, while in others, it is induced by the activation of relatively undifferentiated cells in somatic tissues. However, this review covers the most important factors involved in the process of plant regeneration and discusses the mechanisms by which plants monitor this process.

Somatic genetic drift and multilevel selection in a clonal seagrass

All multicellular organisms are genetic mosaics owing to somatic mutations. The accumulation of somatic genetic variation in clonal species undergoing asexual (or clonal) reproduction may lead to phenotypic heterogeneity among autonomous modules (termed ramets). However, the abundance and dynamics of somatic genetic variation under clonal reproduction remain poorly understood. Here we show that branching events in a seagrass (Zostera marina) clone or genet lead to population bottlenecks of tissue that result in the evolution of genetically differentiated ramets in a process of somatic genetic drift. By studying inter-ramet somatic genetic variation, we uncovered thousands of single nucleotide polymorphisms that segregated among ramets. Ultra-deep resequencing of single ramets revealed that the strength of purifying selection on mosaic genetic variation was greater within than among ramets. Our study provides evidence for multiple levels of selection during the evolution of seagrass genets. Somatic genetic drift during clonal propagation leads to the emergence of genetically unique modules that constitute an elementary level of selection and individuality in long-lived clonal species.

Epigenetic changes and their relationship to somaclonal variation: a need to monitor the micropropagation of plantation crops

Chromatin modulation plays important roles in gene expression regulation and genome activities. In plants, epigenetic changes, including variations in histone modification and DNA methylation, are linked to alterations in gene expression. Despite the significance and potential of in vitro cell and tissue culture systems in fundamental research and marketable applications, these systems threaten the genetic and epigenetic networks of intact plant organs and tissues. Cell and tissue culture applications can lead to DNA variations, methylation alterations, transposon activation, and finally, somaclonal variations. In this review, we discuss the status of the current understanding of epigenomic changes that occur under in vitro conditions in plantation crops, including coconut, oil palm, rubber, cotton, coffee and tea. It is hoped that comprehensive knowledge of the molecular basis of these epigenomic variations will help researchers develop strategies to enhance the totipotent and embryogenic capabilities of tissue culture systems for plantation crops.

Genome-wide discovery of DNA variants in cucumber somaclonal lines

The emergence of somaclonal variability in in vitro cultures is undesirable during micropropagation, but this phenomenon may be a source of genetic variability sought by breeders. The main factors that affect the appearance of variability are known, but the exact mechanism has not yet been determined. In this paper, we used next-generation sequencing and comparative genomics to study changes in the genomes of cucumber lines resulting from in vitro regeneration and somaclonal mutation in comparison to a reference, the highly inbred B10 line. The total number of obtained polymorphisms differed between the three somaclonal lines S1, S2 and S3, with 8369, 7591 and 44510, respectively. Polymorphisms occurred most frequently in non-coding regions and were mainly SNPs. High-impact changes accounted for 1%-3% of all polymorphisms and most often caused an open reading frame shift. Functional analysis of genes affected by high impact variants showed that they were related to transport, biosynthetic processes, nucleotide-containing compounds and cellular protein modification processes. The obtained results indicated significant factors affecting somaclonal variability and the appearance of changes in the genome, and demonstrated a lack of dependence between phenotype and the number of genomic polymorphisms.

Indirect regeneration and genetic fidelity analysis of acclimated plantlets through SCoT and ISSR markers in Morus alba L. cv. Chinese white

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A reliable protocol developed for micropropagation of Morus alba L.cv. Chinese white through indirect regeneration using different explants.

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Friable callus was induced in maximum amounts from leaf and nodal explants on MS media supplemented with 2,4-D and NAA respectively.

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Highest frequency of regeneration was obtained from the leaf and node derived callus on MS media with BAP + TDZ and plantlets were rooted on IBA.

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Genetic homogeneity of in vitro raised plants was confirmed by SCoT and ISSR primers based molecular analysis.

