Intragenesis and cisgenesis as alternatives to transgenic crop development

Modern Breeding Strategies and Tools for Durable Late Blight Resistance in Potato

Cultivated potato (Solanum tuberosum) is a major crop worldwide. It occupies the second place after cereals (corn, rice, and wheat). This important crop is threatened by the Oomycete Phytophthora infestans, the agent of late blight disease. This pathogen was first encountered during the Irish famine during the 1840s and is a reemerging threat to potatoes. It is mainly controlled chemically by using fungicides, but due to health and environmental concerns, the best alternative is resistance. When there is no disease, no treatment is required. In this study, we present a summary of the ongoing efforts concerning resistance breeding of potato against this devastating pathogen, P. infestans. This work begins with the search for and selection of resistance genes, whether they are from within or from outside the species. The genetic methods developed to date for gene mining, such as effectoromics and GWAS, provide researchers with the ability to identify genes of interest more efficiently. Once identified, these genes are cloned using molecular markers (MAS or QRL) and can then be introduced into different cultivars using somatic hybridization or recombinant DNA technology. More innovative technologies have been developed lately, such as gene editing using the CRISPR system or gene silencing, by exploiting iRNA strategies that have emerged as promising tools for managing Phytophthora infestans, which can be employed. Also, gene pyramiding or gene stacking, which involves the accumulation of two or more R genes on the same individual plant, is an innovative method that has yielded many promising results. All these advances related to the development of molecular techniques for obtaining new potato cultivars resistant to P. infestans can contribute not only to reducing losses in agriculture but especially to ensuring food security and safety.

Regulation of gene-edited plants in Europe: from the valley of tears into the shining sun?

Some 20 years ago, the EU introduced complex regulatory rules for the growth of transgenic crops, which resulted in a de facto ban to grow these plants in fields within most European countries. With the rise of novel genome editing technologies, it has become possible to improve crops genetically in a directed way without the need for incorporation of foreign genes. Unfortunately, in 2018, the European Court of Justice ruled that such gene-edited plants are to be regulated like transgenic plants. Since then, European scientists and breeders have challenged this decision and requested a revision of this outdated law. Finally, after 5 years, the European Commission has now published a proposal on how, in the future, to regulate crops produced by new breeding technologies. The proposal tries to find a balance between the different interest groups in Europe. On one side, genetically modified plants, which cannot be discerned from their natural counterparts, will exclusively be used for food and feed and are-besides a registration step-not to be regulated at all. On the other side, plants expressing herbicide resistance are to be excluded from this regulation, a concession to the strong environmental associations and NGOs in Europe. Moreover, edited crops are to be excluded from organic farming to protect the business interests of the strong organic sector in Europe. Nevertheless, if this law passes European parliament and council, unchanged, it will present a big step forward toward establishing a more sustainable European agricultural system. Thus, it might soon be possible to develop and grow crops that are more adapted to global warming and whose cultivation will require lower amounts of pesticides. However, there is still a long way to go until the law is passed. Too often, the storm of arguments raised by the opponents, based on irrational fears of mutations and a naive understanding of nature, has fallen on fruitful ground in Europe.

Identification of a sugarcane bacilliform virus promoter that is activated by drought stress in plants

Sugarcane (Saccharum spp.) is an important sugar and biofuel crop in the world. It is frequently subjected to drought stress, thus causing considerable economic losses. Transgenic technology is an effective breeding approach to improve sugarcane tolerance to drought using drought-inducible promoter(s) to activate drought-resistance gene(s). In this study, six different promoters were cloned from sugarcane bacilliform virus (SCBV) genotypes exhibiting high genetic diversity. In β-glucuronidase (GUS) assays, expression of one of these promoters (PSCBV-YZ2060) is similar to the one driven by the CaMV 35S promoter and >90% higher compared to the other cloned promoters and Ubi1. Three SCBV promoters (PSCBV-YZ2060, PSCBV-TX, and PSCBV-CHN2) function as drought-induced promoters in transgenic Arabidopsis plants. In Arabidopsis, GUS activity driven by promoter PSCBV-YZ2060 is also upregulated by abscisic acid (ABA) and is 2.2-5.5-fold higher when compared to the same activity of two plant native promoters (PScRD29A from sugarcane and PAtRD29A from Arabidopsis). Mutation analysis revealed that a putative promoter region 1 (PPR1) and two ABA response elements (ABREs) are required in promoter PSCBV-YZ2060 to confer drought stress response and ABA induction. Yeast one-hybrid and electrophoretic mobility shift assays uncovered that transcription factors ScbZIP72 from sugarcane and AREB1 from Arabidopsis bind with two ABREs of promoter PSCBV-YZ2060. After ABA treatment or drought stress, the expression levels of endogenous ScbZIP72 and heterologous GUS are significantly increased in PSCBV-YZ2060:GUS transgenic sugarcane plants. Consequently, promoter PSCBV-YZ2060 is a possible alternative promoter for genetic engineering of drought-resistant transgenic crops such as sugarcane.

Advanced Biotechnological Interventions in Mitigating Drought Stress in Plants

This comprehensive article critically analyzes the advanced biotechnological strategies to mitigate plant drought stress. It encompasses an in-depth exploration of the latest developments in plant genomics, proteomics, and metabolomics, shedding light on the complex molecular mechanisms that plants employ to combat drought stress. The study also emphasizes the significant advancements in genetic engineering techniques, particularly CRISPR-Cas9 genome editing, which have revolutionized the creation of drought-resistant crop varieties. Furthermore, the article explores microbial biotechnology's pivotal role, such as plant growth-promoting rhizobacteria (PGPR) and mycorrhizae, in enhancing plant resilience against drought conditions. The integration of these cutting-edge biotechnological interventions with traditional breeding methods is presented as a holistic approach for fortifying crops against drought stress. This integration addresses immediate agricultural needs and contributes significantly to sustainable agriculture, ensuring food security in the face of escalating climate change challenges.

Application of new breeding techniques in fruit trees

Climate change and rapid adaption of invasive pathogens pose a constant pressure on the fruit industry to develop improved varieties. Aiming to accelerate the development of better-adapted cultivars, new breeding techniques have emerged as a promising alternative to meet the demand of a growing global population. Accelerated breeding, cisgenesis, and CRISPR/Cas genome editing hold significant potential for crop trait improvement and have proven to be useful in several plant species. This review focuses on the successful application of these technologies in fruit trees to confer pathogen resistance and tolerance to abiotic stress and improve quality traits. In addition, we review the optimization and diversification of CRISPR/Cas genome editing tools applied to fruit trees, such as multiplexing, CRISPR/Cas-mediated base editing and site-specific recombination systems. Advances in protoplast regeneration and delivery techniques, including the use of nanoparticles and viral-derived replicons, are described for the obtention of exogenous DNA-free fruit tree species. The regulatory landscape and broader social acceptability for cisgenesis and CRISPR/Cas genome editing are also discussed. Altogether, this review provides an overview of the versatility of applications for fruit crop improvement, as well as current challenges that deserve attention for further optimization and potential implementation of new breeding techniques.

