Somaclonal variations and their applications in horticultural crops improvement

In Vitro Culture Technology and Advanced Biotechnology Tools Toward Improvement in Gladiolus (Gladiolus species): Present Scenario and Future Prospects

In the world's flower trade, gladiolus (Gladiolus spp.) is ranked first among bulbous flowers and eighth among cut flowers, with more than 30,000 different cultivars being grown. Mass multiplication and commercialization are restricted by the traditional propagation methods. However, the large-scale proliferation and improvement of the gladiolus have been accomplished with the aid of plant tissue culture and other biotechnological techniques. The current review includes a thorough examination of the growth and development parameters required for successful in vitro gladiolus development as well as cormel formation. Moreover, focus is being given to various techniques and methods such as in vitro cytogenetic stability and modification of chromosome number, in vitro mutagenesis and selection of pest resistance, in vitro identification and selection to develop virus-free germplasm, cryopreservation, synthetic seed technology, identifying virus diseases by RT-PCR, somaclonal variation, and protoplast and somatic hybridization. Molecular markers and their applications for genetic diversity analysis, relationships between different genotypes, and clonal stability analysis in Gladiolus species have been conducted by several research groups worldwide and are also being discussed. The article also covers efforts to enhance the functionality of plant phenotypes through genetic transformation. Future prospects for further improvement of ornamental gladiolus are also explored. Overall, the current review provides insight into the applications of basic and advanced biotechnological tools for gladiolus improvement.

Application of machine learning in in vitro propagation of endemic Lilium akkusianum R. Gämperle

A successful regeneration protocol was developed for micropropagation of Lilium akkusianum R. Gämperle, an endemic species of Türkiye, from scale explants. The study also aimed to evaluate the effects of Meta-Topolin (mT) and N6-Benzyladenine (BA) on in vitro regeneration. The Murashige and Skoog medium (MS) supplemented with different levels of α-naphthaleneacetic acid (NAA)/BA and NAA/mT were used for culture initiation in the darkness. The highest callus rates were observed on explants cultured on MS medium with 2.0 mg/L NAA + 0.5 mg/L mT (83.31%), and the highest adventitious bud number per explant was 4.98 in MS medium with 0.5 mg/L NAA + 1.5 mg/L mT. Adventitious buds were excised and cultured in 16/8 h photoperiod conditions. The highest average shoot number per explant was 4.0 in MS medium with 2.0 mg/L mT + 1.0 mg/L NAA. Shoots were rooted with the highest rate (90%) in the medium with the 1.0 mg/L IBA, and the highest survival rate (87.5%) was recorded in rooted shoots in the same medium. The ISSR marker system showed that regenerated plantlets were genetically stable. Besides traditional tissue culture techniques used in the current study, the potential for improving the effectiveness of L. akkusianum propagation protocols by incorporating machine learning methodologies was evaluated. ML techniques enhance lily micropropagation by analyzing complex biological processes, merging with traditional methods. This collaborative approach validates current protocols, allowing ongoing improvements. Embracing machine learning in endemic L. akkusianum studies contributes to sustainable plant propagation, promoting conservation and responsible genetic resource utilization in agriculture.

Somatic Mutation Accumulations in Micropropagated Cannabis Are Proportional to the Number of Subcultures

Advancements in micropropagation techniques have made it easier to produce large numbers of cannabis clones, but these methods may also introduce genetic instability over successive generations. This instability often manifests as somaclonal variation, characterized by the progressive accumulation of genetic mutations or epigenetic alterations with each subculture. In this study, we examined how mutations accumulate in cannabis clones subjected to 6-11 subcultures. Using genotyping-by-sequencing, we identified 9405 polymorphic variants across 70 clones. The analysis revealed a correlation between the number of subcultures and the frequency of these mutations, revealing that genetic changes accumulate over successive subcultures despite clones sharing the same chronological age. Furthermore, we evaluated the functional impacts of accumulated mutations, with particular attention to implications on gene function and overall plant health. While rare, 14 high-impact variants were identified in genes that are important for plant development. Notably, six variants were also found in genes related to cannabinoid and terpene synthesis pathways, potentially affecting the plant's biochemical composition. These findings highlight the need for genetic assessments in micropropagation protocols, impacting plant breeding and conservation. Understanding genetic variations in clonally propagated plants optimizes practices for stability. Crucial for cannabis and horticultural plants, it emphasizes techniques to prevent genetic decay and ensure viability.

Exploring the Significance of Somaclonal Variations in Horticultural Crops

Genetic and epigenetic variations produced via cell and tissue culture open up new sources of variability intra-species which can be used to improve crops. The use of in vitro generated somaclonal variations for selecting novel variants aids in the development of novel genotypes having desirable agronomic traits that can be released as varieties or utilized for breeding purposes. Horticultural crops give higher yield and productivity per unit area than other crops, as well as provide good economic returns which have led to an increase in their potential benefits throughout time. The last three to four decades have seen the selection and release of a number of valuable somaclonal variants, many of which possess remarkable features including disease resistance, high yield, improved nutritional quality and abiotic stress tolerance. Generating somaclonal variations has given breeders a novel alternative option for obtaining genetic diversity in horticultural crops and without advanced technologies. The variations introduced through tissue culture process, methods to determine and validate genetic changes in vitro regenerated plantlets, along with prospective application of such variations in horticultural crops' improvement are reviewed in the present work.

Effectiveness of light-emitting diodes for arsenic and mercury accumulation by Ceratophyllum demersum L.: An innovative advancement in phytoremediation technology

Light Emitting Diodes (LEDs) have emerged as a tool with great potential in the field of phytoremediation, offering a novel approach to enhance the efficiency of plant-based remediation techniques. In this work investigated the influence of LEDs on the phytoremediation of arsenic (As) and mercury (Hg) by Ceratophyllum demersum L., propagated using tissue culture methods. In addition, the biochemical properties of the plants exposed to metal toxicity were examined. Phytoremediation experiments employed concentrations of As (0.01-1.0 mg/L) and Hg (0.002-0.2 mg/L), with application periods set at 1, 7, 14, and 21 days. In addition to white, red and blue LEDs, white fluorescent light was used for control purposes in the investigations. A positive correlation was observed between higher metal concentrations, extended exposure times, and increased metal accumulation in the plants. Red LED light yielded the highest level of heavy metal accumulation, while white fluorescent light resulted in the lowest accumulation level. Examination of the biochemical parameters of the plants, including photosynthetic pigment levels, protein quantities, and lipid peroxidation, revealed a pronouncedly enhanced performance in specimens subjected to red and blue LED illumination, surpassing outcomes observed in other light treatments. The findings of this study introduce innovative avenues for the effective utilization of red and blue LED lights in the realm of phytoremediation research. Thus, the interaction between LEDs, tissue culture, and the phytoremediation process could lead to synergistic effects that contribute to more effective and sustainable remediation strategies.

Comparative restriction enzyme analysis of methylation (CREAM) reveals methylome variability within a clonal in vitro cannabis population

The primary focus of medicinal cannabis research is to ensure the stability of cannabis lines for consistent administration of chemically uniform products to patients. In recent years, tissue culture has emerged as a valuable technique for genetic preservation and rapid multiplication of cannabis clones. However, there is concern that the physical and chemical conditions of the growing media can induce somaclonal variation, potentially impacting the viability and uniformity of clones. To address this concern, we developed Comparative Restriction Enzyme Analysis of Methylation (CREAM), a novel method to assess DNA methylation patterns and used it to study a population of 78 cannabis clones maintained in tissue culture. Through bioinformatics analysis of the methylome, we successfully detected 2,272 polymorphic methylated regions among the clones. Remarkably, our results demonstrated that DNA methylation patterns were preserved across subcultures within the clonal population, allowing us to distinguish between two subsets of clonal lines used in this study. These findings significantly contribute to our understanding of the epigenetic variability within clonal lines in medicinal cannabis produced through tissue culture techniques. This knowledge is crucial for understanding the effects of tissue culture on DNA methylation and ensuring the consistency and reliability of medicinal cannabis products with therapeutic properties. Additionally, the CREAM method is a fast and affordable technology to get a first glimpse at methylation in a biological system. It offers a valuable tool for studying epigenetic variation in other plant species, thereby facilitating broader applications in plant biotechnology and crop improvement.