A reliable protocol was developed for in vitro micro propagation of Morus alba L.cv. Chinese white. Initially, friable callus was induced (242.8 and 128.5 mg) from in vivo leaf and nodal explants on Murashige and Skoog’s (MS) medium amended with 4.0 μM/L of 2,4-Dichlorophenoxyacetic acid (2,4-D) and 3.0 μM/L of Naphthalene acetic acid (NAA) respectively within 3 weeks. Shoot regeneration (12.2 and 8.6) was obtained from leaf and node derived callus on 6-benzylaminopurine (BAP) + Thidiazuron (TDZ) at 2.5 + 2.0 and 7.5 + 2.0 μM/L concentrations respectively, after 4 weeks of incubation. In vitro shoots were rooted (90 %) on half strength MS medium with 7.5 μM/L indole-3 butyric acid (IBA) and plantlets were hardened in plastic pots contained farmyard manure, sand and garden soil in 1:1:2 ratio. The genetic stability of plantlets were confirmed by start codon targeted (SCoT) and inter simple sequence repeats (ISSR) primers based molecular analysis.

CG hypomethylation leads to complex changes in DNA methylation and transpositional burst of diverse transposable elements in callus cultures of rice

CG methylation (^m CG) is essential for preserving genome stability in mammals, but this link remains obscure in plants. OsMET1-2, a major rice DNA methyltransferase, plays critical roles in maintaining ^m CG in rice. Null mutation of OsMET1-2 causes massive CG hypomethylation, rendering the mutant suitable to address the role of ^m CG in maintaining genome integrity in plants. Here, we analyzed ^m CG dynamics and genome stability in tissue cultures of OsMET1-2 homozygous (-/-) and heterozygous (+/-) mutants, and isogenic wild-type (WT). We found ^m CG levels in cultures of -/- were substantially lower than in those of WT and +/-, as expected. Unexpectedly, ^m CG levels in 1- and 3-year cultures of -/- were 77.6% and 48.7% higher, respectively, than in shoot, from which the cultures were initiated, suggesting substantial regain of ^m CG in -/- cultures, which contrasts to the general trend of ^m CG loss in all WT plant tissue cultures hitherto studied. Transpositional burst of diverse transposable elements (TEs) occurred only in -/- cultures, although no elevation of genome-wide mutation rate in the form of single nucleotide polymorphisms was detected. Altogether, our results establish an essential role of ^m CG in retaining TE immobility and hence genome stability in rice and likely in plants in general.

From cells highly tolerant to Zn and Pb to fully fertile plants - Selection of tolerant lines with in vitro culture

Viola arvensis cells were selected after treatment with Zn or Pb and regenerated into plants likely to have higher tolerance levels than the initial plant. The surviving cells in the suspension treated with 2000 μM of Zn, 2000 μM of Pb or 0 μM for 72 h were maintained on a solidified half-strength MS medium supplemented with 0.5 mg L^-1 TDZ to induce divisions and organogenesis. The adventitious shoots obtained were rooted on a half-strength MS medium with 1 mg L^-1 IBA. Regenerants derived from the Zn- and Pb-treated cells were vigorous and fully fertile. The in vitro conditions and metal impact generated a low genome alteration and overall low genetic diversity of regenerants compared to the initial plant and plants from the natural population. The cells of regenerants obtained after Pb treatment represented an approximately 12% higher tolerance level to Pb than the cells of the initial plant. This is the first report of plant regeneration from highly tolerant cells selected by heavy metal treatment. Regenerants successfully obtained in vitro could be considered as a source material for the recultivation of areas polluted with heavy metals.