A CRISPR/Cas9-based vector system enables the fast breeding of selection-marker-free canola with Rcr1-rendered clubroot resistance

Breeding for disease resistance in major crops is of crucial importance for global food security and sustainability. However, common biotechnologies such as traditional transgenesis or genome editing do not provide an ideal solution, whereas transgenic crops free of selection markers such as cisgenic/intragenic crops might be suitable. In this study, after cloning and functional verification of the Rcr1 gene for resistance to clubroot (Plasmodiophora brassicae), we confirmed that the genes Rcr1, Rcr2, Rcr4, and CRa from Brassica rapa crops and the resistance gene from B. napus oilseed rape cv. 'Mendel' on chromosome A03 were identical in their coding regions. We also determined that Rcr1 has a wide distribution in Brassica breeding materials and renders potent resistance against multiple representative clubroot strains in Canada. We then modified a CRISPR/Cas9-based cisgenic vector system and found that it enabled the fast breeding of selection-marker-free transgenic crops with add-on traits, with selection-marker-free canola (B. napus) germplasms with Rcr1-rendered stable resistance to clubroot disease being successfully developed within 2 years. In the B. napus background, the intragenic vector system was able to remove unwanted residue sequences from the final product with high editing efficiency, and off-target mutations were not detected. Our study demonstrates the potential of applying this breeding strategy to other crops that can be transformed by Agrobacterium. Following the streamlined working procedure, intragenic germplasms can be developed within two generations, which could significantly reduce the breeding time and labor compared to traditional introgression whilst still achieving comparable or even better breeding results.

Beyond skin-deep: targeting the plant surface for crop improvement

The above-ground plant surface is a well-adapted tissue layer that acts as an interface between the plant and its surrounding environment. As such, its primary role is to protect against desiccation and maintain the gaseous exchange required for photosynthesis. Further, this surface layer provides a barrier against pathogens and herbivory, while attracting pollinators and agents of seed dispersal. In the context of agriculture, the plant surface is strongly linked to post-harvest crop quality and yield. The epidermal layer contains several unique cell types adapted for these functions, while the non-lignified above-ground plant organs are covered by a hydrophobic cuticular membrane. This review aims to provide an overview of the latest understanding of the molecular mechanisms underlying crop cuticle and epidermal cell formation, with focus placed on genetic elements contributing towards quality, yield, drought tolerance, herbivory defence, pathogen resistance, pollinator attraction, and sterility, while highlighting the inter-relatedness of plant surface development and traits. Potential crop improvement strategies utilizing this knowledge are outlined in the context of the recent development of new breeding techniques.

From Transgenesis to Genome Editing in Crop Improvement: Applications, Marketing, and Legal Issues

The biotechnological approaches of transgenesis and the more recent eco-friendly new breeding techniques (NBTs), in particular, genome editing, offer useful strategies for genetic improvement of crops, and therefore, recently, they have been receiving increasingly more attention. The number of traits improved through transgenesis and genome editing technologies is growing, ranging from resistance to herbicides and insects to traits capable of coping with human population growth and climate change, such as nutritional quality or resistance to climatic stress and diseases. Research on both technologies has reached an advanced stage of development and, for many biotech crops, phenotypic evaluations in the open field are already underway. In addition, many approvals regarding main crops have been granted. Over time, there has been an increase in the areas cultivated with crops that have been improved through both approaches, but their use in various countries has been limited by legislative restrictions according to the different regulations applied which affect their cultivation, marketing, and use in human and animal nutrition. In the absence of specific legislation, there is an on-going public debate with favorable and unfavorable positions. This review offers an updated and in-depth discussion on these issues.

Reasons and riddance of Agrobacterium tumefaciens overgrowth in plant transformation

Agrobacterium tumefaciens-mediated plant transformation has become routine work across the world to study gene function and the production of genetically modified plants. However, several issues hamper the transformation process in a profound way, both directly and indirectly. One of the major concerns is the overgrowth of Agrobacterium, which occasionally appears after the co-cultivation phase of the explant. This phenomenon is reported in several species and seems to spoil the whole transformation process. There are multiple approaches being employed to counter this unwanted growth of bacteria in a few plant species. In reality, once the overgrowth appears, it becomes nearly impossible to cure it. Hence, for the prevention of this phenomenon, numerous factors are regulated. These factors are: explant nature, A. tumefaciens strain, T-DNA vector, co-cultivation (time and condition), acetosyringone, washing medium, antibiotics (type, concentration, combination, incubation period), etc. In this article, we discuss these factors based on available reports. It can be of immense help in formulating viable strategies to control A. tumefaciens overgrowth.

The Role of Italy in the Use of Advanced Plant Genomic Techniques on Fruit Trees: State of the Art and Future Perspectives

Climate change is deeply impacting the food chain production, lowering quality and yield. In this context, the international scientific community has dedicated many efforts to enhancing resilience and sustainability in agriculture. Italy is among the main European producers of several fruit trees; therefore, national research centers and universities undertook several initiatives to maintain the specificity of the 'Made in Italy' label. Despite their importance, fruit crops are suffering from difficulties associated with the conventional breeding approaches, especially in terms of financial commitment, land resources availability, and long generation times. The 'new genomic techniques' (NGTs), renamed in Italy as 'technologies for assisted evolution' (TEAs), reduce the time required to obtain genetically improved cultivars while precisely targeting specific DNA sequences. This review aims to illustrate the role of the Italian scientific community in the use of NGTs, with a specific focus on Citrus, grapevine, apple, pear, chestnut, strawberry, peach, and kiwifruit. For each crop, the key genes and traits on which the scientific community is working, as well as the technological improvements and advancements on the regeneration of local varieties, are presented. Lastly, a focus is placed on the legal aspects in the European and in Italian contexts.

Genetically engineered crops for sustainably enhanced food production systems

Genetic modification of crops has substantially focused on improving traits for desirable outcomes. It has resulted in the development of crops with enhanced yields, quality, and tolerance to biotic and abiotic stresses. With the advent of introducing favorable traits into crops, biotechnology has created a path for the involvement of genetically modified (GM) crops into sustainable food production systems. Although these plants heralded a new era of crop production, their widespread adoption faces diverse challenges due to concerns about the environment, human health, and moral issues. Mitigating these concerns with scientific investigations is vital. Hence, the purpose of the present review is to discuss the deployment of GM crops and their effects on sustainable food production systems. It provides a comprehensive overview of the cultivation of GM crops and the issues preventing their widespread adoption, with appropriate strategies to overcome them. This review also presents recent tools for genome editing, with a special focus on the CRISPR/Cas9 platform. An outline of the role of crops developed through CRSIPR/Cas9 in achieving sustainable development goals (SDGs) by 2030 is discussed in detail. Some perspectives on the approval of GM crops are also laid out for the new age of sustainability. The advancement in molecular tools through plant genome editing addresses many of the GM crop issues and facilitates their development without incorporating transgenic modifications. It will allow for a higher acceptance rate of GM crops in sustainable agriculture with rapid approval for commercialization. The current genetic modification of crops forecasts to increase productivity and prosperity in sustainable agricultural practices. The right use of GM crops has the potential to offer more benefit than harm, with its ability to alleviate food crises around the world.