Micropropagation and Genetic Fidelity of Fegra Fig (Ficus palmata Forssk.) and Grafting Compatibility of the Regenerated Plants with Ficus carica

Ficus palmata is an important fig species that produces edible and nutritious fruit and possesses several therapeutic uses. This study reports an effective method for the micropropagation of F. palmata using nodal explants. In vitro shoots were cultured for 7 weeks onto MS medium fortified with different concentrations of cytokinins, light intensities, sucrose concentrations, and light/dark incubation treatments. Optimal axillary shoot proliferation (10.9 shoots per explant) was obtained on a medium containing 30 g/L sucrose and supplemented with 2 mg/L 6-benzylaminopurine (BAP) under 35 μmol/m2/s light intensity. Dark incubation limited the foliage growth but favored shoot elongation and rooting compared with light incubation. Elongated shoots, under dark conditions, were rooted (100%; 6.67 roots per explant) onto MS medium containing 1 mg/L indole-3-acetic acid (IAA) and 1.5 g/L activated charcoal. The micropropagated plantlets were acclimatized with a 95% survival rate. In this study, the genetic fidelity of micropropagated F. palmata clones along with their mother plant was tested using randomly amplified polymorphic DNA (RAPD), inter-simple sequence repeats (ISSR), and start codon targeted (SCoT) molecular markers. The genetic similarity between the micropropagated plantlets and the mother plant of F. palmata was nearly 95.9%, assuring high uniformity and true-to-type regenerated plants. Using micropropagated F. palmata plantlets as a rootstock proved appropriate for the grafting F. carica 'Brown Turkey'. These findings contribute to the commercial propagation and production of the fig crop.

An insight into tissue culture-induced variation origin shared between anther culture-derived triticale regenerants

BACKGROUND

The development of the plant in vitro techniques has brought about the variation identified in regenerants known as somaclonal or tissue culture-induced variation (TCIV). S-adenosyl-L-methionine (SAM), glutathione (GSH), low methylated pectins (LMP), and Cu(II) ions may be implicated in green plant regeneration efficiency (GPRE) and TCIV, according to studies in barley (Hordeum vulgare L.) and partially in triticale (× Triticosecale spp. Wittmack ex A. Camus 1927). Using structural equation models (SEM), these metabolites have been connected to the metabolic pathways (Krebs and Yang cycles, glycolysis, transsulfuration), but not for triticale. Using metabolomic and (epi)genetic data, the study sought to develop a triticale regeneration efficiency statistical model. The culture's induction medium was supplemented with various quantities of Cu(II) and Ag(I) ions for regeneration. The period of plant regeneration has also changed. The donor plant, anther-derived regenerants, and metAFLP were utilized to analyze TCIV concerning DNA in symmetric (CG, CHG) and asymmetric (CHH) sequence contexts. Attenuated Total Reflectance-Fourier Transfer Infrared (ATR-FTIR) spectroscopy was used to gather the metabolomic information on LMP, SAM, and GSH. To frame the data, a structural equation model was employed.

RESULTS

According to metAFLP analysis, the average sequence change in the CHH context was 8.65%, and 0.58% was de novo methylation. Absorbances of FTIR spectra in regions specific for LMP, SAM, and GSH were used as variables values introduced to the SEM model. The average number of green regenerants per 100 plated anthers was 2.55.

CONCLUSIONS

The amounts of pectin demethylation, SAM, de novo methylation, and GSH are connected in the model to explain GPRE. By altering the concentration of Cu(II) ions in the medium, which influences the amount of pectin, triticale's GPRE can be increased.

Comprehensive Analysis of Highbush Blueberry Plants Propagated In Vitro and Conventionally

In vitro culture allows the production of numerous plants with both desirable and undesirable traits. To investigate the impact of the propagation method on highbush blueberry plants, an analysis was performed on four groups of differentially propagated plants: in vitro with axillary (TC-Ax) or adventitious shoots (TC-Ad), conventionally (SC) and using a mixed method (TC/SC). The analysis included plant features (shoot length and branching, chlorophyll and fluorescence and DNA methylation) and fruit properties (antioxidant compounds). The data obtained indicated significant differences between plants propagated conventionally and in vitro, as well as variations among plants derived from in vitro cultures with different types of explants. SC plants generally exhibited the lowest values of morphological and physiological parameters but produced fruits richest in antioxidant compounds. TC/SC plants were dominant in length, branching and fluorescence. Conversely, TC-Ax plants produced fruits with the lowest levels of antioxidant compounds. The methylation-sensitive amplified polymorphism (MSAP) technique was employed to detect molecular differences. TC-Ad plants showed the highest methylation level, whereas SC plants had the lowest. The overall methylation level varied among differentially propagated plants. It can be speculated that the differences among the analysed plants may be attributed to variations in DNA methylation.

Assessment of antibacterial activity and cytotoxic effects of in vitro and in vivo plant parts of a medicinal plant Gynura procumbens (Lour.) Merr

The goal of this study was to evaluate the antibacterial and cytotoxic effects of both the in vitro and in vivo plant part extracts of the medicinal plant Gynura procumbens. An effective protocol for regeneration and callus formation was developed using nodal segments and regenerated leaf explants, respectively. The highest fresh and dry weight calli were produced after four weeks of culture on Murashige and Skoog (MS) medium containing 2.0 mg/L BAP and 2.0 mg/L NAA, while the most shoots were produced on MS medium containing 1.0 mg/L BAP and 0.5 mg/L IAA. The in vitro shoots developed roots on MS media with 0.1 mg/L IBA. The antibacterial activity of extracts against various bacteria was examined to determine their significance (p < 0.05). The least significant difference (LSD) test results showed that the regenerated leaf extract had the highest antibacterial activity while the callus extract had the lowest. The minimum bactericidal concentration (MBC) and the minimum inhibitory concentration (MIC) were also established. Regenerated leaf extract had the highest toxicity and the lowest lethal concentration (LC50) value (1.21 ± 0.03 μg/mL) in a brine shrimp lethality bioassay. In contrast, callus extract had the lowest toxicity and the highest LC50 (11.09 ± 0.4 μg/mL). In addition, the in vitro cytotoxicity test results revealed that the callus and field leaf extracts had anti-cell-proliferative properties. The regenerated leaf and stem extract, however, could induce cell growth.

Comprehensive Phenotypic Characterization of Diverse Drug-Type Cannabis Varieties from the Canadian Legal Market

Cannabis (Cannabis sativa L.) stands as a historically significant and culturally important plant, embodying economic, social, and medicinal relevance for human societies. However, years of prohibition and stigmatization have hindered the cannabis research community, which is hugely undersized and suffers from a scarcity of understanding of cannabis genetics and how key traits are expressed or inherited. In this study, we conducted a comprehensive phenotypic characterization of 176 drug-type cannabis accessions, representative of Canada's legal market. We assessed germination methods, evaluated various traits including agronomic, morphological, and cannabinoid profiles, and uncovered significant variation within this population. Notably, the yield displayed a negative correlation with maturity-related traits but a positive correlation with the fresh biomass. Additionally, the potential THC content showed a positive correlation with maturity-related traits but a negative correlation with the yield. Significant differences were observed between the plants derived from regular female seeds and feminized seeds, as well as between the plants derived from cuttings and seeds for different traits. This study advances our understanding of cannabis cultivation, offering insights into germination practices, agronomic traits, morphological characteristics, and biochemical diversity. These findings establish a foundation for precise breeding and cultivar development, enhancing cannabis's potential in the legal market.