In Vitro Regeneration and ISSR-Based Genetic Fidelity Analysis of Orthosiphon stamineus Benth

Orthosiphon stamineus has been widely used as traditional remedy for various illnesses and diseases, such as cardiovascular diseases and epileptic seizures. In this study, direct regeneration through nodal segment of this species was attempted using Kinetin (6-Furfurylaminopurine) and IAA (indole-3-acetic acid). Optimum regeneration media was identified as MS media supplemented with 2.0 mg L−1 Kin plus 0.5 mg L−1 IAA. This yielded the highest number of shoots (5.57 ± 0.42) and leaves (20.53 ± 1.91) per explant. Acclimatization of the resulting in vitro regenerants was successful in all potting mixtures tested. However, potting mixture PF (1:1:1 ratio of black soil/red soil/compost) was identified as the best medium for acclimatization of this species, as it yielded 100% survival percentage after 90 days of acclimatization. Ten in vitro regenerants of O. stamineus were randomly collected after the third subculture and subjected to genetic variation analysis using inter-simple sequence repeat (ISSR) markers. Out of 20 ISSR markers tested, 10 working primers were observed to produce satisfactory amplification of bands, with an average of 7.11 bands per primer. A total of 610 bands were produced by the 10 primers. The percentage of polymorphism was observed to be very low, yielding only 7.32% polymorphism among all samples. Jaccard dissimilarity analysis was also conducted and very low genetic distance (about 0.1) was found among the in vitro regenerants and between the regenerants with the mother plant, thus ascertaining the clonal nature of the plantlets produced in this study.

Detection of mPing mobilization in transgenic rice plants

BACKGROUND

Various kinds of transposable elements (TEs) constitute high proportions of eukaryotic genomes. Although most of these TEs are not actively mobile, genome stress can induce mobilization of dormant TEs. Transgenic plants undergo tissue culture and subsequent whole-plant regeneration, which can cause genomic stress and in turn induce mobilization of inactive TEs.

OBJECTIVES

To investigate the activation of transposable elements on the genome wide of the GM plant.

METHODS

Transposon activities were analyzed in three transgenic rice plants carrying the insect resistance gene Cry1Ac and an herbicide resistance gene by the transposon display technique. These three transgenic plants were derived from a leading Korean rice variety, Illmi.

RESULTS

We detected seven mobile activities in the mPing element, which is a MITE family transposon. The identity of the novel fragments in the gel display was confirmed by checking TAA target site duplication via sequence analysis. The genomic integration sites were all on different chromosomes, and the integrations were specific to either one or two T1 transgenic lines, except for one common integration on chromosome 4. One integration was in the 5'-UTR of the Glycerol-3-phosphate acyltransferase 8 gene, two integrations were in introns of expressed genes, and the other four integrations were in intergenic regions.

CONCLUSION

Thus, novel mobilization of dormant TEs occurs in transgenic plants, which must be considered in the generation of genetically modified crops (GM crops).

Plant Regeneration via Somatic Embryogenesis in Mature Wild Olive Genotypes Resistant to the Defoliating Pathotype of Verticillium dahliae

Regeneration capacity, via somatic embryogenesis, of four wild olive genotypes differing in their response to defoliating Verticillium dahliae (resistant genotypes StopVert, OutVert, Ac-18 and the susceptible one, Ac-15) has been evaluated. To induce somatic embryogenesis, methodologies previously used in wild or cultivated olive were used. Results revealed the importance of genotype, explant type, and hormonal balance in the induction process. Use of apical buds obtained from micropropagated shoots following a methodology used in cultivated olive (4 days induction in liquid 1/2 MS medium supplemented with 30 µM TDZ-0.54 µM NAA, followed by 8 weeks in basal 1/2 MS medium) was adequate to obtain somatic embryos in two genotypes, StopVert and Ac-18, with a 5.0 and 2.5% induction rates, respectively; however, no embryogenic response was observed in the other two genotypes. Embryogenic cultures were transferred to basal ECO medium supplemented with 0.5 µM 2iP, 0.44 µM BA, and 0.25 µM indole-3-butyric acid (IBA) for further proliferation. Somatic embryos from StopVert were maturated and germinated achieving a 35.4% conversion rate. An analysis of genetic stability on StopVert, using Simple Sequence Repeats (SSRs) and Random Amplified Polymorphic DNA (RAPDs) markers, was carried out in embryogenic callus, plants regenerated from this callus and two controls, micropropagated shoots used as explant source, and the original mother plant. Polymorphism was only observed in the banding pattern generated by RAPDs in 1 of the 10 callus samples evaluated, resulting in a variation rate of 0.07%. This is the first time in which plants have been regenerated via somatic embryogenesis in wild olive.

