An efficient genetic transformation system mediated by Rhizobium rhizogenes in fruit trees based on the transgenic hairy root to shoot conversion

Plant genetic transformation: achievements, current status and future prospects

Regeneration represents a fundamental biological process wherein an organism's tissues or organs repair and replace themselves following damage or environmental stress. In plant systems, injured tree branches can regenerate adventitious buds and develop new crowns through propagation techniques like cuttings and canopy pruning, while transgenic plants emerge via tissue culture in genetic engineering processes intimately connected to plant regeneration mechanisms. The advancement of plant regeneration technology is critical for addressing complex and dynamic climate challenges, ultimately ensuring global agricultural sustainability. This review comprehensively synthesizes the latest genetic transformation technologies, including transformation systems across woody, herbaceous and algal species, organellar genetic modifications, crucial regeneration factors facilitating Agrobacterium-mediated transformations, the intricate hormonal networks regulating plant regeneration, comparative analyses of transient transformation approaches and marker gene dynamics throughout transformation processes. Ultimately, the review offers novel perspectives on current transformation bottlenecks and proposes future research trajectories.

Non-tissue culture genetic modifications for plant improvement

Gene delivery systems are essential for investigating gene regulation mechanisms and enhancing the genetic improvement of functional traits in plants. However, fewer than 0.1% of higher plant species on Earth can be genetically modified. Even for these species, the genetic modification process relies on complex tissue culture methods, which are time-consuming, costly, and often require specialized technical skills. Additionally, the efficiency of genetic modification is extremely low in some species. Notably, over the past five years, significant progress has been made in establishing non-tissue culture genetic modification systems. This advancement effectively resolved a series of previously mentioned challenges and innovated in biotechnology for the improvement of many valuable plant species. This review summarizes the research advancements in non-tissue culture genetic modification technologies and presents examples of successful species modified using various methods, including fast-treated Agrobacterium co-culture (Fast-TrACC), cut-dip-budding (CDB), particle bombardment, and nano-mediated delivery systems. Additionally, we propose a working guideline to classify, analyze, evaluate, and select non-tissue culture genetic modification systems for plant species of interest. Our review also discusses the potential for enhancing plant regeneration capacity, improving genetic modification efficiency, and the future application prospects for plant improvement.

Agrobacterium rhizogenes-Mediated Hairy Root Genetic Transformation Using Agrobacterium Gel Inoculation and RUBY Reporter Enables Efficient Gene Function Analysis in Sacha Inchi (Plukenetia volubilis)

Plukenetia volubilis L., a woody oilseed plant rich in α-linolenic acid, represents a promising source of polyunsaturated fatty acids. However, the lack of an efficient genetic transformation system has significantly hindered gene function research and molecular breeding in P. volubilis. In this study, we developed a highly efficient Agrobacterium rhizogenes-mediated hairy root transformation system for P. volubilis via the use of Agrobacterium gel in combination with the visually detectable RUBY reporter for gene function analysis in roots. The results indicate that the optimal transformation method involves infecting P. volubilis seedlings with Agrobacterium gel containing acetosyringone and inducing hairy root formation in perlite. This approach resulted in more than 18.97% of the seedlings producing positive hairy roots overexpressing the RUBY gene. Using this genetic transformation system, we successfully overexpressed the antimicrobial peptide-encoding gene CEMA in hairy roots, which enhanced the resistance of P. volubilis to Fusarium oxysporum. Furthermore, by combining this transformation system with the CRISPR-Cas9 tool, we validated the regulatory role of PvoSHR in the development of root epidermal cells in P. volubilis. Unexpectedly, a 123-bp DNA fragment from the T-DNA region of the A. rhizogenes Ri plasmid was found to be knocked in to the P. volubilis genome, replacing a 110-bp fragment of PvoSHR at CRISPR-Cas9 induced double-strand DNA breaks. Conclusively, this system provides a powerful tool for gene function research in P. volubilis and provides novel insights into the development of transformation and gene editing systems for other woody plants.