Plant regeneration from embryogenic callus-derived from immature leaves of Momordica charantia L

Bitter melon (Momordica charantia L.), a widely cultivated food and medicinal plant native to the world's subtropics and tropics, is a Cucurbitaceae rich in carotenoids. However, the low seed germination frequency and progeny variability associated with the production of this plant have a substantial impact on its growth and yield. These constraints affect the availability and exploitation of this crop, especially the fruits, which are rich in secondary metabolites such as β-carotene and α-carotene. In vitro regeneration would help overcome the obstacle linked to the germination of this plant and increase its yield and utilization. A reproducible in vitro organogenesis protocol was established using bitter melon embryogenic callus derived from immature leaf explants of in vivo grown seedlings and in vitro plantlets. Regeneration via callus was conducted on MSB5 media augmented with different plant growth regulator concentrations. The maximum frequency of callus formation (95.09 %) was produced in MSB5 media incorporated with 1.2 mg L-1 NAA augmented with 0.5 mg L-1 TDZ. MSB5 medium with no growth regulators was observed to be the most suitable for the shoot and root formation from the callus, producing a significantly high shoot percentage of 90.91 % and 21.53 shoots per explants, and the highest rooting frequency and root number of 88.92 % and 6.23 roots per explant, respectively, from leaf-derived callus of in vitro plantlets. The elongated plantlets had grown to a significantly higher average height of 12.20 cm on media added with 0.75 mg L-1 GA3. This reproducible method for regenerating bitter melon plantlets could facilitate mass multiplication, conservation, and commercial field production.

Optimization of Plant Growth Regulators for In Vitro Mass Propagation of a Disease-Free 'Shine Muscat' Grapevine Cultivar

This study addresses the propagation challenges faced by 'Shine Muscat', a newly introduced premium grapevine cultivar in South Korea, where multiple viral infections pose considerable economic loss. The primary objective was to establish a robust in vitro propagation method for producing disease-free grapes and to identify effective plant growth regulators to facilitate large-scale mass cultivation. After experimentation, 2.0 µM 6-benzyladenine (BA) exhibited superior shoot formation in the Murashige and Skoog medium compared with kinetin and thidiazuron. Conversely, α-naphthaleneacetic acid (NAA) hindered shoot growth and induced callus formation, while indole-3-butyric acid (IBA) and indole-3-acetic acid (IAA) demonstrated favorable root formation, with IBA showing better results overall. Furthermore, inter simple sequence repeat analysis confirmed the genetic stability of in vitro-cultivated seedlings using 2.0 μM BA and 1.0 μM IBA, validating the suitability of the developed propagation method for generating disease-free 'Shine Muscat' grapes. These findings offer promising prospects for commercial grape cultivation, ensuring a consistent supply of healthy grapes in the market.

Recalcitrance to transformation, a hindrance for genome editing of legumes

Plant genome editing, a recently discovered method for targeted mutagenesis, has emerged as a promising tool for crop improvement and gene function research. Many genome-edited plants, such as rice, wheat, and tomato, have emerged over the last decade. As the preliminary steps in the procedure for genome editing involve genetic transformation, amenability to genome editing depends on the efficiency of genetic engineering. Hence, there are numerous reports on the aforementioned crops because they are transformed with relative ease. Legume crops are rich in protein and, thus, are a favored source of plant proteins for the human diet in most countries. However, legume cultivation often succumbs to various biotic/abiotic threats, thereby leading to high yield loss. Furthermore, certain legumes like peanuts possess allergens, and these need to be eliminated as these deprive many people from gaining the benefits of such crops. Further genetic variations are limited in certain legumes. Genome editing has the potential to offer solutions to not only combat biotic/abiotic stress but also generate desirable knock-outs and genetic variants. However, excluding soybean, alfalfa, and Lotus japonicus, reports obtained on genome editing of other legume crops are less. This is because, excluding the aforementioned three legume crops, the transformation efficiency of most legumes is found to be very low. Obtaining a higher number of genome-edited events is desirable as it offers the option to genotypically/phenotypically select the best candidate, without the baggage of off-target mutations. Eliminating the barriers to genetic engineering would directly help in increasing genome-editing rates. Thus, this review aims to compare various legumes for their transformation, editing, and regeneration efficiencies and discusses various solutions available for increasing transformation and genome-editing rates in legumes.

Regulation of plant epigenetic memory in response to cold and heat stress: towards climate resilient agriculture

Plants have evolved to adapt and grow in hot and cold climatic conditions. Some also adapt to daily and seasonal temperature changes. Epigenetic modifications play an important role in regulating plant tolerance under such conditions. DNA methylation and post-translational modifications of histone proteins influence gene expression during plant developmental stages and under stress conditions, including cold and heat stress. While short-term modifications are common, some modifications may persist and result in stress memory that can be inherited by subsequent generations. Understanding the mechanisms of epigenomes responding to stress and the factors that trigger stress memory is crucial for developing climate-resilient agriculture, but such an integrated view is currently limited. This review focuses on the plant epigenetic stress memory during cold and heat stress. It also discusses the potential of machine learning to modify stress memory through epigenetics to develop climate-resilient crops.

Engineering traits through CRISPR/cas genome editing in woody species to improve forest diversity and yield

Dangers confronting forest ecosystems are many and the strength of these biological systems is deteriorating, thus substantially affecting tree physiology, phenology, and growth. The establishment of genetically engineered trees into degraded woodlands, which would be adaptive to changing climate, could help in subsiding ecological threats and bring new prospects. This should not be resisted due to the apprehension of transgene dispersal in forests. Consequently, it is important to have a deep insight into the genetic structure and phenotypic limits of the reproductive capability of tree stands/population(s) to endure tolerance and survival. Importantly, for a better understanding of genes and their functional mechanisms, gene editing (GeEd) technology is an excellent molecular tool to unravel adaptation progressions. Therefore, GeEd could be harnessed for resolving the allelic interactions for the creation of gene diversity, and transgene dispersal may be alleviated among the population or species in different bioclimatic zones around the globe. This review highlights the potential of the CRISPR/Cas tools in genomic, transcriptomic, and epigenomic-based assorted and programmable alterations of genes in trees that might be able to fix the trait-specific gene function. Also, we have discussed the application of diverse forms of GeEd to genetically improve several traits, such as wood density, phytochemical constituents, biotic and abiotic stress tolerance, and photosynthetic efficiency in trees. We believe that the technology encourages fundamental research in the forestry sector besides addressing key aspects, which might fasten tree breeding and germplasm improvement programs worldwide.

Generation of the transgene-free canker-resistant Citrus sinensis using Cas12a/crRNA ribonucleoprotein in the T0 generation

Citrus canker caused by Xanthomonas citri subsp. citri (Xcc) is a destructive citrus disease worldwide. Generating disease-resistant cultivars is the most effective, environmentally friendly and economic approach for disease control. However, citrus traditional breeding is lengthy and laborious. Here, we develop transgene-free canker-resistant Citrus sinensis lines in the T0 generation within 10 months through transformation of embryogenic protoplasts with Cas12a/crRNA ribonucleoprotein to edit the canker susceptibility gene CsLOB1. Among the 39 regenerated lines, 38 are biallelic/homozygous mutants, demonstrating a 97.4% biallelic/homozygous mutation rate. No off-target mutations are detected in the edited lines. Canker resistance of the cslob1-edited lines results from both abolishing canker symptoms and inhibiting Xcc growth. The transgene-free canker-resistant C. sinensis lines have received regulatory approval by USDA APHIS and are exempted from EPA regulation. This study provides a sustainable and efficient citrus canker control solution and presents an efficient transgene-free genome-editing strategy for citrus and other crops.