Biotechnological Advances to Improve Abiotic Stress Tolerance in Crops

The major challenges that agriculture is facing in the twenty-first century are increasing droughts, water scarcity, flooding, poorer soils, and extreme temperatures due to climate change. However, most crops are not tolerant to extreme climatic environments. The aim in the near future, in a world with hunger and an increasing population, is to breed and/or engineer crops to tolerate abiotic stress with a higher yield. Some crop varieties display a certain degree of tolerance, which has been exploited by plant breeders to develop varieties that thrive under stress conditions. Moreover, a long list of genes involved in abiotic stress tolerance have been identified and characterized by molecular techniques and overexpressed individually in plant transformation experiments. Nevertheless, stress tolerance phenotypes are polygenetic traits, which current genomic tools are dissecting to exploit their use by accelerating genetic introgression using molecular markers or site-directed mutagenesis such as CRISPR-Cas9. In this review, we describe plant mechanisms to sense and tolerate adverse climate conditions and examine and discuss classic and new molecular tools to select and improve abiotic stress tolerance in major crops.

A paired-end whole-genome sequencing approach enables comprehensive characterization of transgene integration in rice

Efficient, accurate molecular characterization of genetically modified (GM) organisms is challenging, especially for those transgenic events transferred with genes/elements of recipient species. Herein, we decipher the comprehensive molecular characterization of one novel GM rice event G281 which was transferred with native promoters and an RNA interference (RNAi) expression cassette using paired-end whole genome sequencing (PE-WGS) and modified TranSeq approach. Our results show that transgenes integrate at rice chromosome 3 locus 16,439,674 included a 36 bp deletion of rice genomic DNA, and the whole integration contains two copies of the complete transfer DNA (T-DNA) in a head-to-head arrangement. No unintended insertion or backbone sequence of the transformed plasmid is observed at the whole genome level. Molecular characterization of the G281 event will assist risk assessment and application for a commercial license. In addition, we speculate that our approach could be further used for identifying the transgene integration of cisgenesis/intragenesis crops since both ends of T-DNA in G281 rice were from native gene or elements which is similar with that of cisgenesis/intrasgenesis. Our results from the in silico mimicking cisgenesis event confirm that the mimic rice Gt1 gene insertion and its flanking sequences are successfully identified, demonstrating the applicability of PE-WGS for molecular characterization of cisgenesis/intragenesis crops.

Coupling paired-end whole-genome sequencing with droplet digital PCR enabled precise identification of a transgene insertion in the genetically modified rice event G281 on chromosome 3 and the potential for exploring the native gene integration.

An Erwinia amylovora inducible promoter for improvement of apple fire blight resistance

pPPO16, the first Ea-inducible promoter cloned from apple, can be a useful component of intragenic strategies to create fire blight resistant apple genotypes. Intragenesis is an important alternative to transgenesis to produce modified plants containing native DNA only. A key point to develop such a strategy is the availability of regulatory sequences controlling the expression of the gene of interest. With the aim of finding apple gene promoters either inducible by the fire blight pathogen Erwinia amylovora (Ea) or moderately constitutive, we focused on polyphenoloxidase genes (PPO). These genes encode oxidative enzymes involved in many physiological processes and have been previously shown to be upregulated during the Ea infection process. We found ten PPO and two PPO-like sequences in the apple genome and characterized the promoters of MdPPO16 (pPPO16) and MdKFDV02 PPO-like (pKFDV02) for their potential as Ea-inducible and low-constitutive regulatory sequences, respectively. Expression levels of reporter genes fused to these promoters and transiently or stably expressed in apple were quantified after various treatments. Unlike pKFDV02 which displayed a variable activity, pPPO16 allowed a fast and strong expression of transgenes in apple following Ea infection in a Type 3 Secretion System dependent manner. Altogether our results does not confirmed pKFDV02 as a constitutive and weak promoter whereas pPPO16, the first Ea-inducible promoter cloned from apple, can be a useful component of intragenic strategies to create fire blight resistant apple genotypes.

Genetic Improvement of Wheat for Drought Tolerance: Progress, Challenges and Opportunities

Wheat production and productivity are challenged by recurrent droughts associated with climate change globally. Drought and heat stress resilient cultivars can alleviate yield loss in marginal production agro-ecologies. The ability of some crop genotypes to thrive and yield in drought conditions is attributable to the inherent genetic variation and environmental adaptation, presenting opportunities to develop drought-tolerant varieties. Understanding the underlying genetic, physiological, biochemical, and environmental mechanisms and their interactions is key critical opportunity for drought tolerance improvement. Therefore, the objective of this review is to document the progress, challenges, and opportunities in breeding for drought tolerance in wheat. The paper outlines the following key aspects: (1) challenges associated with breeding for adaptation to drought-prone environments, (2) opportunities such as genetic variation in wheat for drought tolerance, selection methods, the interplay between above-ground phenotypic traits and root attributes in drought adaptation and drought-responsive attributes and (3) approaches, technologies and innovations in drought tolerance breeding. In the end, the paper summarises genetic gains and perspectives in drought tolerance breeding in wheat. The review will serve as baseline information for wheat breeders and agronomists to guide the development and deployment of drought-adapted and high-performing new-generation wheat varieties.

A CRISPR/Cas9-Based System with Controllable Auto-Excision Feature Serving Cisgenic Plant Breeding and Beyond

Transgenic or genetically modified crops have great potential in modern agriculture but still suffer from heavy regulations worldwide due to biosafety concerns. As a promising alternative route, cisgenic crops have received higher public acceptance and better reviews by governing authorities. To serve the purpose of cisgenic plant breeding, we have developed a CRISPR/Cas9-based vector system, which is capable of delivering target gene-of-interest (GOI) into recipient plants while removing undesired genetic traces in the plants. The new system features a controllable auto-excision feature, which is realized by a core design of embedded multi-clonal sequence and the use of inducible promoters controlling the expression of Cas9 nuclease. In the current proof-of-concept study in Arabidopsis thaliana (L.) Heynh., we have successfully incorporated a GOI into the plant and removed the selection marker and CRISPR/Cas9 components from the final product. Following the designed workflow, we have demonstrated that novel cisgenic plant germplasms with desired traits could be developed within one to two generations. Further characterizations of the vector system have shown that heat treatment at 37 °C could significantly improve the editing efficiency (up to 100%), and no off-target mutations were identified in the Arabidopsis background. This novel vector system is the first CRISPR/Cas9-based genome editing tool for cisgenic plant breeding and should prove powerful for other similar applications in the bright future of precision molecular breeding.