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

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.

Changes in DNA methylation pattern of apple long-term in vitro shoot culture and acclimatized plants

DNA methylation is a process of epigenetic modification that can alter the functionality of a genome. Using whole-genome bisulfite sequencing, this study quantify the level of DNA methylation in the epigenomes of two diploid apple (Malus x domestica) scion cultivars ('McIntosh' and 'Húsvéti rozmaring') derived from three environmental conditions: in vivo mother plants in an orchard, in vitro culture, and acclimatized in vitro plants. The global DNA methylation levels were not dependent on the source of plant material, and the average level of DNA methylation was 49.77%, 34.65% and 8.77% in CpG, CHG and CHH contexts, respectively. Significant differences in DNA methylation were identified in 586 (specifically 334, 201 and 131 in CpG, CHG and CHH contexts, respectively) out of 45,116 genes, including promoter and coding sequences. These were classified as differentially methylated genes (DMGs). This is a 1.3% difference in the level of DNA methylation of genes in response to a change in the environment. Differential methylation was visualised by MA plots and functional genomic maps were established for biological processes, molecular functions and cellular components. When the DMGs were considered, in vitro tissue culture resulted in the highest level of methylation, but it was lower in acclimatized in vitro plants which was similar to that in the mother tree. Methylation patterns of the two scions differed, indicating cultivar-specific epigenetic regulation of gene expression during adaptation to various environments. After selecting genes that displayed differences larger than ±10% in CpG and CHG contexts, or larger than ±1.35% in the CHH context from among the DMGs, they were annotated in Blast2 GO v5.1.12 for Gene Ontology. DMGs identified as MD07G1113000 (protein transport), MD08G1041600 (extracellular space), MD09G1054800 (phosphatidic acid binding), and MD10G1265800 (not annotated) were methylated in all three contexts in in vitro shoots. These DNA methylation results suggest that epigenetic changes may contribute to the adaptation of apple to environmental changes by modifying the epigenome and thereby gene expression.

Phenotypic and genetic characterization of tomato mutants provides new insights into leaf development and its relationship to agronomic traits

BACKGROUND

Tomato mutants altered in leaf morphology are usually identified in the greenhouse, which demands considerable time and space and can only be performed in adequate periods. For a faster but equally reliable scrutiny method we addressed the screening in vitro of 971 T-DNA lines. Leaf development was evaluated in vitro in seedlings and shoot-derived axenic plants. New mutants were characterized in the greenhouse to establish the relationship between in vitro and in vivo leaf morphology, and to shed light on possible links between leaf development and agronomic traits, a promising field in which much remains to be discovered.

RESULTS

Following the screening in vitro of tomato T-DNA lines, putative mutants altered in leaf morphology were evaluated in the greenhouse. The comparison of results in both conditions indicated a general phenotypic correspondence, showing that in vitro culture is a reliable system for finding mutants altered in leaf development. Apart from providing homogeneous conditions, the main advantage of screening in vitro lies in the enormous time and space saving. Studies on the association between phenotype and nptII gene expression showed co-segregation in two lines (P > 99%). The use of an enhancer trap also allowed identifying gain-of-function mutants through reporter expression analysis. These studies suggested that genes altered in three other mutants were T-DNA tagged. New mutants putatively altered in brassinosteroid synthesis or perception, mutations determining multiple pleiotropic effects, lines affected in organ curvature, and the first tomato mutant with helical growth were discovered. Results also revealed new possible links between leaf development and agronomic traits, such as axillary branching, flower abscission, fruit development and fruit cracking. Furthermore, we found that the gene tagged in mutant 2635-MM encodes a Sterol 3-beta-glucosyltransferase. Expression analysis suggested that abnormal leaf development might be due to the lack-off-function of this gene.