Rindera graeca (A. DC.) Boiss. & Heldr. (Boraginaceae) In Vitro Cultures Targeting Lithospermic Acid B and Rosmarinic Acid Production

The in vitro cultures of Rindera graeca, a rare endemic plant, were developed as a sustainable source of phenolic acids. Various shoot and root cultures were established and scaled up in a sprinkle bioreactor. A multiplication rate of 7.2 shoots per explant was achieved. HPLC-PDA-ESI-HRMS analysis revealed the presence of rosmarinic acid (RA) and lithospermic acid B (LAB) as the main secondary metabolites in both the shoot and root cultures. The maximum RA (30.0 ± 3.2 mg/g DW) and LAB (49.3 ± 15.5 mg/g DW) yields were determined in root-regenerated shoots. The strongest free radical scavenging activity (87.4 ± 1.1%), according to 2,2-diphenyl-1-picrylhydrazyl-hydrate assay, was noted for roots cultivated in a DCR medium. The highest reducing power (2.3 µM ± 0.4 TE/g DW), determined by the ferric-reducing antioxidant power assay, was noted for shoots cultivated on an SH medium containing 0.5 mg/L 6-benzylaminopurine. A genetic analysis performed using random amplified polymorphic DNA and start codon targeted markers revealed genetic variation of 62.8% to 96.5% among the investigated shoots and roots. This variability reflects the capacity of cultivated shoots and roots to produce phenolic compounds.

In vitro and in vivo screening for the identification of salt-tolerant sugarcane (Saccharum officinarum L.) clones: molecular, biochemical, and physiological responses to salt stress

Sugarcane is a glycophyte whose growth and yield can be negatively affected by salt stress. As the arable lands with potential saline soils expand annually, the increase of salt-tolerance in sugarcane cultivars is highly desired. We, herein, employed in vitro and in vivo conditions in order to screen sugarcane plants for salt tolerance at the cellular and at the whole plant levels. Calli of sugarcane cv. Khon Kaen 3 (KK3) were selected after culturing in selective media containing various NaCl concentrations, and regenerated plants were then reselected after culturing in selective media containing higher NaCl concentrations. The surviving plants were finally selected after an exposure to 254 mM NaCl under greenhouse conditions. A total of 11 sugarcane plants survived the selection process. Four plants that exhibited tolerance to the four different salt concentrations applied during the aforementioned screening process were then selected for the undertaking of further molecular, biochemical, and physiological studies. The construction of a dendrogram has revealed that the most salt-tolerant plant was characterized by the lowest genetic similarity to the original cultivar. The relative expression levels of six genes (i.e., SoDREB, SoNHX1, SoSOS1, SoHKT, SoBADH, and SoMIPS) were found to be significantly higher in the salt-tolerance clones than those measured in the original plant. The measured proline levels, the glycine betaine content, the relative water content, the SPAD unit, the contents of chlorophyll a and b, as well as the K⁺/Na⁺ ratios of the salt-tolerant clones were also found to be significantly higher than those of the original plant.When the salt-tolerant clones were grown in a low saline soil, they exhibited a higher Brix percentage than that of the original cultivar.

Effect of Explant Source on Phenotypic Changes of In Vitro Grown Cannabis Plantlets over Multiple Subcultures

Drug-type cannabis is often multiplied using micropropagation methods to produce genetically uniform and disease/insect-free crops. However, micropropagated plantlets often exhibit phenotypic variation, leading to culture decline over time. In cannabis, the source of these changes remains unknown, though several factors (e.g., explant’s sources and prolonged in vitro culture) can result in such phenotypical variations. The study presented herein evaluates the effects of explant sources (i.e., nodal segments derived from the basal, near-basal, middle, and apical parts of the greenhouse-grown mother plant) over multiple subcultures (4 subcultures during 235 days) on multiplication parameters and leaf morphological traits of in vitro cannabis plantlets. While initial in vitro responses were similar among explants sourced from different regions of the plant, there were significant differences in performance over the course of multiple subcultures. Specifically, explant source and/or the number of subcultures significantly impacted plantlet height, number of nodes, and canopy surface area. The explants derived from the basal and near-basal parts of the plant resulted in the tallest shoots with the greatest number of nodes, while the explants derived from the middle and apical regions led to shorter shoots with fewer nodes. Moreover, the basal-derived explants produced cannabis plantlets with shorter but wider leaves which demonstrated the potential of such explants for in vitro rejuvenation practices with minimal culture decline. This study provides new evidence into the long-term impacts of explant source in cannabis micropropagation.

Start codon targeted (SCoT) polymorphism marker in plant genome analysis: current status and prospects

The present review illustrates a comprehensive overview of the start codon targeted (SCoT) polymorphism marker and their utilization in various applications related to genetic and genomic studies. Start codon targeted (SCoT) polymorphism marker, a targeted fingerprinting marker technique, has gained considerable importance in plant genetics, genomics, and molecular breeding due to its many desirable features. SCoT marker targets the region flanking the start codon, a highly conserved region in plant genes. Therefore, it can distinguish genetic variations in a specific gene that link to a specific trait. It is a simple, novel, cost-effective, highly polymorphic, and reproducible molecular marker for which there is no need for prior sequence information. In the recent past, SCoT markers have been employed in many commercially important and underutilized plant species for a variety of applications, including genetic diversity analysis, interspecific/generic genetic relationships, cultivar/hybrid/species identification, sex determination, construction of linkage map, association mapping/analysis, differential gene expression, and genetic fidelity analysis of tissue culture-raised plants. The main aim of this review is to provide up-to-date information on SCoT markers and their application in many commercially important and underutilized plant species, mainly progress made in the last 8-10 years.

Somaclonal Variation for Genetic Improvement of Starch Accumulation in Potato (Solanum tuberosum) Tubers

Starch content is one of the major quality criteria targeted by potato breeding programs. Traditional potato breeding is a laborious duty due to the tetraploid nature and immense heterozygosity of potato genomes. In addition, screening for functional genetic variations in wild relatives is slow and strenuous. Moreover, genetic diversity, which is the raw material for breeding programs, is limited due to vegetative propagation used in the potato industry. Somaclonal variation provides a time-efficient tool to breeders for obtaining genetic variability, which is essential for breeding programs, at a reasonable cost and independent of sophisticated technology. The present investigation aimed to create potato somaclones with an improved potential for starch accumulation. Based on the weight and starch content of tubers, the somaclonal variant Ros 119, among 105 callus-sourced clones, recorded a higher tuberization potential than the parent cv Lady Rosetta in a field experiment. Although this somaclone was similar to the parent in the number of tubers produced, it exhibited tubers with 42 and 61% higher fresh and dry weights, respectively. Additionally, this clone recorded 10 and 75% increases in starch content based on the dry weight and average content per plant, respectively. The enhanced starch accumulation was associated with the upregulation of six starch-synthesis-related genes, namely, the AGPase, GBSS I, SBE I, SBE II, SS II and SS III genes. AGPase affords the glycosyl moieties required for the synthesis of amylose and amylopectin. GBSS is required for amylose elongation, while SBE I, SBE II, SS II and SS III are responsible for amylopectin.

Somaclonal Variation-Advantage or Disadvantage in Micropropagation of the Medicinal Plants

Cell and tissue plant cultures are used either to save vulnerable species from extinction or to multiply valuable genotypes, or both, and are widely applied for economically important plant species. For medicinal plants, the use of in vitro technologies for the production of secondary metabolites and pathogen-free plants has been greatly developed. Two opposite aspects characterize the in vitro micropropagation of medicinal plants: maintaining genetic fidelity for the perpetuation and preservation of elites, and the identification and exploitation of somaclonal variations associated with new, useful traits. A balance between what is advantageous and what is undesirable is necessary, and this implies the identification of somaclonal variability at all levels, from the phenotypic to molecular ones. This review addresses the somaclonal variation arising from the in vitro multiplication of medicinal plants from three perspectives: cytogenetics, genetics, and epigenetics. The possible causes of the appearance of somaclones, the methods for their identification, and the extent to which they are desirable are presented comparatively for different plant species with therapeutic properties. The emphasis is on the subtle changes at the genetic and epigenetic level, as it results from the application of methods based on DNA markers.