Engineering Agrobacterium for improved plant transformation

Outside of a few model systems and selected taxa, the insertion of transgenes and regeneration of modified plants are difficult or impossible. This is a major bottleneck both for biotechnology and scientific research with many important species. Agrobacterium-mediated transformation (AMT) remains the most common approach to insert DNA into plant cells, and is also an important means to stimulate regeneration of organized tissues. However, the strains and transformation methods available today have been largely unchanged since the 1990s. New sources of Agrobacterium germplasm and associated genomic information are available for hundreds of wild strains in public repositories, providing new opportunities for research. Many of these strains contain novel gene variants or arrangements of genes in their T-DNA, potentially providing new tools for strain enhancement. There are also several new techniques for Agrobacterium modification, including base editing, CRISPR-associated transposases, and tailored recombineering, that make the process of domesticating wild strains more precise and efficient. We review the novel germplasm, genomic resources, and new methods available, which together should lead to a renaissance in Agrobacterium research and the generation of many new domesticated strains capable of promoting plant transformation and/or regeneration in diverse plant species.

Efficient genetic transformation and gene editing of Chinese cabbage using Agrobacterium rhizogenes

A method using Agrobacterium rhizogenes-mediated callus production and plant regeneration enables efficient genetic transformation and gene editing in Chinese cabbage.

Novel methods for genetic transformation of watermelon (Citrullus lanatus) without tissue culture via Agrobacterium rhizogenes

Factors that restrict the development of genetic transformation include the long cycle, extensive requirements for experimental conditions, and low survival and transformation rates. Especially for plants that obtain offspring through sexual reproduction. This study established the genetic transformation methods that are particularly suitable for it. First, a rapid in vivo transformation system of adventitious roots was developed using A. rhizogenes to infect normally growing watermelon stem nodes without requiring plant treatment, enabling the stable genetic transformation of adventitious roots. And the genetic transformation efficiency of adventitious roots reaches 100%. Second, the traditional genetic transformation system was improved using A. rhizogenes which induces rooting of explants and promotes the regeneration of adventitious buds. The genetic transformation efficiency of adventitious roots reaches 100% and adventitious buds reaches 40%, which is much higher than using A. tumefaciens. Third, in order to achieve shorten the regeneration cycle and high transformation efficiency, the genetic transformation method without tissue culture was established using A. rhizogenes to infect the seed. This genetic transformation efficiency of transgenic plants reaches 80%, and it is not limited by genotype. This study significantly improves the plant regeneration and low genetic transformation efficiency while promoting the rapid development of watermelon molecular breeding.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-025-01544-6.

New strategies to advance plant transformation

Plants are an important source of food, energy, and bioproducts. Advances in genetics, genomics-assisted breeding, and biotechnology have facilitated the combining of desirable traits into elite cultivars. To ensure sustainable crop production in the face of climate challenges and population growth, it is essential to develop and implement techniques that increase crop yield and resilience in environments facing water scarcity, nutrient deficiencies, and other abiotic and biotic stressors. Plant transformation and genome editing are critical tools in the development of new cultivars. Here, we discuss recent advances in plant transformation technologies aimed at enhancing efficiency, throughput, and the number of transformable genotypes. These advancements include the use of morphogenic regulators, virus-mediated genetic modifications, and in planta transformation with Rhizobium rhizogenes.

New Integrative Vectors Increase Agrobacterium rhizogenes Transformation and Help Characterise Roles for Soybean GmTML Gene Family Members

Hairy-root transformation is widely used to generate transgenic plant roots for genetic functional characterisation studies. However, transformation efficiency can be limited, largely due to the use of binary vectors. Here, we report on the development of novel integrative vectors that significantly increase the transformation efficiency of hairy roots. This includes pHGUS7, for promoter::reporter visualisation studies, and pHOG13, for genetic insertion and overexpression studies. These vectors have been designed to simplify cloning workflows, enhance the selection of positively transformed Agrobacterium colonies, and increase the transformation efficiency and ease of selection of genetically modified hairy roots. To demonstrate the efficacy of the new vectors, Too Much Love (TML) encoding genes acting in the Autoregulation Of Nodulation (AON) pathway of soybeans were investigated. Both constructs provided significantly higher transformation rates than the binary vector control, often resulting in > 70% of the roots being transformed. This was achieved using either whole-plant seedlings or cotyledonary nodes in tissue culture. Overexpression of each individual TML encoding gene (GmTML1a, GmTML1b and GmTML2) using pHOG13 resulted in a significant reduction in nodule number, demonstrating the role of all three in inhibiting nodule organogenesis. Moreover, reporter-fusions with the promoter of each TML encoding gene using pHGUS7 revealed that each exhibits a unique pattern of expression in nodules, with GmTML1b displaying considerably stronger expression than GmTML1a or GmTML2. Taken together, these results demonstrate the utility and efficiency of the new pHOG13 and pHGUS7 integrative vectors in hairy-root transformation, and improve our understanding of the critical TML-encoding genes in soybean nodulation control.