Applications of Genomic Tools in Plant Breeding: Crop Biofortification

Crop breeding has mainly been focused on increasing productivity, either directly or by decreasing the losses caused by biotic and abiotic stresses (that is, incorporating resistance to diseases and enhancing tolerance to adverse conditions, respectively). Quite the opposite, little attention has been paid to improve the nutritional value of crops. It has not been until recently that crop biofortification has become an objective within breeding programs, through either conventional methods or genetic engineering. There are many steps along this long path, from the initial evaluation of germplasm for the content of nutrients and health-promoting compounds to the development of biofortified varieties, with the available and future genomic tools assisting scientists and breeders in reaching their objectives as well as speeding up the process. This review offers a compendium of the genomic technologies used to explore and create biodiversity, to associate the traits of interest to the genome, and to transfer the genomic regions responsible for the desirable characteristics into potential new varieties. Finally, a glimpse of future perspectives and challenges in this emerging area is offered by taking the present scenario and the slow progress of the regulatory framework as the starting point.

Potential of Industrial Hemp for Phytoremediation of Heavy Metals

The accumulation of anthropogenic heavy metals in soil is a major form of pollution. Such potentially toxic elements are nonbiodegradable and persist for many years as threats to human and environmental health. Traditional forms of remediation are costly and potentially damaging to the land. An alternative strategy is phytoremediation, where plants are used to capture metals from the environment. Industrial hemp (Cannabis sativa) is a promising candidate for phytoremediation. Hemp has deep roots and is tolerant to the accumulation of different metals. In addition, the crop biomass has many potential commercial uses after harvesting is completed. Furthermore, the recent availability of an annotated genome sequence provides a powerful tool for the bioengineering of C. sativa for better phytoremediation.

Specialized metabolites: Physiological and biochemical role in stress resistance, strategies to improve their accumulation, and new applications in crop breeding and management

Specialized plant metabolites (SPMs), traditionally referred to as 'secondary metabolites', are chemical compounds involved in a broad range of biological functions, including plant responses to abiotic and biotic stresses. Moreover, some of them have a role in end-product quality with potential health benefits in humans. For this reason, they became an important target of studies focusing on their mechanisms of action and use in crop breeding and management. In this review we summarize the specific role of SPMs in physiological processes and in plant resistance to abiotic and biotic stresses, and the different strategies to enhance their production/accumulation in plant tissues under stress, including genetic approaches (marker-assisted selection and biotechnological tools) and agronomic management (fertilizer applications, cultivation method and beneficial microorganisms). New crop management strategies based on the direct application of the most promising compounds in form of plant residuals or liquid formulations are also described.

The Intragenesis and Synthetic Biology Approach towards Accelerating Genetic Gains on Strawberry: Development of New Tools to Improve Fruit Quality and Resistance to Pathogens

Under climate change, the spread of pests and pathogens into new environments has a dramatic effect on crop protection control. Strawberry (Fragaria spp.) is one the most profitable crops of the Rosaceae family worldwide, but more than 50 different genera of pathogens affect this species. Therefore, accelerating the improvement of fruit quality and pathogen resistance in strawberry represents an important objective for breeding and reducing the usage of pesticides. New genome sequencing data and bioinformatics tools has provided important resources to expand the use of synthetic biology-assisted intragenesis strategies as a powerful tool to accelerate genetic gains in strawberry. In this paper, we took advantage of these innovative approaches to create four RNAi intragenic silencing cassettes by combining specific strawberry new promoters and pathogen defense-related candidate DNA sequences to increase strawberry fruit quality and resistance by silencing their corresponding endogenous genes, mainly during fruit ripening stages, thus avoiding any unwanted effect on plant growth and development. Using a fruit transient assay, GUS expression was detected by the two synthetic FvAAT2 and FvDOF2 promoters, both by histochemical assay and qPCR analysis of GUS transcript levels, thus ensuring the ability of the same to drive the expression of the silencing cassettes in this strawberry tissue. The approaches described here represent valuable new tools for the rapid development of improved strawberry lines.

Citrus Genetic Transformation: An Overview of the Current Strategies and Insights on the New Emerging Technologies

Citrus are among the most prevailing fruit crops produced worldwide. The implementation of effective and reliable breeding programs is essential for coping with the increasing demands of satisfactory yield and quality of the fruit as well as to deal with the negative impact of fast-spreading diseases. Conventional methods are time-consuming and of difficult application because of inherent factors of citrus biology, such as their prolonged juvenile period and a complex reproductive stage, sometimes presenting infertility, self-incompatibility, parthenocarpy, or polyembryony. Moreover, certain desirable traits are absent from cultivated or wild citrus genotypes. All these features are challenging for the incorporation of the desirable traits. In this regard, genetic engineering technologies offer a series of alternative approaches that allow overcoming the difficulties of conventional breeding programs. This review gives a detailed overview of the currently used strategies for the development of genetically modified citrus. We describe different aspects regarding genotype varieties used, including elite cultivars or extensively used scions and rootstocks. Furthermore, we discuss technical aspects of citrus genetic transformation procedures via Agrobacterium, regular physical methods, and magnetofection. Finally, we describe the selection of explants considering young and mature tissues, protoplast isolation, etc. We also address current protocols and novel approaches for improving the in vitro regeneration process, which is an important bottleneck for citrus genetic transformation. This review also explores alternative emerging transformation strategies applied to citrus species such as transient and tissue localized transformation. New breeding technologies, including cisgenesis, intragenesis, and genome editing by clustered regularly interspaced short palindromic repeats (CRISPR), are also discussed. Other relevant aspects comprising new promoters and reporter genes, marker-free systems, and strategies for induction of early flowering, are also addressed. We provided a future perspective on the use of current and new technologies in citrus and its potential impact on regulatory processes.

A Strategy for the Production and Molecular Validation of Agrobacterium-Mediated Intragenic Octoploid Strawberry

Intragenesis is an all-native engineering technology for crop improvement. Using an intragenic strategy to bring genes from wild species to cultivated strawberry could expand the genetic variability. A robust regeneration protocol was developed for the strawberry cv. ‘Shanghai Angel’ by optimizing the dose of Thidiazuron and identifying the most suitable explants. The expression cassette was assembled with all DNA fragments from F. vesca, harboring a sugar transporter gene FvSTP8 driven by a fruit-specific FvKnox promoter. Transformed strawberry was developed through an Agrobacterium-mediated strategy without any selectable markers. Other than PCR selection, probe-based duplex droplet digital PCR (ddPCR) was performed to determine the T-DNA insert. Four independent transformed shoots were obtained with a maximum of 5.3% efficiency. Two lines were confirmed to be chimeras, while the other two were complete transformants with six and 11 copies of the intragene, respectively. The presence of a vector backbone beyond the T-DNA in these transformants indicated that intragenic strawberries were not obtained. The current work optimized the procedures for producing transformed strawberry without antibiotic selection, and accurately determined the insertion copies by ddPCR in the strawberry genome for the first time. These strategies might be promising for the engineering of ‘Shanghai Angel’ and other cultivars to improve agronomic traits.