Potential of In Vitro Culture of Scutellaria baicalensis in the Formation of Genetic Variation Confirmed by ScoT Markers

The in vitro culture technique can be used for micropropagation of medicinal plants as well as for creating genotypes with an improved profile of phytochemical compounds. For this purpose, somaclonal variability may be used for the induction of genetic diversity among regenerants. The paper presents a protocol for obtaining Scutellaria baicalensis regenerants by indirect organogenesis and the assessment of their genetic variability with the use of start codon-targeted markers. The most intense process of indirect shoot organogenesis was observed on Murashige and Skoog medium supplemented with kinetin and 6-Benzylaminopurine (0.5 mg × dm-3 each)-7.4 shoot per explant on average. The callogenesis process occurred on the medium supplemented with TDZ, while the medium supplemented with GA3 allowed for direct shoot organogenesis and was used for the micropropagation of regenerants. In the analysis of plantlets obtained by indirect organogenesis, 11 ScoT markers generated a total of 130 amplicons, 45 of which were polymorphic. This analysis showed genetic diversity of regenerants in relation to the donor plant as well as within them, with mean similarity among the analyzed genotypes at the level of 0.90. This study confirms that the use of in vitro cultures allows for the possibility to generate genetic variability in Scutellaria baicalensis, which can be effectively revealed with the use of the SCoT marker.

Efficient shoot regeneration of medicinal plant Haplophyllum tuberculatum by direct and indirect organogenesis and genetic fidelity assessment using Inter Simple Sequence Repeats markers

In vitro plant cell and tissue cultures are potent tools to propagating germplasm resources in conserving and managing plant genetic resources. A reliable micropropagation protocol was developed for efficient callus proliferation and direct and indirect shoot regeneration of Meseika (Haplophyllum tuberculatum). With the applied sterilization procedure, immature, unopened H. tuberculatum seed pods can be identified as a potent explant with high viability and low contamination percentage. Multiple shoots were regenerated from leaf and stem explants through direct organogenesis on Murashige and Skoog's (MS) + 3% sucrose medium amended with BAP. Indirect regeneration of several shoots was achieved on 1/2 MS + 1% sucrose media amended with 2 and 4 mg/l BAP. An efficient callus proliferation from both explants can be achieved by supplementing the MS media with NAA and BAP. All the cultures were incubated in a controlled growth chamber under 5/19 h light/dark photoperiod, temperature (25 ± 2°C), and 60% relative humidity (RH).10 ISSR (Inter Simple Sequence Repeat) markers were screened to test the genetic fidelity of regenerated H. tuberculatum shoots. Callus development was observed after 15 days and shoot regeneration was occurred after 30 days after callus initiation. 10 ISSR primers produced a total of 39 clear, distinct amplicons. 75, 60, 40, and 16% polymorphism percentages were recorded by the ISSR primer 11, 7, 5, and 4, respectively. The developed micropropagation protocol is appropriate for rapid in-vitro multiplication of H. tuberculatum shoots and callus.

Flower color mutation, pink to orange, through CmGATA4 - CCD4a-5 module regulates carotenoids degradation in chrysanthemum

The carotenoids biosynthesis pathway in plants has been studied extensively, yet little is known about the regulatory mechanisms underlying this process, especially for ornamental horticulture plants. In this study, a natural variation of chrysanthemum with orange coloration was identified and compared with the wild type with pink coloration; the content and component of carotenoids were largely enriched in the mutant with orange coloration. CmCCD4a-5, the DNA sequence in both 'Pink yan' and the mutant, was identified and shown to function as a carotenoid degradation enzyme. Compared with 'Pink yan', the mutant shows lower expression level of CmCCD4a-5. Furthermore, CmGATA4 was found to have an opposite expression trend to CmCCD4a-5, and it could directly bind with the CmCCD4a-5 promoter. Taken together, this study demonstrates that CmGATA4 acts as a negative regulator of CmCCD4a-5 and, furthermore, low expression of CmCCD4a-5 resulted in carotenoid accumulation in the mutant.

Applications of In Vitro Tissue Culture Technologies in Breeding and Genetic Improvement of Wheat

Sources of new genetic variability have been limited to existing germplasm in the past. Wheat has been studied extensively for various agronomic traits located throughout the genome. The large size of the chromosomes and the ability of its polyploid genome to tolerate the addition or loss of chromosomes facilitated rapid progress in the early study of wheat genetics using cytogenetic techniques. At the same time, its large genome size has limited the progress in genetic characterization studies focused on diploid species, with a small genome and genetic engineering procedures already developed. Today, the genetic transformation and gene editing procedures offer attractive alternatives to conventional techniques for breeding wheat because they allow one or more of the genes to be introduced or altered into an elite cultivar without affecting its genetic background. Recently, significant advances have been made in regenerating various plant tissues, providing the essential basis for regenerating transgenic plants. In addition, Agrobacterium-mediated, biolistic, and in planta particle bombardment (iPB) gene delivery procedures have been developed for wheat transformation and advanced transgenic wheat development. As a result, several useful genes are now available that have been transferred or would be helpful to be transferred to wheat in addition to the current traditional effort to improve trait values, such as resistance to abiotic and biotic factors, grain quality, and plant architecture. Furthermore, the in planta genome editing method will significantly contribute to the social implementation of genome-edited crops to innovate the breeding pipeline and leverage unique climate adaptations.

Triticale doubled haploid plant regeneration factors linked by structural equation modeling

Triticale regeneration via anther culture faces many difficulties, e.g., a low percentage of regenerated plants and the presence of albinos. Plant regeneration may be affected by abiotic stresses and by ingredients added to the induction medium. The latter influences biochemical pathways and plant regeneration efficiency. Among such ingredients, copper and silver ions acting as cofactors for enzymatic reactions are of interest. However, their role in plant tissue cultures and relationships with biochemical pathways has not been studied yet.

The study evaluated relationships between DNA methylation, changes in DNA sequence variation, and green plant regeneration efficiency influenced by copper and silver ions during triticale plant regeneration. For this purpose, a biological model based on donor plants and their regenerants, a methylation-sensitive amplified fragment length polymorphism, and structural equation modeling were employed.

The green plant regeneration efficiency varied from 0.71 to 6.06 green plants per 100 plated anthers. The values for the components of tissue culture-induced variation related to cytosine methylation in a CHH sequence context (where H is A, C, or T) were 8.65% for sequence variation, 0.76% for DNA demethylation, and 0.58% for de novo methylation. The proposed model states that copper ions affect the regeneration efficiency through cytosine methylation and may induce mutations through, e.g., oxidative processes, which may interfere with the green plant regeneration efficiency. The linear regression confirms that the plant regeneration efficiency rises with increasing copper ion concentration in the absence of Ag ions in the induction medium. The least absolute shrinkage and selection operator regression shows that de novo methylation, demethylation, and copper ions may be involved in the green plant regeneration efficiency. According to structural equation modeling, copper ions play a central role in the model determining the regeneration efficiency.

Gamma ray-induced tissue responses and improved secondary metabolites accumulation in Catharanthus roseus