Development of a robust and efficient virus-induced gene silencing system for reverse genetics in recalcitrant Camellia drupifera capsules

BACKGROUND

Virus-induced gene silencing (VIGS) is a rapid and powerful method for gene functional analysis in plants that pose challenges in stable transformation. Numerous VIGS systems based on Agrobacterium infiltration has been widely developed for tender tissues of various plant species, yet none is available for recalcitrant perennial woody plants with firmly lignified capsules, such as tea oil camellia. Therefore, there is an urgent need for an efficient, robust, and cost-effective VIGS system for recalcitrant tissues.

RESULTS

Herein, we initiated the Tobacco rattle virus (TRV)-elicited VIGS in Camellia drupifera capsules with an orthogonal analysis including three factors: silencing target, virus inoculation approach, and capsule developmental stage. To facilitate observation and statistical analysis, two genes predominantly involved in pericarp pigmentation were selected for silencing efficiency: CdCRY1 (coding for a key photoreceptor affecting light-responsive perceivable anthocyanin accumulation in exocarps) and CdLAC15 (coding for an oxidase catalyzing the oxidative polymerization of proanthocyanidins in mesocarps, resulting in unperceivable red-hued mesocarps). The infiltration efficiency achieved for each gene was ~ 93.94% by pericarp cutting immersion. The optimal VIGS effect for each gene was observed at early (~ 69.80% for CdCRY1) and mid stages (~ 90.91% for CdLAC15) of capsule development.

CONCLUSIONS

Using our optimized VIGS system, CdCRY1 and CdLAC15 expression was successfully knocked down in Camellia drupifera pericarps, leading to fading phenotypes in exocarps and mesocarps, respectively. The established VIGS system may facilitate functional genomic studies in tea oil camellia and other recalcitrant fruits of woody plants.

Unlocking regeneration potential: harnessing morphogenic regulators and small peptides for enhanced plant engineering

Plant genetic transformation is essential for understanding gene functions and developing improved crop varieties. Traditional methods, often genotype-dependent, are limited by plants' recalcitrance to gene delivery and low regeneration capacity. To overcome these limitations, new approaches have emerged that greatly improve efficiency and genotype flexibility. This review summarizes key strategies recently developed for plant transformation, focusing on groundbreaking technologies enhancing explant- and genotype flexibility. It covers the use of morphogenic regulators (MRs), stem cell-based methods, and in planta transformation methods. MRs, such as maize Babyboom (BBM) with Wuschel2 (WUS2), and GROWTH-REGULATING FACTORs (GRFs) with their cofactors GRF-interacting factors (GIFs), offer great potential for transforming many monocot species, including major cereal crops. Optimizing BBM/WUS2 expression cassettes has further enabled successful transformation and gene editing using seedling leaves as starting material. This technology lowers the barriers for academic laboratories to adopt monocot transformation systems. For dicot plants, tissue culture-free or in planta transformation methods, with or without the use of MRs, are emerging as more genotype-flexible alternatives to traditional tissue culture-based transformation systems. Additionally, the discovery of the local wound signal peptide Regeneration Factor 1 (REF1) has been shown to enhance transformation efficiency by activating wound-induced regeneration pathways in both monocot and dicot plants. Future research may combine these advances to develop truly genotype-independent transformation methods.