Maize Transformation: From Plant Material to the Release of Genetically Modified and Edited Varieties

Over the past decades, advances in plant biotechnology have allowed the development of genetically modified maize varieties that have significantly impacted agricultural management and improved the grain yield worldwide. To date, genetically modified varieties represent 30% of the world's maize cultivated area and incorporate traits such as herbicide, insect and disease resistance, abiotic stress tolerance, high yield, and improved nutritional quality. Maize transformation, which is a prerequisite for genetically modified maize development, is no longer a major bottleneck. Protocols using morphogenic regulators have evolved significantly towards increasing transformation frequency and genotype independence. Emerging technologies using either stable or transient expression and tissue culture-independent methods, such as direct genome editing using RNA-guided endonuclease system as an in vivo desired-target mutator, simultaneous double haploid production and editing/haploid-inducer-mediated genome editing, and pollen transformation, are expected to lead significant progress in maize biotechnology. This review summarises the significant advances in maize transformation protocols, technologies, and applications and discusses the current status, including a pipeline for trait development and regulatory issues related to current and future genetically modified and genetically edited maize varieties.

Novel and emerging biotechnological crop protection approaches

Traditional breeding or genetically modified organisms (GMOs) have for a long time been the sole approaches to effectively cope with biotic and abiotic stresses and implement the quality traits of crops. However, emerging diseases as well as unpredictable climate changes affecting agriculture over the entire globe force scientists to find alternative solutions required to quickly overcome seasonal crises. In this review, we first focus on cisgenesis and genome editing as challenging biotechnological approaches for breeding crops more tolerant to biotic and abiotic stresses. In addition, we take into consideration a toolbox of new techniques based on applications of RNA interference and epigenome modifications, which can be adopted for improving plant resilience. Recent advances in these biotechnological applications are mainly reported for non-model plants and woody crops in particular. Indeed, the characterization of RNAi machinery in plants is fundamental to transform available information into biologically or biotechnologically applicable knowledge. Finally, here we discuss how these innovative and environmentally friendly techniques combined with traditional breeding can sustain a modern agriculture and be of potential contribution to climate change mitigation.

Role of information in consumers' preferences for eco-sustainable genetic improvements in plant breeding

Consumers' preferences for products derived from genetic improvements and innovations in plant breeding are often conditioned by technophobia and negative public imaginaries. The current study addresses this issue by analyzing consumers' monetary preferences for a win-win innovation (generating gains for both private actors and the community) in the viticulture sector, namely fungus resistant grapes (FRG). The use of these grapes reduces the quantity of chemical inputs applied to vineyards, simultaneously improving firms' economic performance. This study aimed to assess whether consumers prefer wines originating from FRG varieties to conventional wines. In particular, through an experimental online survey involving 627 Italian regular wine drinkers, the study compares individuals' willingness to pay (WTP) for conventional wines with the WTP for two FRG wines produced with two different techniques: horticultural hybridization and genome editing. The study also assesses the potential effect of polarized media coverage on preferences by testing, in a between-subjects experimental design, two diverging (positive/negative) information scenarios, and the core drivers of these preferences. The findings suggest that respondents express a premium price for horticultural FRG wines compared to conventional wines (+9.14%) and a strong discount for genome edited FRG wines (-21.13%). The results also reveal that negative information reduces consumers' WTP for horticultural FRG wines, while positive information increases their WTP for genome edited FRG wines. Last, the study highlights that individuals concerned with food sustainability issues and knowledgeable about wine are more likely to accept both FRG typologies. Overall, the study confirms the crucial role of appropriate information for market acceptance of innovations based on plant genetics to foster the adoption of sustainable pest-reducing practices in wine production.

Genomic Approaches to Identify Molecular Bases of Crop Resistance to Diseases and to Develop Future Breeding Strategies

Plant diseases are responsible for substantial crop losses each year and affect food security and agricultural sustainability. The improvement of crop resistance to pathogens through breeding represents an environmentally sound method for managing disease and minimizing these losses. The challenge is to breed varieties with a stable and broad-spectrum resistance. Different approaches, from markers to recent genomic and 'post-genomic era' technologies, will be reviewed in order to contribute to a better understanding of the complexity of host-pathogen interactions and genes, including those with small phenotypic effects and mechanisms that underlie resistance. An efficient combination of these approaches is herein proposed as the basis to develop a successful breeding strategy to obtain resistant crop varieties that yield higher in increasing disease scenarios.

A Roadmap to Modulated Anthocyanin Compositions in Carrots

Anthocyanins extracted from black carrots have received increased interest as natural colorants in recent years. The reason is mainly their high content of acylated anthocyanins that stabilizes the color and thereby increases the shelf-life of products colored with black carrot anthocyanins. Still, the main type of anthocyanins synthesized in all black carrot cultivars is cyanidin limiting their use as colorants due to the narrow color variation. Additionally, in order to be competitive against synthetic colors, a higher percentage of acylated anthocyanins and an increased anthocyanin content in black carrots are needed. However, along with the increased interest in black carrots there has also been an interest in identifying the structural and regulatory genes associated with anthocyanin biosynthesis in black carrots. Thus, huge progress in the identification of genes involved in anthocyanin biosynthesis has recently been achieved. Given this information it is now possible to attempt to modulate anthocyanin compositions in black carrots through genetic modifications. In this review we look into genetic modification opportunities for generating taproots of black carrots with extended color palettes, with a higher percentage of acylated anthocyanins or a higher total content of anthocyanins.

New plant breeding techniques and their regulatory implications: An opportunity to advance metabolomics approaches

Over the previous decades, biotechnological innovations have led to improved agricultural productivity, more nutritious foods and lower chemical usage. Both in western societies and Low Medium Income Countries (LMICs). However, the projected increases in the global population, means the production of nutritious food stuffs must increase dramatically. Building on existing genetic modification technologies a series of New Plant Breeding Technologies (NPBT) has recently emerged. These approaches include, Agro-infiltration, grafting, cis and intragenesis and gene editing technologies. How these new techniques should be regulated has fostered considerable debate. Concerns have also been raised, to ensure over-regulation does not arise, creating administrative and economic burden. In this article the existing landscape of genetically modified crops is reviewed and the potential of several New Plant Breeding Techniques (NPBT) described. Metabolomics is an omic technology that has developed in a concurrent manner with biotechnological advances in plant breeding. There is potentially further opportunities to advance our metabolomic technologies to characterise the outputs of New Plant Breeding Technologies, in a manner that is beneficial both from an academic, biosafety and industrial perspective.

Genomics Armed With Diversity Leads the Way in Brassica Improvement in a Changing Global Environment

Meeting the needs of a growing world population in the face of imminent climate change is a challenge; breeding of vegetable and oilseed Brassica crops is part of the race in meeting these demands. Available genetic diversity constituting the foundation of breeding is essential in plant improvement. Elite varieties, land races, and crop wild species are important resources of useful variation and are available from existing genepools or genebanks. Conservation of diversity in genepools, genebanks, and even the wild is crucial in preventing the loss of variation for future breeding efforts. In addition, the identification of suitable parental lines and alleles is critical in ensuring the development of resilient Brassica crops. During the past two decades, an increasing number of high-quality nuclear and organellar Brassica genomes have been assembled. Whole-genome re-sequencing and the development of pan-genomes are overcoming the limitations of the single reference genome and provide the basis for further exploration. Genomic and complementary omic tools such as microarrays, transcriptomics, epigenetics, and reverse genetics facilitate the study of crop evolution, breeding histories, and the discovery of loci associated with highly sought-after agronomic traits. Furthermore, in genomic selection, predicted breeding values based on phenotype and genome-wide marker scores allow the preselection of promising genotypes, enhancing genetic gains and substantially quickening the breeding cycle. It is clear that genomics, armed with diversity, is set to lead the way in Brassica improvement; however, a multidisciplinary plant breeding approach that includes phenotype = genotype × environment × management interaction will ultimately ensure the selection of resilient Brassica varieties ready for climate change.

