Agrobacterium-mediated transient transformation of sorghum leaves for accelerating functional genomics and genome editing studies

Development and optimization of in vitro shoot regeneration in Physalis peruviana using cotyledon explants

The genetic improvement of Physalis peruviana L. faces important challenges because it is a recalcitrant species, which limits its use in breeding and conservation programs. In the present research, the objective was to develop an effective regeneration protocol using cotyledon cultures. For this purpose, the effects of zeatin (ZT) and meta-topoline (mT) at concentrations of 0, 0.5, 1.0 and 2.0 mg/L and the effects of several auxins, including indolbutyric acid (IBA), indolacetic acid (IAA), naphthaleneacetic acid (NAA) and 2.4-dichlorophenoxyacetic acid (2.4-D), on morphogenetic responses were evaluated. A maximum regeneration of 62.5 % was achieved with the combination of 2 mg/L ZT, 2 mg/L mT, and 0.5-1 mg/L IBA. For root formation, the best results were obtained with the combination of 2 mg/L ZT, 2 mg/L mT, and 1 mg/L NAA, reaching a maximum rate of 87.5 %. In conclusion, specific combinations of cytokinins and auxins can overcome the resistance of P. peruviana to regeneration and provide a solid basis for biotechnological applications such as genetic transformation and germplasm conservation.

Plant Engineering to Enable Platforms for Sustainable Bioproduction of Terpenoids

Terpenoids represent the most diverse class of natural products, with a broad spectrum of industrial relevance including applications in green solvents, flavors and fragrances, nutraceuticals, colorants, and therapeutics. They are typically challenging to extract from their natural sources, where they occur in small amounts and mixtures of related but unwanted byproducts. Formal chemical synthesis, where established, is reliant on petrochemistry. Hence, there is great interest in developing sustainable solutions to assemble biosynthetic pathways in engineered host organisms. Metabolic engineering for chemical production has largely focused on microbial hosts, yet plants offer a sustainable production platform. In addition to containing the precursor pathways that generate the terpenoid building blocks as well as the cell structures and compartments required, or tractable localization for the enzymes involved, plants may provide a low input system to produce these chemicals using carbon dioxide and sunlight only. There have been significant recent advancements in the discovery of pathways to terpenoids of interest as well as strategies to boost yields in host plants. While part of the phytochemical field is focusing on the discovery of biosynthetic pathways, this review will focus on advancements using the pathway toolbox and toward engineering plants for the production of terpenoids. We will highlight strategies currently used to produce target products, optimization of known pathways to improve yields, compartmentalization of pathways within cells, and genetic tools developed to facilitate complex engineering of biosynthetic pathways. These advancements in Synthetic Biology are bringing engineered plant systems closer to commercially relevant hosts for the bioproduction of terpenoids.

Isolation, Purification, and Application of Protoplasts and Transient Expression Systems in Plants

Protoplasts, derived from plant cells, exhibit remarkable totipotency and hold significant value across a wide spectrum of biological and biotechnological applications. These versatile applications encompass protein subcellular localization and interaction analysis, gene expression regulation, functional characterization, gene editing techniques, and single-cell sequencing. Protoplasts' usability stems from their inherent accessibility and their ability to efficiently incorporate exogenous genes. In this review, we provide a comprehensive overview, including details on isolation procedures and influencing factors, purification and viability assessment methodologies, and the utilization of the protoplast transient expression system. The aim is to provide a comprehensive overview of current applications and offer valuable insights into protoplast isolation and the establishment of transient expression systems in a diverse range of plant species, thereby serving as a valuable resource for the plant science community.

Identification of a suitable method of inoculation for reducing background effect in mock-inoculated controls during gene expression studies in Arabidopsis thaliana