Establishment of an Agrobacterium-mediated transformation system for the genetic engineering of Linum grandiflorum Desf

Genetic transformation is a powerful tool in plant biotechnology. However, its application is limited to species that are well-studied and easy to transform. There is a critical need to establish transformation protocols for non-model species. A stable transformation method using Agrobacterium rhizogenes for hairy root transformation and regeneration of transgenic Linum grandiflorum was established. This protocol shows the successful co-transformation of different T-DNA fragments from both the native Ri plasmid and the binary vector with the reporter gene. Hairy roots were produced after inoculation with Agrobacterium rhizogenes from which later shoots were formed from the callus, and subsequently, whole plants were regenerated. This protocol significantly facilitates genomic studies in Linum grandiflorum, particularly in investigating genes at the S-locus supergene, which are crucial for understanding self-incompatibility. Moreover, the established transformation method enables the production of hairy root lines, which can be utilized for the biosynthesis of medically useful and commercially valuable plant metabolites.

Overview on Current Selectable Marker Systems and Novel Marker Free Approaches in Fruit Tree Genetic Engineering

Selectable marker genes are useful for recognizing which cells have integrated specific sequences in their genome after genetic transformation processes. They are especially important for fruit trees genetic transformation to individuate putatively genetically modified events, because most of the protocols used to genetic engineer these species are often unsuccessful or with low efficiency. Traditional selectable marker genes, mainly of bacterial origin, confer antibiotics/herbicides-resistance or metabolic advantages to transformed cells. Genes that allow the visual recognition of engineered tissues without using any selective agent, such as morphogenic regulators and reporter genes, are also used as selection tools to in vitro identify genetically modified regenerated lines. As final step, genetic engineered plants should be tested in field conditions, where selectable marker genes are no longer necessary, and strongly unpopular especially for the commercial development of the new products. Thus, different approaches, mainly based on the use of site-specific recombinases and/or editing nucleases, are being now used to recover marker-free fruit crops. This review describes and comments the most used and suitable selection tools of interest, particularly for fruit tree genetic engineering. Lastly, a spotlight highlights the biosafety aspects related to the use of selectable marker genes exploited for fruit species genetic engineering.

Exploring an economic and highly efficient genetic transformation and genome-editing system for radish through developmental regulators and visible reporter

Radish (Raphanus sativus L.) is one of the most important root vegetable crops worldwide. However, gene function exploration and germplasm innovation still face tremendous challenges due to its extremely low transformation efficiency. Here, an economic and highly efficient genetic transformation method for radish was explored by Agrobacterium rhizogenes-mediated transformation with the help of combining special developmental regulator (DR) genes and the visual identification reporter. Firstly, the RUBY gene, a betalain biosynthesis system, could result in a visual red-violet color used as a convenient and effective reporter for monitoring transgenic hairy roots screening of radish. However, the hairy roots-to-shoots conversion system of radish still stands as a barrier to the obtainment of whole transgenic plants, although different hormone combinations and various culture conditions were tried. Following, two DR genes including Wuschel2 (Wus2) and isopentenyl transferase (ipt), as well as their combination Wus2-ipt were introduced for the shoot regeneration capacity improvement. The results showed that the transgenic shoots could be directly generated without externally supplying any hormones in the presence of a Wus2-ipt combination. Then, Wus2-ipt along with the RUBY reporter was employed to establish an efficient genetic transformation system of radish. Moreover, this system was applied in generating gene-edited radish plants and the phytoene desaturase (RsPDS) gene was effectively knockout through albino phenotype observation and sequencing analysis. These findings have the potential to be widely applied in genetic transformation and genome-editing genetic improvement of other vegetable species.

Advancements in delivery strategies and non-tissue culture regeneration systems for plant genetic transformation

Plant genetic transformation is a pivotal and essential step in modifying important agronomic traits using biotechnological tools, which primarily depend on the efficacy of transgene delivery and the plant regeneration system. Over the years, advancements in the development of delivery methods and regeneration systems have contributed to plant engineering and molecular breeding. Recent studies have demonstrated that the efficiency of plant transformation can be improved by simultaneously delivering meristem-developmental regulators, utilizing virus-mediated gene editing, and executing non-sterile in planta manipulations. Efficient genetic delivery and non-tissue culture regeneration systems are gradually being developed. This review summarizes diverse delivery strategies and in planta regeneration techniques aimed at improving the efficiency of plant genetic transformation. We also emphasize the integration and utilization of these emerging transgenic approaches for expediting future crop engineering.