Characterization of an algal phosphomannose isomerase gene and its application as a selectable marker for genetic manipulation of tomato

Establishing a transgenic plant largely relies on a selectable marker gene that can confer antibiotic or herbicide resistance to plant cells. The existence of such selectable marker genes in genetically modified foods has long been criticized. Plant cells generally exhibit too low an activity of phosphomannose isomerase (PMI) to grow with mannose as a sole carbon source. In this study, we characterized PMI from the green microalga Chlorococcum sp. and assessed its feasibility as a selectable marker for plant biotechnology. Chlorococcum sp. PMI (ChlPMI) was shown to be closely related to higher plants but more distant to bacterial counterparts. Overexpression of ChlPMI in tomato induced callus and shoot formation in media containing mannose (6 g/L) and had an average transformation rate of 3.9%. Based on this transformation system, a polycistronic gene cluster containing crtB, HpBHY, CrBKT and SlLCYB (BBBB) was co-expressed in a different tomato cultivar. Six putative transformants were achieved with a transformation rate of 1.4%, which produced significant amounts of astaxanthin due to the expression of the BBBB genes. Taken together, these findings indicate that we have established an additional tool for plant biotechnology that may be suitable for genetically modifying foods safely.

Potato improvement through genetic engineering

Potato (Solanum tuberosum L.) is the third most important crop worldwide and a staple food for many people worldwide. Genetically, it poses many challenges for traditional breeding due to its autotetraploid nature and its tendency toward inbreeding depression. Breeding programs have focused on productivity, nutritional quality, and disease resistance. Some of these traits exist in wild potato relatives but their introgression into elite cultivars can take many years and, for traits such as pest resistance, their effect is often short-lasting. These problems can be addressed by genetic modification (GM) or gene editing (GE) and open a wide horizon for potato crop improvement. Current genetically modified and gene edited varieties include those with Colorado potato beetle and late blight resistance, reduction in acrylamide, and modified starch content. RNAi hairpin technology can be used to silence the haplo-alleles of multiple genes simultaneously, whereas optimization of newer gene editing technologies such as base and prime editing will facilitate the routine generation of advanced edits across the genome. These technologies will likely gain further relevance as increased target specificity and decreased off-target effects are demonstrated. In this Review, we discuss recent work related to these technologies in potato improvement.

Metabolic Engineering Strategies of Industrial Hemp (Cannabis sativa L.): A Brief Review of the Advances and Challenges

Industrial hemp (Cannabis sativa L.) is a diploid (2n = 20), dioecious plant that is grown for fiber, seed, and oil. Recently, there has been a renewed interest in this crop because of its panoply of cannabinoids, terpenes, and other phenolic compounds. Specifically, hemp contains terpenophenolic compounds such as cannabidiol (CBD) and cannabigerol (CBG), which act on cannabinoid receptors and positively regulate various human metabolic, immunological, and physiological functions. CBD and CBG have an effect on the cytokine metabolism, which has led to the examination of cannabinoids on the treatment of viral diseases, including COVID-19. Based on genomic, transcriptomic, and metabolomic studies, several synthetic pathways of hemp secondary metabolite production have been elucidated. Nevertheless, there are few reports on hemp metabolic engineering despite obvious impact on scientific and industrial sectors. In this article, recent status and current perspectives on hemp metabolic engineering are reviewed. Three distinct approaches to expedite phytochemical yield are discussed. Special emphasis has been placed on transgenic and transient gene delivery systems, which are critical for successful metabolic engineering of hemp. The advent of new tools in synthetic biology, particularly the CRISPR/Cas systems, enables environment-friendly metabolic engineering to increase the production of desirable hemp phytochemicals while eliminating the psychoactive compounds, such as tetrahydrocannabinol (THC).

Transcriptomic and proteomic responses to brown plant hopper (Nilaparvata lugens) in cultivated and Bt-transgenic rice (Oryza sativa) and wild rice (O. rufipogon)

Strategies are still employed to reduce insect damage in crop production, including conventional breeding with wild germplasm resources and transgenic technology with foreign genes' insertion. Cultivated and Bt-transgenic rice (Oryza sativa) and two ecotypes of wild rice (O. rufipogon) were treated by a 72 h feeding of brown plant hopper (Nilaparvata lugens). Under the feeding of N. lugens, compared with the cultivated rice (568 and 4), more differentially expressed genes (DEGs) and differentially accumulated proteins (DAPs) were identified in transgenic rice (2098 and 11) and two wild ecotypes (1990, 39 and 1932, 25, respectively). The iTRAQ analysis showed 79 DAPs and confirmed the results of RNA-seq, which showed the least GO terms and KEGG pathways responding to herbivory in the cultivated rice. DAPs significantly enriched two GO terms that are related with Bph14 and Bph33 genes in rice. Most of DEGs and DAPs were related to plant biological processes of plant-pathogen interaction and plant hormone signal transduction, and hormone signaling and transcription factors regulate the immune response of rice to BPH. Our results demonstrated the similarity in the wild rice and Bt-transgenic rice for their transcriptomic and proteomic response to herbivory, while cultivated rice lacked enough pathways in response to herbivory. STATEMENT OF SIGNIFICANCE OF THE STUDY: The iTRAQ analysis and RNA-seq were employed 39 to identify differentially expressed genes (DEGs) and differentially accumulated proteins (DAPs) in seedlings of cultivated, Bt-transgenic and two wild rice ecotypes under feeding of brown plant hopper. Wild rice showed DEGs and DAPs related to biochemical pathways of plant pathogen interactions and plant hormone signal transductions, while cultivated rice lacked enough pathways in response to herbivory. Crop domestication weakened the response of plants to herbivory, while the insertion of Bt gene might promote the response of plants to herbivory. Growing environment plays an important role in regulating gene networks of plant response to herbivory. Our results highlighted the importance of conservation of crop wild species. SIGNIFICANCE: Insect damage is one of main factors in reducing agricultural production, and technologies and methods were employed to control insect pests in agricultural systems. Transgenic technology is developed to produce insect-resistant crops, but receive concerns on biosafety risks. Alternatively, crop wild species are important genetic resource in crop breeding to produce trait-specific varieties. Here, we investigated the molecular mechanisms of plant response to herbivory in wild, Bt-transgenic and cultivated rice, and found crop domestication weakened the response of plants to herbivory. The insertion of foreign Bt gene may promote the expression of other genes. In addition, our results showed growing environment plays an important role in regulating gene networks of plant response to herbivory. These results highlight the importance of wild species conservation, with the strategy of in situ conservation.