The recent advancement in the field of transcriptome and methylome sequencing helped scientists to analyse the gene expression and epigenetic status of different genes. Several genes and their regulatory pathways have been discovered due to research into plant-microbe interactions. Previous research on plant-Agrobacterium interactions found that the method of inoculation (wounding using a syringe), resulted in altered DNA methylation of the host DNA repair gene promoters. The expression study of host defence genes revealed that the method of inoculation masked the host response to bacteria. It could be possible that these method-induced changes could interfere with various defence regulatory pathways, which otherwise would not be triggered by the bacteria alone. Hence, it would be critical to identify an appropriate method of inoculation that could provide more unambiguous interpretation of studies involving gene expression and regulation in plants under bacterial stress. The expression dynamics of two defence genes, PR1 and NPR1, under various combinations of parameters such as three different methods of inoculation, treatment with five different bacterial re-suspending solutions, and at three different post-inoculation time intervals were examined in the model plant Arabidopsis thaliana. The H2O2 and superoxide (O2-) production due to various inoculation methods and re-suspending solutions on the host was also studied. The flood inoculation method, which used sterile deionized water (SDW) to re-suspend bacteria, elicited the slightest response in mock-inoculated plants. Under this method, Agrobacterium strains carrying the GUS reporter gene were used to test bacterial infectivity. Blue sectors were found in plants infected for 24 and 48 h. PR1 and NPR1 expression were significantly altered at various time intervals after inoculation. So, for experiments involving Arabidopsis-Agrobacterium interaction with minimal background influences, such as gene expression and epigenetic analyses, the flood inoculation method using SDW as the resuspension liquid is proposed.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01381-x.

Agrobacterium-mediated in planta transformation of cut coleoptile: a new, simplified, and tissue culture-independent method to deliver the CRISPR/Cas9 system in rice

BACKGROUND

Agrobacterium-mediated transformation and particle bombardment are the two common approaches for genome editing in plant species using CRISPR/Cas9 system. Both methods require careful manipulations of undifferentiated cells and tissue culture to regenerate the potentially edited plants. However, tissue culture techniques are laborious and time-consuming.

METHODS AND RESULTS

In this study, we have developed a simplified, tissue culture-independent protocol to deliver the CRISPR/Cas9 system through in planta transformation in Malaysian rice (Oryza sativa L. subsp. indica cv. MR 219). Sprouting seeds with cut coleoptile were used as the target for the infiltration by Agrobacterium tumefaciens and we achieved 9% transformation efficiency. In brief, the dehusked seeds were surface-sterilised and imbibed, and the coleoptile was cut to expose the apical meristem. Subsequently, the cut coleoptile was inoculated with A. tumefaciens strain EHA105 harbouring CRISPR/Cas9 expression vector. The co-cultivation was conducted for five to six days in a dark room (25 ± 2 °C) followed by rooting, acclimatisation, and growing phases. Two-month-old plant leaves were then subjected to a hygromycin selection, and hygromycin-resistant plants were identified as putative transformants. Further validation through the polymerase chain reaction verified the integration of the Cas9 gene in four putative T0 lines. During the fruiting stage, it was confirmed that the Cas9 gene was still present in three randomly selected tillers from two 4-month-old transformed plants.

CONCLUSION

This protocol provides a rapid method for editing the rice genome, bypassing the need for tissue culture. This article is the first to report the delivery of the CRISPR/Cas9 system for in planta transformation in rice.

An efficient method for protoplast-mediated production of transformed castor bean (Ricinus communis) lines

OBJECTIVE

The purpose of this study was to develop a method for the isolation, culture, and PEG-mediated protoplast transfection from leaves of in vitro-grown plants of Ricinus communis.

RESULTS

Factors such as the enzymatic composition and the incubation time were evaluated. The enzymatic solution, containing 1.6% Cellulase-R10 and 0.8% Macerozyme-R10, with 16 h of incubation, was the best condition to achieve a high protoplast yield (481.16 × 10⁴ protoplasts/g FW) with a high percentage of viability (95%). The combination and concentration of enzymes have been shown to affect the protoplast isolation efficiency significantly. Furthermore, we found that a higher number of protoplasts (8.5 × 10⁵ protoplast/g FW) was obtained at a longer incubation time, but their viability decreased. We obtained a simple and efficient protocol to isolate protoplast from Ricinus communis leaves and culture. A PEG-mediated protoplast transfection protocol was also established to introduce plasmid DNA into Ricinus communis genotypes cultivated in Colombia. Thus, strengthening advances in the genetic improvement processes for this crop are presented.