CONCLUSION

In vitro culture is a quick, efficient and reliable tool for identifying tomato mutants altered in leaf morphology. The characterization of new mutants in vivo revealed new links between leaf development and some agronomic traits. Moreover, the possible implication of a gene encoding a Sterol 3-beta-glucosyltransferase in tomato leaf development is reported.

Analysis of DNA Methylation Patterns Associated with In Vitro Propagated Globe Artichoke Plants Using an EpiRADseq-Based Approach

Globe artichoke represents one of the main horticultural species of the Mediterranean basin, and 'Spinoso sardo' is the most widespread and economically relevant varietal type in Sardinia, Italy. In the last decades, in vitro culture of meristematic apices has increased the frequency of aberrant plants in open-field production. These off-type phenotypes showed highly pinnate-parted leaves and late inflorescence budding, and emerged from some branches of the true-to-type 'Spinoso sardo' plants. This phenomenon cannot be foreseen and is reversible through generations, suggesting the occurrence of epigenetic alterations. Here, we report an exploratory study on DNA methylation patterns in off-type/true-to-type globe artichoke plants, using a modified EpiRADseq technology, which allowed the identification of 2,897 differentially methylated loci (DML): 1,998 in CG, 458 in CHH, and 441 in CHG methylation contexts of which 720, 88, and 152, respectively, were in coding regions. Most of them appeared involved in primary metabolic processes, mostly linked to photosynthesis, regulation of flower development, and regulation of reproductive processes, coherently with the observed phenotype. Differences in the methylation status of some candidate genes were integrated with transcriptional analysis to test whether these two regulation levels might interplay in the emergence and spread of the 'Spinoso sardo' non-conventional phenotype.

Carbon and nitrogen partitioning of transgenic rice T2A-1 (Cry2A*) with different nitrogen treatments

Nitrogen (N) and carbon(C) metabolisms in plants were investigated to assess different responses of Bt and non-Bt rice to different N treatments. T2A-1 (Bt rice variety) inserted with Cry2A* protein to resist Lepidoptera and its parental line MH63 was adopted in this study. The total N accumulation presented no statistical difference. But nitrogen contents in different parts of rice plant were significantly different between the two lines, especially on leaf and spike part. This study revealed that the nitrogen in leaf of T2A-1 was far more than that of MH63; however, the nitrogen in spike of T2A-1 was less than that of MH63. In addition, MH63 assimilated more carbon than T2A-1. However, the distribution proportion of carbon in leaf, stem and spike of T2A-1 and MH63 were both 1:1:1. What’s more, our study of the difference in metabolism pathway based on proteomics analysis provided more insights on the responses of two lines of Bt and non-Bt rice to different N treatments. And amino acid metabolism, energy metabolism, and carbohydrate metabolism presented significant difference between two lines. In addition, the number of differentially expressed proteins with N deficiency treatment was almost twice as many as that with normal N treatment. It could be inferred that the insertion of Cry2A* in T2A-1 may bring about effects on carbon and nitrogen allocation and related metabolisms, especially under N deficiency environment.

Evaluation of in vitro shoot multiplication and ISSR marker based assessment of somaclonal variants at different subcultures of vanilla (Vanilla planifolia Jacks)

The effect of subculture cycles on somaclonal variation of V. planifolia using intersimple sequence repeat (ISSR) markers was analyzed. Nodal segments of 2 cm in length were established in vitro and multiplied by 10 subculture cycles in Murashige and Skoog (MS) medium supplemented with 8.86 μM BAP (benzylaminopurine). After 45 days in each culture, the length and number of shoots per explant were evaluated. For ISSR markers, ten shoots per each subculture and the mother plant were used. Ten ISSR primers were used and a total of 118 bands were obtained. The polymorphism (%) was calculated and a dendrogram based on Jaccard's genetic distance between the subcultures and the donor plant was obtained. These results show that the multiplication rate tends to increase until subculture five, whereas shoot length decreases as the number of subcultures increases. The ISSR markers revealed an increase in the polymorphism percentage after the fifth culture cycle. The dendrogram showed the formation of two groups. The first group, with less genetic variability, is the donor plant and subcultures 1-5; the second group has greater genetic distance and is formed by subcultures 6-10. The results revealed that the number of subcultures with 8.86 μM BAP is a factor that affects the somaclonal variation during in vitro regeneration of V. planifolia. In conclusion, the subculture number affects somaclonal variation and in vitro development of V. planifolia.