Evaluation of Plant-Derived Promoters for Constitutive and Tissue-Specific Gene Expression in Potato

Various plant-derived promoters can be used to regulate ectopic gene expression in potato. In the present study, four promoters derived from the potato genome have been characterized by the expression of identical cassettes carrying the fusion with the reporter β-glucuronidase (gusA) gene. The strengths of StUbi, StGBSS, StPat, and StLhca3 promoters were compared with the conventional constitutive CaMV 35S promoter in various organs (leaves, stems, roots, and tubers) of greenhouse-grown plants. The final amount of gene product was determined at the post-transcriptional level using histochemical analysis, fluorometric measurements, and Western blot analysis. The promoter strength comparison demonstrated that the StUbi promoter generally provided a higher level of constitutive β-glucuronidase accumulation than the viral CaMV 35S promoter. Although the StLhca3 promoter was predominantly expressed in a green tissue-specific manner (leaves and stems) while StGBSS and StPat mainly provided tuber-specific activity, a “promoter leakage” was also found. However, the degree of unspecific activity depended on the particular transgenic line and tissue. According to fluorometric data, the functional activity of promoters in leaves could be arranged as follows: StLhca3 > StUbi > CaMV 35S > StPat > StGBSS (from highest to lowest). In tubers, the higher expression was detected in transgenic plants expressing StPat-gusA fusion construct, and the strength order was as follows: StPat > StGBSS > StUbi > CaMV 35S > StLhca3. The observed differences between expression patterns are discussed considering the benefits and limitations for the usage of each promoter to regulate the expression of genes in a particular potato tissue.

Biotechnological Approaches: Gene Overexpression, Gene Silencing, and Genome Editing to Control Fungal and Oomycete Diseases in Grapevine

Downy mildew, powdery mildew, and grey mold are some of the phytopathological diseases causing economic losses in agricultural crops, including grapevine, worldwide. In the current scenario of increasing global warming, in which the massive use of agrochemicals should be limited, the management of fungal disease has become a challenge. The knowledge acquired on candidate resistant (R) genes having an active role in plant defense mechanisms has allowed numerous breeding programs to integrate these traits into selected cultivars, even though with some limits in the conservation of the proper qualitative characteristics of the original clones. Given their gene-specific mode of action, biotechnological techniques come to the aid of breeders, allowing them to generate simple and fast modifications in the host, without introducing other undesired genes. The availability of efficient gene transfer procedures in grapevine genotypes provide valid tools that support the application of new breeding techniques (NBTs). The expertise built up over the years has allowed the optimization of these techniques to overexpress genes that directly or indirectly limit fungal and oomycetes pathogens growth or silence plant susceptibility genes. Furthermore, the downregulation of pathogen genes which act as virulence effectors by exploiting the RNA interference mechanism, represents another biotechnological tool that increases plant defense. In this review, we summarize the most recent biotechnological strategies optimized and applied on Vitis species, aimed at reducing their susceptibility to the most harmful fungal and oomycetes diseases. The best strategy for combating pathogenic organisms is to exploit a holistic approach that fully integrates all these available tools.

Non-coding RNAs as emerging targets for crop improvement

Food security is affected by climate change, population growth, as well as abiotic and biotic stresses. Conventional and molecular marker assisted breeding and genetic engineering techniques have been employed extensively for improving resistance to biotic stress in crop plants. Advances in next-generation sequencing technologies have permitted the exploration and identification of parts of the genome that extend beyond the regions with protein coding potential. These non-coding regions of the genome are transcribed to generate many types of non-coding RNAs (ncRNAs). These ncRNAs are involved in the regulation of growth, development, and response to stresses at transcriptional and translational levels. ncRNAs, including long ncRNAs (lncRNAs), small RNAs and circular RNAs have been recognized as important regulators of gene expression in plants and have been suggested to play important roles in plant immunity and adaptation to abiotic and biotic stresses. In this article, we have reviewed the current state of knowledge with respect to lncRNAs and their mechanism(s) of action as well as their regulatory functions, specifically within the context of biotic stresses. Additionally, we have provided insights into how our increased knowledge about lncRNAs may be used to improve crop tolerance to these devastating biotic stresses.

Conventional and Molecular Techniques from Simple Breeding to Speed Breeding in Crop Plants: Recent Advances and Future Outlook

In most crop breeding programs, the rate of yield increment is insufficient to cope with the increased food demand caused by a rapidly expanding global population. In plant breeding, the development of improved crop varieties is limited by the very long crop duration. Given the many phases of crossing, selection, and testing involved in the production of new plant varieties, it can take one or two decades to create a new cultivar. One possible way of alleviating food scarcity problems and increasing food security is to develop improved plant varieties rapidly. Traditional farming methods practiced since quite some time have decreased the genetic variability of crops. To improve agronomic traits associated with yield, quality, and resistance to biotic and abiotic stresses in crop plants, several conventional and molecular approaches have been used, including genetic selection, mutagenic breeding, somaclonal variations, whole-genome sequence-based approaches, physical maps, and functional genomic tools. However, recent advances in genome editing technology using programmable nucleases, clustered regularly interspaced short palindromic repeats (CRISPR), and CRISPR-associated (Cas) proteins have opened the door to a new plant breeding era. Therefore, to increase the efficiency of crop breeding, plant breeders and researchers around the world are using novel strategies such as speed breeding, genome editing tools, and high-throughput phenotyping. In this review, we summarize recent findings on several aspects of crop breeding to describe the evolution of plant breeding practices, from traditional to modern speed breeding combined with genome editing tools, which aim to produce crop generations with desired traits annually.

New Plant Breeding Techniques in Citrus for the Improvement of Important Agronomic Traits. A Review

New plant breeding techniques (NPBTs) aim to overcome traditional breeding limits for fruit tree species, in order to obtain new varieties with improved organoleptic traits and resistance to biotic and abiotic stress, and to maintain fruit quality achieved over centuries by (clonal) selection. Knowledge on the gene(s) controlling a specific trait is essential for the use of NPBTs, such as genome editing and cisgenesis. In the framework of the international scientific community working on fruit tree species, including citrus, NPBTs have mainly been applied to address pathogen threats. Citrus could take advantage of NPBTs because of its complex species biology (seedlessness, apomixis, high heterozygosity, and long juvenility phase) and aptitude for in vitro manipulation. To our knowledge, genome editing in citrus via transgenesis has successful for induced resistance to Citrus bacterial canker in sweet orange and grapefruit using the resistance gene CsLOB1. In the future, NPBTs will also be used to improve fruit traits, making them healthier. The regeneration of plants following the application of NPBTs is a bottleneck, making it necessary to optimize the efficiency of current protocols. The strengths and weaknesses of using explants from young in vitro plantlets, and from mature plants, will be discussed. Other major issues addressed in this review are related to the requirement for marker-free systems and shortening the long juvenility phase. This review aims to summarize methods and approaches available in the literature that are suitable to citrus, focusing on the principles observed before the use of NPBTs.