New methods for sorghum transformation in temperate climates

Sorghum (Sorghum bicolor) is an emerging cereal crop in temperate climates due to its high drought tolerance and other valuable traits. Genetic transformation is an important tool for the improvement of cereals. However, sorghum is recalcitrant to genetic transformation which is almost only successful in warmer climates. Here, we test the application of two new techniques for sorghum transformation in temperate climates, namely transient transformation by Agrobacterium tumefaciens-mediated agroinfiltration and stable transformation using gold particle bombardment and leaf whorls as explants. We optimized the transient transformation method, including post-infiltration incubation of plants in the dark and using Agrobacterium grown on plates with a high cell density (OD600 = 2.0). Expression of the green fluorescence protein (GFP)-tagged endogenous sorghum gene SbDHR2 was achieved with low transformation efficiency, and our results point out a potential weakness in using this approach for localization studies. Furthermore, we succeeded in the production of callus and somatic embryos from leaf whorls, although no genetic transformation was accomplished with this method. Both methods show potential, even if they seem to be influenced by climatic conditions and therefore need further optimization to be applied routinely in temperate climates.

SbPHO2, a conserved Pi starvation signalling gene, is involved in the regulation of the uptake of multiple nutrients in sorghum

Sorghum is one of the five most productive crops worldwide, but its yield is seriously limited by phosphate (Pi) availability. Although inorganic Pi signalling is well studied in Arabidopsis and rice, it remains largely unknown in sorghum. The sorghum sbpho2 mutant was identified, showing leaf necrosis and short roots. Map-based cloning identified SbPHO2 as Sobic.009G228100, an E2 conjugase gene that is a putative orthologue of the PHO2 genes in rice and Arabidopsis, which play important roles in Pi signalling. Pi starvation experiments and transformation of SbPHO2 into the rice ospho2 mutant further revealed that SbPHO2 is likely involved in Pi accumulation and root architecture alteration in sorghum. qRTPCR results showed that SbPHO2 was expressed in almost the entire plant, especially in the leaves. Furthermore, some typical Pi starvation-induced genes were induced in sbpho2 even under Pi-sufficient conditions, including Pi transporters, SPXs, phosphatases and lipid composition alteration-related genes. In addition to P accumulation in the shoots of sbpho2, concentrations of N, K, and other metal elements were also altered significantly in the sbpho2 plants. Nitrate uptake was also suppressed in the sbpho2 mutant. Consistent with this finding, the expression of several nitrate-, potassium- and other metal element-related genes was also altered in sbpho2. Furthermore, the results indicated that N-dependent control of the P starvation response is regulated via SbPHO2 in sorghum. Our results suggest that SbPHO2 participates in the regulation of the absorption of multiple nutrients, although PHO2 is a crucial and conserved component of Pi starvation signalling.

Progress and challenges in sorghum biotechnology, a multipurpose feedstock for the bioeconomy

Sorghum [Sorghum bicolor (L.) Moench] is the fifth most important cereal crop globally by harvested area and production. Its drought and heat tolerance allow high yields with minimal input. It is a promising biomass crop for the production of biofuels and bioproducts. In addition, as an annual diploid with a relatively small genome compared with other C4 grasses, and excellent germplasm diversity, sorghum is an excellent research species for other C4 crops such as maize. As a result, an increasing number of researchers are looking to test the transferability of findings from other organisms such as Arabidopsis thaliana and Brachypodium distachyon to sorghum, as well as to engineer new biomass sorghum varieties. Here, we provide an overview of sorghum as a multipurpose feedstock crop which can support the growing bioeconomy, and as a monocot research model system. We review what makes sorghum such a successful crop and identify some key traits for future improvement. We assess recent progress in sorghum transformation and highlight how transformation limitations still restrict its widespread adoption. Finally, we summarize available sorghum genetic, genomic, and bioinformatics resources. This review is intended for researchers new to sorghum research, as well as those wishing to include non-food and forage applications in their research.

Development and Adoption of Genetically Engineered Plants for Virus Resistance: Advances, Opportunities and Challenges