Modern Technologies Provide New Opportunities for Somatic Hybridization in the Breeding of Woody Plants

Advances in cell fusion technology have propelled breeding into the realm of somatic hybridization, enabling the transfer of genetic material independent of sexual reproduction. This has facilitated genome recombination both within and between species. Despite its use in plant breeding for over fifty years, somatic hybridization has been limited by cumbersome procedures, such as protoplast isolation, hybridized-cell selection and cultivation, and regeneration, particularly in woody perennial species that are difficult to regenerate. This review summarizes the development of somatic hybridization, explores the challenges and solutions associated with cell fusion technology in woody perennials, and outlines the process of protoplast regeneration. Recent advancements in genome editing and plant cell regeneration present new opportunities for applying somatic hybridization in breeding. We offer a perspective on integrating these emerging technologies to enhance somatic hybridization in woody perennial plants.

A comprehensive review of in planta stable transformation strategies

Plant transformation remains a major bottleneck to the improvement of plant science, both on fundamental and practical levels. The recalcitrant nature of most commercial and minor crops to genetic transformation slows scientific progress for a large range of crops that are essential for food security on a global scale. Over the years, novel stable transformation strategies loosely grouped under the term "in planta" have been proposed and validated in a large number of model (e.g. Arabidopsis and rice), major (e.g. wheat and soybean) and minor (e.g. chickpea and lablab bean) species. The in planta approach is revolutionary as it is considered genotype-independent, technically simple (i.e. devoid of or with minimal tissue culture steps), affordable, and easy to implement in a broad range of experimental settings. In this article, we reviewed and categorized over 300 research articles, patents, theses, and videos demonstrating the applicability of different in planta transformation strategies in 105 different genera across 139 plant species. To support this review process, we propose a classification system for the in planta techniques based on five categories and a new nomenclature for more than 30 different in planta techniques. In complement to this, we clarified some grey areas regarding the in planta conceptual framework and provided insights regarding the past, current, and future scientific impacts of these techniques. To support the diffusion of this concept across the community, this review article will serve as an introductory point for an online compendium about in planta transformation strategies that will be available to all scientists. By expanding our knowledge about in planta transformation, we can find innovative approaches to unlock the full potential of plants, support the growth of scientific knowledge, and stimulate an equitable development of plant research in all countries and institutions.

Arbuscular Mycorrhizal Fungi Improve Lycium barbarum Potassium Uptake by Activating the Expression of LbHAK

Arbuscular mycorrhizal (AM) fungi can establish a mutualistic relationship with the roots of most terrestrial plants to increase plant nutrient uptake. The effects of potassium uptake and transport by AM symbiosis are much less reported compared to other nutrients. In this research, a heterologous yeast system was used to verify that the LbHAK has capacity for potassium uptake. The split-roots system implemented using seedlings of Lycium barbarum confirmed that R. irregularis locally induced LbHAK expression, which means that LbHAK is only expressed in mycorrhizal roots. Furthermore, the impacts of overexpression of LbHAK on the growth, nutrients and water uptake, and transport of mycorrhizal tobacco (inoculation with Rhizophagus irregularis) at 0.2 mM and 2 mM K conditions were assessed. The mycorrhizal tobacco growth and potassium accumulation were significantly enhanced through LbHAK overexpression in tobacco. In addition, overexpression of LbHAK substantially enhanced phosphorus content, while stimulating the expression of NtPT4, Rir-AQP1, and Rir-AQP2 in mycorrhizal tobacco. Moreover, LbHAK overexpression greatly promoted AM colonization. LbHAK has a potential role in facilitating potassium absorption through the mycorrhizal pathway, and overexpression of LbHAK in tobacco may promote the transport of potassium, phosphorus, and water from AM fungi to tobacco. These data imply the important roles played by the LbHAK in AM-fungi-induced potassium uptake in L. barbarum and in improving plant nutrients and AM colonization.