The present study investigated the impact of gamma ray irradiation on callus biomass growth and the yield of vincristine and vinblastine of in vitro grown tissues of Catharanthus roseus. The biochemical alteration underlying the synthesis of secondary metabolites has also been studied and a comparison of yield was prepared. The embryogenic tissues were exposed to 20, 40, 60, 80, and 100 Gy gamma ray doses and the callus biomass fresh weight, the embryogenesis (the embryo numbers, germination, plant regeneration), the alteration of protein, proline, and sugar attributes at different morphogenetic stages were monitored. The callus biomass growth was maximum (1.65 g) in 20 Gy exposed tissues and was less in 100 Gy treatment (0.33 g). The gamma-irradiated embryogenic tissues differentiated into embryos but the embryogenesis % and somatic embryo number per culture reduced with increasing doses. It was least in 80 Gy where very low numbers of embryos were formed (3.45 and 3.30 mean torpedo and cotyledonary embryo numbers per callus mass, respectively) which later germinated into plantlets. Protein, proline, sugar, and different antioxidant enzymes, i.e., superoxide dismutase (SOD), ascorbate peroxidase (APX), and catalase (CAT) activities, were investigated as the tissues were exposed to gamma ray elicitation/signaling, evoking cellular stress. Increased 80 Gy gamma dose inhibited a 42.73% decrease in protein accumulation at initiation stages of embryogenic tissue. Soluble sugar level also declined gradually being least in 80 Gy treated tissues (14.51 mg gm^-1 FW) compared to control (20.2 mg gm^-1 FW). Proline content, however, increased with increasing gamma doses, maximum at 80 Gy (8.28 mg gm^-1 FW). The SOD, APX, and CAT activity increased linearly with enhanced level of gamma doses and maximum, i.e., 3.91 EU min^-1 mg^-1, 1.71 EU min^-1 mg^-1, and 4.89 EU min^-1 mg^-1, protein activity was noted for SOD, APX, and CAT, respectively, at 80 Gy gamma rays treated tissues. The quantification of vinblastine and vincristine in gamma ray elicitated tissues was made by using high-pressure thin layer chromatography (HPTLC). Somatic embryo-regenerated plant's leaves had the maximum yield of vinblastine (15.13 µgm gm^-1 DW) at 40 Gy irradiation dose compared to control (13.30 µgm gm^-1 DW)-the increased yield % is 13.75. The stem is also rich source producing 11.98 µgm gm^-1 DW of vinblastine. Among the various developmental stages of embryos, vinblastine content was highest in germinating stage of embryos (10.14 µgm gm^-1 DW) compared to other three, i.e., initiation, proliferation, and maturation embryo stages. Similarly, highest accumulation of vincristine (6.32 µg gm^-1 DW) was noted at low gamma irradiation dose (20 Gy) in leaf tissues. The present study indicates that the synthesis of vinblastine and vincristine was growth- and development-specific and the lower 20-40 Gy gamma levels were more effective in enriching alkaloids while higher doses declined yield. KEY POINTS: • Vinblastine and vincristine yield was quantified in in vitro grown tissues and leaves of embryo regenerated Catharanthus roseus after gamma ray treatment. • The accumulation of vinblastine and vincristine was maximum in regenerated leaves; low doses were more efficient in improving yield. • Gamma ray irradiation impacted biochemical profiles, caused cellular stress, and perhaps responsible for improved alkaloid yield.

Phylogeography and conservation gaps of Musa balbisiana Colla genetic diversity revealed by microsatellite markers

Collection and storage of crop wild relative (CWR) germplasm is crucial for preserving species genetic diversity and crop improvement. Nevertheless, much of the genetic variation of CWRs is absent in ex situ collections and detailed passport data are often lacking. Here, we focussed on Musa balbisiana, one of the two main progenitor species of many banana cultivars. We investigated the genetic structure of M. balbisiana across its distribution range using microsatellite markers. Accessions stored at the International Musa Germplasm Transit Centre (ITC) ex situ collection were compared with plant material collected from multiple countries and home gardens from Vietnam. Genetic structure analyses revealed that accessions could be divided into three main clusters. Vietnamese and Chinese populations were assigned to a first and second cluster respectively. A third cluster consisted of ITC and home garden accessions. Samples from Papua New Guinea were allocated to the cluster with Chinese populations but were assigned to a separate fourth cluster if the number of allowed clusters was set higher. Only one ITC accession grouped with native M. balbisiana populations and one group of ITC accessions was nearly genetically identical to home garden samples. This questioned their wild status, including accessions used as reference for wild M. balbisiana. Moreover, most ITC accessions and home garden samples were genetically distinct from wild populations. Our results highlight that additional germplasm should be collected from the native distribution range, especially from Northeast India, Myanmar, China, and the Philippines and stored for ex situ conservation at the ITC. The lack of passport data for many M. balbisiana accessions also complicates the interpretation of genetic information in relation to cultivation and historical dispersal routes.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10722-022-01389-4.

miRNA Profiling and Its Role in Multi-Omics Regulatory Networks Connected with Somaclonal Variation in Cucumber (Cucumis sativus L.)

The role of miRNAs in connection with the phenomenon of somaclonal variation, which occurs during plant in vitro culture, remains uncertain. This study aims to investigate the possible role of miRNAs in multi-omics regulatory pathways in cucumber somaclonal lines. For this purpose, we performed sRNA sequencing (sRNA-seq) from cucumber fruit samples identified 8, 10 and 44 miRNAs that are differentially expressed between somaclones (S1, S2, S3 lines) and the reference B10 line of Cucumis sativus. For miRNA identification, we use ShortStack software designed to filter miRNAs from sRNAs according to specific program criteria. The identification of predicted in-silico targets revealed 2,886 mRNAs encoded by 644 genes. The functional annotation of miRNA's target genes and gene ontology classification revealed their association with metabolic processes, response to stress, multicellular organism development, biosynthetic process and catalytic activity. We checked with bioinformatic analyses for possible interactions at the level of target proteins, differentially expressed genes (DEGs) and genes affected by genomic polymorphisms. We assume that miRNAs can indirectly influence molecular networks and play a role in many different regulatory pathways, leading to somaclonal variation. This regulation is supposed to occur through the process of the target gene cleavage or translation inhibition, which in turn affects the proteome, as we have shown in the example of molecular networks. This is a new approach combining levels from DNA-seq through mRNA-seq, sRNA-seq and in silico PPI in the area of plants' somaclonal variation.

Assessment of genetic fidelity of lacy tree philodendron (Philodendron bipinnatifidum Schott ex Endl.) micro propagated plants

Tissue culture is a potent means for producing clonally propagated plants. However, genetically identical regenerants are of great concern due to their economic consequences. Therefore, polymerase chain reaction (PCR)-based molecular markers are employed to detect somaclonal variations. In this study, the genetic fidelity of in vitro raised Philodendron bipinnatifidum clones, and their mother plant was tested using 11 randomly amplified polymorphic DNA (RAPD) markers. The RAPD decamers produced 92 amplicons with 8.4 bands ranging from 260-5000 bp. The bands varied from one to fifteen for primer 8 and primer 7, respectively. The genetic similarity between the micro propagated plantlets and mother plant of P. bipinnatifidum was nearly 100%, assuring uniformity and true-to-type regenerated plantlets for this commercially crucial ornamental plant.

Establishment of In Vitro Regeneration Protocol for Sabah’s Jewel Orchid, Macodes limii J.J. Wood & A.L. Lamb

Habitat disturbance and excessive collection of wild orchids from their natural habitat have threatened many orchids species at risk of extinction. In this study, the in vitro regeneration protocol for Macodes limii, a jewel orchid endemic to Sabah was established. The effects of explant source and plant growth regulators (PGRs) including naphthaleneacetic acid, picloram, 2,4-dichlorophenoxyacetic acid, 6-benzylaminopurine, kinetin, and thidiazuron on the in vitro regeneration capacity of M. limii plantlets were examined. Both factors showed a significant interaction in promoting axillary shoot formation. Nodal explants from the third and fourth positions cultured with 1.0 mg/L TDZ, induced 95% of shoot regeneration, with an average of three shoots/explant (1.6–1.8 cm of shoot length) after 90 days of culture. The well-developed plantlets went through an acclimatization phase for 60 days with a 60% of survival rate. An inter simple sequence repeat (ISSR) marker analysis confirmed the genetic stability of the in vitro regenerated plants to the mother plant. The successfully acclimatized plantlets were finally transferred to Poring Orchid Conservation Centre for reintroduction. The established protocol provides the means for large-scale production of this endemic jewel orchid, as well as a basis for further research aimed at the conservation and genetic improvement of this plant.