Plant viruses cause yield losses to crops of agronomic and economic significance and are a challenge to the achievement of global food security. Although conventional plant breeding has played an important role in managing plant viral diseases, it will unlikely meet the challenges posed by the frequent emergence of novel and more virulent viral species or viral strains. Hence there is an urgent need to seek alternative strategies of virus control that can be more readily deployed to contain viral diseases. The discovery in the late 1980s that viral genes can be introduced into plants to engineer resistance to the cognate virus provided a new avenue for virus disease control. Subsequent advances in genomics and biotechnology have led to the refinement and expansion of genetic engineering (GE) strategies in crop improvement. Importantly, many of the drawbacks of conventional breeding, such as long lead times, inability or difficulty to cross fertilize, loss of desirable plant traits, are overcome by GE. Unfortunately, public skepticism towards genetically modified (GM) crops and other factors have dampened the early promise of GE efforts. These concerns are principally about the possible negative effects of transgenes to humans and animals, as well as to the environment. However, with regards to engineering for virus resistance, these risks are overstated given that most virus resistance engineering strategies involve transfer of viral genes or genomic segments to plants. These viral genomes are found in infected plant cells and have not been associated with any adverse effects in humans or animals. Thus, integrating antiviral genes of virus origin into plant genomes is hardly unnatural as suggested by GM crop skeptics. Moreover, advances in deep sequencing have resulted in the sequencing of large numbers of plant genomes and the revelation of widespread endogenization of viral genomes into plant genomes. This has raised the possibility that viral genome endogenization is part of an antiviral defense mechanism deployed by the plant during its evolutionary past. Thus, GM crops engineered for viral resistance would likely be acceptable to the public if regulatory policies were product-based (the North America regulatory model), as opposed to process-based. This review discusses some of the benefits to be gained from adopting GE for virus resistance, as well as the challenges that must be overcome to leverage this technology. Furthermore, regulatory policies impacting virus-resistant GM crops and some success cases of virus-resistant GM crops approved so far for cultivation are discussed.

Agroinfiltration Mediated Scalable Transient Gene Expression in Genome Edited Crop Plants

Agrobacterium-mediated transformation is one of the most commonly used genetic transformation method that involves transfer of foreign genes into target plants. Agroinfiltration, an Agrobacterium-based transient approach and the breakthrough discovery of CRISPR/Cas9 holds trending stature to perform targeted and efficient genome editing (GE). The predominant feature of agroinfiltration is the abolishment of Transfer-DNA (T-DNA) integration event to ensure fewer biosafety and regulatory issues besides showcasing the capability to perform transcription and translation efficiently, hence providing a large picture through pilot-scale experiment via transient approach. The direct delivery of recombinant agrobacteria through this approach carrying CRISPR/Cas cassette to knockout the expression of the target gene in the intercellular tissue spaces by physical or vacuum infiltration can simplify the targeted site modification. This review aims to provide information on Agrobacterium-mediated transformation and implementation of agroinfiltration with GE to widen the horizon of targeted genome editing before a stable genome editing approach. This will ease the screening of numerous functions of genes in different plant species with wider applicability in future.

Leaf infiltration in plant science: old method, new possibilities

The penetration of substances from the surface to deep inside plant tissues is called infiltration. Although various plant tissues may be effectively saturated with externally applied fluid, most described infiltration strategies have been developed for leaves. The infiltration process can be spontaneous (under normal atmospheric pressure) or forced by a pressure difference generated between the lamina surface and the inside of the leaf. Spontaneous infiltration of leaf laminae is possible with the use of liquids with sufficiently low surface tension. Forced infiltration is most commonly performed using needle-less syringes or vacuum pumps.Leaf infiltration is widely used in plant sciences for both research and application purposes, usually as a starting technique to obtain plant material for advanced experimental procedures. Leaf infiltration followed by gentle centrifugation allows to obtain the apoplastic fluid for further analyses including various omics. In studies of plant-microorganism interactions, infiltration is used for the controlled introduction of bacterial suspensions into leaf tissues or for the isolation of microorganisms inhabiting apoplastic spaces of leaves. The methods based on infiltration of target tissues allow the penetration of dyes, fixatives and other substances improving the quality of microscopic imaging. Infiltration has found a special application in plant biotechnology as a method of transient transformation with the use of Agrobacterium suspension (agroinfiltration) enabling genetic modifications of mature plant leaves, including the local induction of mutations using genome editing tools. In plant nanobiotechnology, the leaves of the target plants can be infiltrated with suitably prepared nanoparticles, which can act as light sensors or increase the plant resistance to environmental stress. In addition the infiltration has been also intensively studied due to the undesirable effects of this phenomenon in some food technology sectors, such as accidental contamination of leafy greens with pathogenic bacteria during the vacuum cooling process.This review, inspired by the growing interest of the scientists from various fields of plant science in the phenomenon of infiltration, provides the description of different infiltration methods and summarizes the recent applications of this technique in plant physiology, phytopathology and plant (nano-)biotechnology.