Genetic homogeneity revealed in micropropagated Bauhinia racemosa Lam. using gene targeted markers CBDP and SCoT

Two gene targeted markers i.e. CAAT box-derived polymorphism (CBDP) and start codon targeted (SCoT) polymorphism were applied to analyze the genetic stability of in vitro propagated plants of Bauhinia racemosa Lam. multiplied by enhanced axillary shoot proliferation of mature tree derived nodal explant. Nine randomly selected micropropagated plants of 1 year age were subjected to molecular analysis. The isolated genomic DNA samples were subjected to PCR amplification with a total of 61 primers (25 CBDP and 36 SCoT) out of which 39 primers (21 CBDP and 18 SCoT) produced scorable amplicons. A total of 97 and 88 clear, distinct and reproducible amplicons were produced by CBDP and SCoT primers, respectively. The monomorphic banding pattern obtained through all the tested primers corroborated the true to type nature of in vitro propagated plants of B. racemosa.

Induction of potato variants with enhanced resistance to common scab disease via cell culture is applicable to a cultivar developed in Japan, but the effect of using the phytotoxin thaxtomin A is restrictive

To induce potato variants with enhanced resistance to common scab disease that retain the desirable agronomic traits of the original cultivars, we used a cell culture technique that employs thaxtomin A, the primary phytotoxin that induces scab symptoms. We induced 24 variants from the potato cultivar 'Saya-akane', developed in Japan, and selected two with enhanced resistance to the disease by growing them in planters with bacteriainoculated soil and in a field infested with the disease. We also examined toxin tolerance in micro-tubers of variants that showed a lower degree or percentage of infection in the glasshouse screening, and found no significant difference relative to the original cultivar. To clarify the effect of using thaxtomin A, we examined the efficiency of induction of the potential enhanced resistance by comparing the degree of infection among variants grown in planters with inoculated soil. We observed no significant difference between variants induced on culture medium with and without the toxin. These results suggest that the effect of using the toxin as a positive selection agent is restrictive and that most resistance-enhancing mutations are induced by the cell culture procedure itself.

Micropropagation protocol for Antigonon leptopus an important ornamental and medicinal plant

The effect of some factors on in vitro consecutive micropropagation behavior of Antigonon leptopus was examined including those of culture establishment, shootlets multiplication, rooting and acclimatization stages. The highest percent of aseptic cultures and survival of explants (100%) were obtained as a result of using Clorox 10% for 3 min followed by MC 0.1% for 2 min while, using each of them individually (Clorox 20% or MC 0.1%) for 5 min caused the highest percent of shoot formation. During the multiplication stage, the highest percent of shoot formation was reached to 100% with repeating culture of explants (two times) on MS medium supplemented with 2ip at 1.0 and IBA at 0.2 mg/l. The highest numbers of shootlets/explant were obtained when 2.0 mg/l of BAP or 0.5 mg/l BA + 0.2 mg/l of IBA were added to MS culture medium. Culturing the explants on MS medium supplemented with 2ip at 0.5 or 1.0 mg/l each combined with 0.2 mg/l of IBA showed the longest shootlets. Reducing the strength of culture media to ½ or ¾ had promotion effect on rooting formation of shootlets. The best results of plant acclimatization (survival percent, plant height and root length) were obtained by using sand or peat moss soil. The amplified DNA fragments using B7, B9 and C19 primers for mother and micropropagated plants showed that the produced pattern by primer B7 had a maximum number of 10 bands of DNA fragments with molecular size ranging between 1025.57 and 176.36 bp, micropropagated plants showed 95.2% similarity in relation to mother plant.