Variation burst during dedifferentiation and increased CHH-type DNA methylation after 30 years of in vitro culture of sweet orange

Somaclonal variation arising from tissue culture may provide a valuable resource for the selection of new germplasm, but may not preserve true-to-type characteristics, which is a major concern for germplasm conservation or genome editing. The genomic changes associated with dedifferentiation and somaclonal variation during long-term in vitro culture are largely unknown. Sweet orange was one of the earliest plant species to be cultured in vitro and induced via somatic embryogenesis. We compared four sweet orange callus lines after 30 years of constant tissue culture with newly induced calli by comprehensively determining the single-nucleotide polymorphisms, copy number variations, transposable element insertions, methylomic and transcriptomic changes. We identified a burst of variation during early dedifferentiation, including a retrotransposon outbreak, followed by a variation purge during long-term in vitro culture. Notably, CHH methylation showed a dynamic pattern, initially disappearing during dedifferentiation and then more than recovering after 30 years of in vitro culture. We also analyzed the effects of somaclonal variation on transcriptional reprogramming, and indicated subgenome dominance was evident in the tetraploid callus. We identified a retrotransposon insertion and DNA modification alternations in the potential regeneration-related gene CLAVATA3/EMBRYO SURROUNDING REGION-RELATED 16. This study provides the foundation to harness in vitro variation and offers a deeper understanding of the variation introduced by tissue culture during germplasm conservation, somatic embryogenesis, gene editing, and breeding programs.

In Vitro Regeneration of Miscanthus x giganteus through Indirect Organogenesis: Effect of Explant Type and Growth Regulators

Miscanthus x giganteus is a spontaneous sterile hybrid therefore the creation of useful genetic diversity by conventional breeding methods is restricted. Plant regeneration through indirect organogenesis may be a useful approach to create genetic variability of this important agricultural crop. The present study aimed to evaluate the effect of the explant type and growth regulators on indirect organogenesis of Miscanthus x giganteus and to determine the ploidy level of plant regenerants by flow cytometry. On average, the highest percentage of morphogenic callus tested explants formed in the medium supplemented with 2.5 mg L^-1 IBA + 0.1 mg L^-1 BAP + 4.0 mg L^-1&nbsp;l-proline. The most intensive secondary differentiation of callus cells was observed in the medium supplemented with 4.0 mg L^-1 ZEA + 1.0 mg L^-1 NAA. The highest root formation frequency with the highest number of roots was determined in the MS nutrient medium supplemented with 0.4 mg L^-1 IBA, where more than 95% of plant regenerants survived and were growing normally.

Establishment of a Novel and Efficient Agrobacterium-Mediated in Planta Transformation System for Passion Fruit (Passiflora edulis)

Passion fruit (Passiflora edulis) is an important fruit crop with high economic value. Genetic engineering plays an important role in crop improvement with desired traits and gene functional studies. The lack of a simple, efficient, and stable transformation system for passion fruit has greatly limited gene functional studies. In this study, a simple and efficient Agrobacterium-mediated in planta transformation system for passion fruit was established, using Agrobacterium virulent strain EHA105 harboring the binary vectors pCAMBIA1301 and pCAMBIA1302 with GUS and GFP reporter genes. The system requires less time and labor costs than conventional transformation systems, and no additional phytohormones and sterile conditions are required. Regeneration efficiency of 86% and transformation efficiency of 29% were achieved, when the wounds were wrapped with Parafilm and the plants were kept in darkness for 15 days. Approximately 75% of the regenerated plants had a single shoot and 26% multiple shoots. The transformation was confirmed at the DNA and RNA levels as well as by GUS staining and GFP fluorescent measurements. The developed protocol will contribute to the genetic improvement of passion fruit breeding.

Elevated transcription of transposable elements is accompanied by het-siRNA-driven de novo DNA methylation in grapevine embryogenic callus

Background

Somatic variation is a valuable source of trait diversity in clonally propagated crops. In grapevine, which has been clonally propagated worldwide for centuries, important phenotypes such as white berry colour are the result of genetic changes caused by transposable elements. Additionally, epiallele formation may play a role in determining geo-specific (‘terroir’) differences in grapes and thus ultimately in wine. This genomic plasticity might be co-opted for crop improvement via somatic embryogenesis, but that depends on a species-specific understanding of the epigenetic regulation of transposable element (TE) expression and silencing in these cultures. For this reason, we used whole-genome bisulphite sequencing, mRNA sequencing and small RNA sequencing to study the epigenetic status and expression of TEs in embryogenic callus, in comparison with leaf tissue.

Results

We found that compared with leaf tissue, grapevine embryogenic callus cultures accumulate relatively high genome-wide CHH methylation, particularly across heterochromatic regions. This de novo methylation is associated with an abundance of transcripts from highly replicated TE families, as well as corresponding 24 nt heterochromatic siRNAs. Methylation in the TE-specific CHG context was relatively low over TEs located within genes, and the expression of TE loci within genes was highly correlated with the expression of those genes.

Conclusions

This multi-‘omics analysis of grapevine embryogenic callus in comparison with leaf tissues reveals a high level of genome-wide transcription of TEs accompanied by RNA-dependent DNA methylation of these sequences in trans. This provides insight into the genomic conditions underlying somaclonal variation and epiallele formation in plants regenerated from embryogenic cultures, which is an important consideration when using these tissues for plant propagation and genetic improvement.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07973-9.

Can the Caper (Capparis spinosa L.) Still Be Considered a Difficult-to-Propagate Crop?

As a perennial xerophytic shrub, characterized by plesiomorphic features, the caper (Capparis spinosa L.) is naturally spread throughout the Mediterranean basin and occupies an important ecological role, as well as an economic one, in traditional and specialized systems for commercial production. This species, in spite of its wide diffusion, is currently considered at risk of genetic erosion, mainly due to overgrazing and overharvesting for domestic uses and for trade. This situation is made more serious because of the lack of efficient propagation techniques, determining the caper as a “difficult-to-propagate species”. In this review, we report the main available sexual and vegetative propagation techniques with the aim of assessing whether, and to what extent, this criticality is still true for caper as a horticultural crop. In terms of seed propagation, germination rates have generally been considered quite low or unsatisfactory, and are also affected by hybridization phenomena that are likely to occur among both the wild and cultivated forms. The seeds show a physiological dormancy that can be lowered by adopting hormonal treatments, but in situ germination remains a critical phase. Vegetative propagation appears quite effective, mostly as related to in vitro techniques that allow caper cultivation that is no longer affected by propagation for an economic dissemination of the species in more intensive orchards. The research needs for Caper spinosa L. as a horticultural crop, especially in the field of genetic improvement and breeding, are also underlined.

Epigenetic and somaclonal divergence in Dendrocalamus farinosus for physiological augmentation and lignin degradation

Epigenetic and molecular variation is a key approach for the improvement of plants. From in vitro tissue culture of Dendrocalamus farinosus; 30 plants were regenerated and after 2 years, the physiological, biochemical, and genomic studies were conducted. The results highlighted that for all phenotypic characteristics, the 30 regenerated plants were superior in comparison with the control (CK). From genetical analysis, a total of 97 bands were witnessed ranging between 212 bp and 2.2 kb. The results for OPU14 showed one additional specific band (723 bp) and one band (700 bp) were missing. The 10 plants were having genetic variability and can be termed as somaclones while the other plants have epigenetic variations. The cellulose and lignin analysis highlighted that somaclone No. 30 has the least cellulose content of 35%; while the somaclones No. 102 and No. 213 have the least 3.21% and 3.48% of lignin contents. Therefore, somaclones No. 30, No. 102, and No. 213 were selected for the histochemical localization. The lignin investigation revealed that somaclone No. 30 is greater while somaclones No. 102 and No. 213 were reduced in vascular bundles in comparison with the CK along with the high expression level of 4CL, C3H, C4H, COMT, and CCoAOMT1 genes.