Advantage of Nanotechnology-Based Genome Editing System and Its Application in Crop Improvement

Agriculture is an important source of human food. However, current agricultural practices need modernizing and strengthening to fulfill the increasing food requirements of the growing worldwide population. Genome editing (GE) technology has been used to produce plants with improved yields and nutritional value as well as with higher resilience to herbicides, insects, and diseases. Several GE tools have been developed recently, including clustered regularly interspaced short palindromic repeats (CRISPR) with nucleases, a customizable and successful method. The main steps of the GE process involve introducing transgenes or CRISPR into plants via specific gene delivery systems. However, GE tools have certain limitations, including time-consuming and complicated protocols, potential tissue damage, DNA incorporation in the host genome, and low transformation efficiency. To overcome these issues, nanotechnology has emerged as a groundbreaking and modern technique. Nanoparticle-mediated gene delivery is superior to conventional biomolecular approaches because it enhances the transformation efficiency for both temporal (transient) and permanent (stable) genetic modifications in various plant species. However, with the discoveries of various advanced technologies, certain challenges in developing a short-term breeding strategy in plants remain. Thus, in this review, nanobased delivery systems and plant genetic engineering challenges are discussed in detail. Moreover, we have suggested an effective method to hasten crop improvement programs by combining current technologies, such as speed breeding and CRISPR/Cas, with nanotechnology. The overall aim of this review is to provide a detailed overview of nanotechnology-based CRISPR techniques for plant transformation and suggest applications for possible crop enhancement.

What is the Molecular Basis of Nonhost Resistance?

This article is part of the Top 10 Unanswered Questions in MPMI invited review series.Nonhost resistance is typically considered the ability of a plant species to repel all attempts of a pathogen species to colonize it and reproduce on it. Based on this common definition, nonhost resistance is presumed to be very durable and, thus, of great interest for its potential use in agriculture. Despite considerable research efforts, the molecular basis of this type of plant immunity remains nebulous. We here stress the fact that "nonhost resistance" is a phenomenological rather than a mechanistic concept that comprises more facets than typically considered. We further argue that nonhost resistance essentially relies on the very same genes and pathways as other types of plant immunity, of which some may act as bottlenecks for particular pathogens on a given plant species or under certain conditions. Thus, in our view, the frequently used term "nonhost genes" is misleading and should be avoided. Depending on the plant-pathogen combination, nonhost resistance may involve the recognition of pathogen effectors by host immune sensor proteins, which might give rise to host shifts or host range expansions due to evolutionary-conditioned gains and losses in respective armories. Thus, the extent of nonhost resistance also defines pathogen host ranges. In some instances, immune-related genes can be transferred across plant species to boost defense, resulting in augmented disease resistance. We discuss future routes for deepening our understanding of nonhost resistance and argue that the confusing term "nonhost resistance" should be used more cautiously in the light of a holistic view of plant immunity.

A Rapid and Highly Efficient Method for Transient Gene Expression in Rice Plants

Rice is the model plant system for monocots and the sequencing of its genome has led to the identification of a vast array of genes for characterization. The tedious and time-consuming effort of raising rice transgenics has significantly delayed the pace of rice research. The lack of highly efficient transient assay protocol for rice has only added to the woes which could have otherwise helped in rapid deciphering of the functions of genes. Here, we describe a technique for efficient transient gene expression in rice seedlings. It makes use of co-cultivation of 6-day-old rice seedlings with Agrobacterium in the presence of a medium containing Silwet^® L-77, acetosyringone and glucose. Seedlings can be visualized 9 days after co-cultivation for transient expression. The use of young seedlings helps in significantly reducing the duration of the experiment and facilitates the visualization of rice cells under the microscope as young leaves are thinner than mature rice leaves. Further, growth of seedlings at low temperature, and the use of surfactant along with wounding and vacuum infiltration steps significantly increases the efficiency of this protocol and helps in bypassing the natural barriers in rice leaves, which hinders Agrobacterium-based transformation in this plant. This technique, therefore, provides a shorter, efficient and cost-effective way to study transient gene function in intact rice seedling without the need for a specialized device like particle gun.