Genome editing in potato via CRISPR-Cas9 ribonucleoprotein delivery

Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein-9 (CRISPR-Cas9) can be used as an efficient tool for genome editing in potato (Solanum tuberosum). From both a scientific and a regulatory perspective, it is beneficial if integration of DNA in the potato genome is avoided. We have implemented a DNA-free genome editing method, using delivery of CRISPR-Cas9 ribonucleoproteins (RNPs) to potato protoplasts, by targeting the gene encoding a granule bound starch synthase (GBSS, EC 2.4.1.242). The RNP method was directly implemented using previously developed protoplast isolation, transfection and regeneration protocols without further adjustments. Cas9 protein was preassembled with RNA produced either synthetically or by in vitro transcription. RNP with synthetically produced RNA (cr-RNP) induced mutations, i.e. indels, at a frequency of up to 9%, with all mutated lines being transgene-free. A mutagenesis frequency of 25% of all regenerated shoots was found when using RNP with in vitro transcriptionally produced RNA (IVT-RNP). However, more than 80% of the shoots with confirmed mutations had unintended inserts in the cut site, which was in the same range as when using DNA delivery. The inserts originated both from DNA template remnants from the in vitro transcription, and from chromosomal potato DNA. In 2-3% of the regenerated shoots from the RNP-experiments, mutations were induced in all four alleles resulting in a complete knockout of the GBSS enzyme function.

Thidiazuron-induced somatic embryogenesis and changes of antioxidant properties in tissue cultures of half-high blueberry plants

An efficient protocol of somatic embryogenesis (SE) has been developed for the first time in four half-high blueberry (Vaccinium corymbosum L. × V. angustifolium Ait.) cultivars. Thidiazuron (TDZ), a plant growth regulator with potential activities for shoot regeneration and shoot proliferation, was found most effective for somatic embryo formation when added to a nutrient medium at high concentration (9 µM). Although TDZ was also best for embryo germination at low concentration (2.3 µM), it was followed by zeatin at 4.6 µM for the same. Plantlets developed from SE were removed from the nutrient medium and transferred on a peat: perlite medium where 100% survival rate was acquired following the acclimatization process in a greenhouse. The concentrations of total phenolic and flavonoid contents were higher in greenhouse-grown conventionally cutting-propagated donor mother plants than those of respective SE plants for 'St. Cloud', 'Patriot' and 'Northblue' but not for 'Chippewa'. The effect of propagation method and/or the older age of donor mother plants were clearly visible exclusively as the 15-year-old donor plants showed higher level of 2,2-diphenyl-1-picrylhydrazyl scavenging activity than the eight-weeks-old SE plants in all four cultivars.

Transcriptome profiling of transgenic potato plants provides insights into variability caused by plant transformation

Crop genetic engineering involves transformation in which transgenic plants are regenerated through tissue culture manipulations that can elicit somaclonal variation due to mutations, translocations, and/or epigenetic alterations. Here, we report on alterations in the transcriptome in a panel of transgenic potato plants engineered to be herbicide resistant. Using an inbred diploid potato clone (DMRH S5 28–5), ten single-insert transgenic lines derived from independent Agrobacterium-mediated transformation events were selected for herbicide resistance using an allelic variant of acetolactate synthase (mALS1). Expression abundances of the single-copy mALS1 transgene varied in individual transgenic lines was correlated with the level of phenotypic herbicide resistance, suggesting the importance of transgene expression in transgenic performance. Using RNA-sequencing, differentially expressed genes were identified with the proportion of genes up-regulated significantly higher than down-regulated genes in the panel, suggesting a differential impact of the plant transformation on gene expression activation compared to repression. Not only were transcription factors among the differentially expressed genes but specific transcription factor binding sites were also enriched in promoter regions of differentially expressed genes in transgenic lines, linking transcriptomic variation with specific transcription factor activity. Collectively, these results provide an improved understanding of transcriptomic variability caused by plant transformation.