A glance at the chemodiversity of Ocimum species: Trends, implications, and strategies for the quality and yield improvement of essential oil

Ocimum species represent commercially important medicinal and aromatic plants. The essential oil biosynthesized by Ocimum species is enriched with specialized metabolites specifically, terpenoids and phenylpropanoids. Interestingly, various Ocimum species are known to exhibit diverse chemical profiles, and this chemical diversity has been at the center of many studies to identify commercially important chemotypes. Here, we present various chemotypes from the Ocimum species and emphasize trends, implications, and strategies for the quality and yield improvement of essential oil. Globally, many Ocimum species have been analyzed for their essential oil composition in over 50 countries. Asia represents the highest number of chemotypes, followed by Africa, South America, and Europe. Ocimum basilicum L. has been the most widespread and well-studied species, followed by O. gratissimum L., O. tenuiflorum L., O. canum Sims, O. americanum and O. kilimandscharicum Gürke. Moreover, various molecular reasons, benefits, adverse health effects and mechanisms behind this vast chemodiversity have been discussed. Different strategies of plant breeding, metabolic engineering, transgenic, and tissue-culture, along with anatomical modifications, are surveyed to enhance specific chemotypic profiles and essential oil yield in numerous Ocimum species. Consequently, chemical characterization of the essential oil obtained from Ocimum species has become indispensable for its proper utilization. The present chemodiversity knowledge from Ocimum species will help to exploit various applications in the industrial, agriculture, biopharmaceutical, and food sectors.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s11101-021-09767-z.

Metabolic profiling, in vitro propagation, and genetic assessment of the endangered rare plant Anarrhinum pubescens

Background

Anarrhinum pubescens Fresen. (Plantaginaceae) is a rare plant, endemic to the Saint Catherine area, of South Sinai, Egypt. Earlier studies have reported the isolation of cytotoxic and anti-cholinesterase iridoid glucosides from the aerial parts of the plant. The present study aimed to investigate the chemical profiling of the wild plant shoots as well as establish efficient protocols for in vitro plant regeneration and proliferation with further assessment of the genetic stability of the in vitro regenerated plants.

Results

Twenty-seven metabolites have been identified in wild plant shoots using the Nuclear Magnetic Resonance (NMR) spectroscopy. The metabolites include alkaloids, amino acids, carbohydrates, organic acids, vitamins, and a phenol. In vitro propagation of the plant was carried out through nodal cutting-micropropagation and leaf segment-direct organogenesis. The best results were obtained when nodal cutting explants were cultured on Murashige and Skoog medium with Gamborg B5 vitamins supplemented with 6-benzylaminopurine (BAP) (1.0 mg/L) and naphthaleneacetic acid (NAA) (0.05 mg/L), which gave a shoot formation capacity of 100% and a mean number of shoots of 27.67 ± 1.4/explant. These shoots were successfully rooted and transferred to the greenhouse and the survival rate was 75%. Genetic fidelity evaluation of the micropropagated clones was carried out using random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) molecular markers. Jaccard’s similarity coefficient indicated a similarity as high as 98% and 95% from RAPD and ISSR markers, respectively.

Conclusions

This study provides the chemical profiling of the aerial part of Anarrhinum pubescens. Moreover, in vitro regeneration through different tissue culture techniques has been established for mass propagation of the plant, and the genetic fidelity of the in vitro regenerated plants was confirmed as well. Our work on the in vitro propagation of A. pubescens will be helpful in ex situ conservation and identification of bioactive metabolites.

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.

Habituation to thaxtomin A increases resistance to common scab in 'Russet Burbank' potato

Common scab is a potato disease characterized by the formation of scab-like lesions on the surface of potato tubers. The actinobacterium Streptomyces scabiei is the main causal agent of common scab. During infection, this bacterium synthesizes the phytotoxin thaxtomin A which is essential for the production of disease symptoms. While thaxtomin A can activate an atypical programmed cell death in plant cell suspensions, it is possible to gradually habituate plant cells to thaxtomin A to provide resistance to lethal phytotoxin concentrations. Potato 'Russet Burbank' calli were habituated to thaxtomin A to regenerate the somaclone RB9 that produced tubers more resistant to common scab than those obtained from the original cultivar. Compared to the Russet Burbank cultivar, somaclone RB9 generated up to 22% more marketable tubers with an infected tuber area below the 5% threshold. Enhanced resistance was maintained over at least two years of cultivation in the field. However, average size of tubers was significantly reduced in somaclone RB9 compared to the parent cultivar. Small RB9 tubers had a thicker phellem than Russet Burbank tubers, which may contribute to improving resistance to common scab. These results show that thaxtomin A-habituation in potato is efficient to produce somaclones with increased and durable resistance to common scab.

Comparative Study of the Genetic and Biochemical Variability of Polyscias filicifolia (Araliaceae) Regenerants Obtained by Indirect and Direct Somatic Embryogenesis as a Source of Triterpenes

Polyscias filicifolia (Araliaceae) is broadly used in traditional medicine in Southeast Asia due to its antimicrobial, immunomodulating and cytotoxic activities. The main groups of compounds responsible for pharmacological effects are believed to be oleanolic triterpene saponins. However, Polyscias plants demonstrate relatively slow growth in natural conditions, which led to applying a developing sustainable source of plant material via primary (PSE), secondary (DSE) and direct somatic embryogenesis from DSE (TSE). The AFLP and metAFLP genotyping resulted in 1277 markers, amplified by a total of 24 pairs of selective primers. Only 3.13% of the markers were polymorphic. The analysis of variance showed that the PSE and TSE regenerants differed only in terms of root number, while the DSE plantlets differed for all studied morphological characteristics. Further, the chemical analysis revealed that oleanolic acid (439.72 µg/g DW), ursolic acid (111.85 µg/g DW) and hederagenin (19.07 µg/g DW) were determined in TSE regenerants. Our results indicate that direct somatic embryogenesis ensures the production of homogeneous plant material, which can serve as a potential source of triterpene compounds. Plants obtained via somatic embryogenesis could also be reintroduced into the natural environment to protect and preserve its biodiversity.

A More Accessible, Time-Saving, and Efficient Method for In Vitro Plant Regeneration from Potato Protoplasts

Both obtaining high-yielding, viable protoplasts and following reliable regeneration protocols are prerequisites for the continuous expansion and development of newly emerging systems involving protoplast utilization. This study determines an efficient process from protoplast isolation to shoot regeneration in vitro. The maximum yield of protoplast extraction, which was 6.36 ± 0.51 × 10⁶ protoplasts/g fresh weight (FW), was approximately 3.7 times higher than that previously reported for potato protoplasts. To obtain data, wounded leaves were used by partially cutting both sides of the midrib, and isolated protoplasts were purified by the sucrose cushion method, with a sucrose concentration of 20%. We confirmed a significant effect on the extraction efficiency by measuring enzymolysis during a 6 h period, with three times more washing buffer than the amount normally used. Protoplasts fixed in alginate lenses with appropriate space were successfully recovered and developed into microcalli 2 weeks after culture. In addition, to induce high efficiency regeneration from protoplasts, calli in which greening occurred for 6 weeks were induced to develop shoots in regeneration medium solidified by Gelrite, and they presented a high regeneration efficiency of 86.24 ± 11.76%.

Analysis of the possible cytogenetic mechanism for overcoming hybrid lethality in an interspecific cross between Nicotiana suaveolens and Nicotiana tabacum

Hybrid lethality is a type of reproductive isolation in which hybrids die before maturation, due to the interaction between the two causative genes derived from each of the hybrid parents. The interspecific hybrid of Nicotiana suaveolens × Nicotiana tabacum is a model plant used in studies on hybrid lethality. While most of the progeny produced from such a cross die, some individuals grow normally and mature. Separately, a technique for producing mature hybrids by artificial culture has been developed. However, the mechanism by which hybrids overcome lethality, either spontaneously or by artificial culture, remains unclear. In the present study, we found that some hybrids that overcome lethality, either spontaneously or by artificial culture, lack the distal part of the Q chromosome, a region that includes the gene responsible for lethality. Quantitative polymerase chain reaction results suggested that the distal deletion of the Q chromosome, detected in some hybrid seedlings that overcome lethality, is caused by reciprocal translocations between homoeologous chromosomes. The results showed that chromosomal instability during meiosis in amphidiploid N. tabacum as well as during artificial culturing of hybrid seedlings is involved in overcoming hybrid lethality in interspecific crosses of the genus Nicotiana.