d-Xylose consumption by nonrecombinant Saccharomyces cerevisiae: A review

Xylose is the second most abundant sugar in nature. Its efficient fermentation has been considered as a critical factor for a feasible conversion of renewable biomass resources into biofuels and other chemicals. The yeast Saccharomyces cerevisiae is of exceptional industrial importance due to its excellent capability to ferment sugars. However, although S. cerevisiae is able to ferment xylulose, it is considered unable to metabolize xylose, and thus, a lot of research has been directed to engineer this yeast with heterologous genes to allow xylose consumption and fermentation. The analysis of the natural genetic diversity of this yeast has also revealed some nonrecombinant S. cerevisiae strains that consume or even grow (modestly) on xylose. The genome of this yeast has all the genes required for xylose transport and metabolism through the xylose reductase, xylitol dehydrogenase, and xylulokinase pathway, but there seems to be problems in their kinetic properties and/or required expression. Self-cloning industrial S. cerevisiae strains overexpressing some of the endogenous genes have shown interesting results, and new strategies and approaches designed to improve these S. cerevisiae strains for ethanol production from xylose will also be presented in this review.

MicroRNAs and new biotechnological tools for its modulation and improving stress tolerance in plants

MicroRNAs (miRNAs) modulate the abundance and spatial-temporal accumulation of target mRNAs and indirectly regulate several plant processes. Transcriptional regulation of the genes encoding miRNAs (MIR genes) can be activated by numerous transcription factors, which themselves are regulated by other miRNAs. Fine-tuning of MIR genes or miRNAs is a powerful biotechnological strategy to improve tolerance to abiotic or biotic stresses in crops of economic importance. Current approaches for miRNA fine-tuning are based on the down- or up-regulation of MIR gene transcription and the use of genetic engineering tools to manipulate the final concentration of these miRNAs in the cytoplasm. Transgenesis, cisgenesis, intragenesis, artificial MIR genes, endogenous and artificial target mimicry, MIR genes editing using Meganucleases, ZNF proteins, TALENs and CRISPR/Cas9 or CRISPR/Cpf1, CRISPR/dCas9 or dCpf1, CRISPR13a, topical delivery of miRNAs and epigenetic memory have been successfully explored to MIR gene or miRNA modulation and improve agronomic traits in several model or crop plants. However, advantages and drawbacks of each of these new biotechnological tools (NBTs) are still not well understood. In this review, we provide a brief overview of the biogenesis and role of miRNAs in response to abiotic or biotic stresses, we present critically the main NBTs used for the manipulation of MIR genes and miRNAs, we show current efforts and findings with the MIR genes and miRNAs modulation in plants, and we summarize the advantages and drawbacks of these NBTs and provide some alternatives to overcome. Finally, challenges and future perspectives to miRNA modulating in important crops are also discussed.

An EU Perspective on Biosafety Considerations for Plants Developed by Genome Editing and Other New Genetic Modification Techniques (nGMs)

The question whether new genetic modification techniques (nGM) in plant development might result in non-negligible negative effects for the environment and/or health is significant for the discussion concerning their regulation. However, current knowledge to address this issue is limited for most nGMs, particularly for recently developed nGMs, like genome editing, and their newly emerging variations, e.g., base editing. This leads to uncertainties regarding the risk/safety-status of plants which are developed with a broad range of different nGMs, especially genome editing, and other nGMs such as cisgenesis, transgrafting, haploid induction or reverse breeding. A literature survey was conducted to identify plants developed by nGMs which are relevant for future agricultural use. Such nGM plants were analyzed for hazards associated either (i) with their developed traits and their use or (ii) with unintended changes resulting from the nGMs or other methods applied during breeding. Several traits are likely to become particularly relevant in the future for nGM plants, namely herbicide resistance (HR), resistance to different plant pathogens as well as modified composition, morphology, fitness (e.g., increased resistance to cold/frost, drought, or salinity) or modified reproductive characteristics. Some traits such as resistance to certain herbicides are already known from existing GM crops and their previous assessments identified issues of concern and/or risks, such as the development of herbicide resistant weeds. Other traits in nGM plants are novel; meaning they are not present in agricultural plants currently cultivated with a history of safe use, and their underlying physiological mechanisms are not yet sufficiently elucidated. Characteristics of some genome editing applications, e.g., the small extent of genomic sequence change and their higher targeting efficiency, i.e., precision, cannot be considered an indication of safety per se, especially in relation to novel traits created by such modifications. All nGMs considered here can result in unintended changes of different types and frequencies. However, the rapid development of nGM plants can compromise the detection and elimination of unintended effects. Thus, a case-specific premarket risk assessment should be conducted for nGM plants, including an appropriate molecular characterization to identify unintended changes and/or confirm the absence of unwanted transgenic sequences.

Agrobacterium-Mediated Transformation of Tree Fruit Crops: Methods, Progress, and Challenges

Genetic engineering based on Agrobacterium-mediated transformation has been a desirable tool to manipulate single or multiple genes of existing genotypes of woody fruit crops, for which conventional breeding is a difficult and lengthy process due to heterozygosity, sexual incompatibility, juvenility, or a lack of natural sources. To date, successful transformation has been reported for many fruit crops. We review the major progress in genetic transformation of these fruit crops made in the past 5 years, emphasizing reproducible transformation protocols as well as the strategies that have been tested in fruit crops. While direct transformation of scion cultivars was mostly used for fruit quality improvement, biotic and abiotic tolerance, and functional gene analysis, transgrafting on genetically modified (GM) rootstocks showed a potential to produce non-GM fruit products. More recently, genome editing technology has demonstrated a potential for gene(s) manipulation of several fruit crops. However, substantial efforts are still needed to produce plants from gene-edited cells, for which tremendous challenge remains in the context of either cell's recalcitrance to regeneration or inefficient gene-editing due to their polyploidy. We propose that effective transient transformation and efficient regeneration are the key for future utilization of genome editing technologies for improvement of fruit crops.

Normative Criteria and Their Inclusion in a Regulatory Framework for New Plant Varieties Derived From Genome Editing

Any legal regulation has to take into account fundamental interests and concerns, whether of private or public nature. This applies in particular to the politically and socially sensitive question of regulating plant biotechnology. With the advent of new breeding techniques, such as genome editing, new challenges are arising for legislators around the world. However, in coping with them not only the technical particularities of the new breeding techniques must be taken into account but also the diverse and sometimes conflicting interests of the various stakeholders. In order to be able to draft a suitable regulatory regime for these new techniques, the different interests and concerns at play are identified. Subsequently, a determination is made on how these interests relate to each other, before regulatory concepts to reconcile the conflicting demands are presented. The examined normative criteria, which can have an impact on regulatory decisions regarding genome edited plants and products derived from them, include: industry interests, farmer interests, public opinion, consumer rights and interests, human health and food safety, food security, environmental protection, consistency, and coherence of the regulatory framework and ethical or religious convictions. Since those interests differ from country to country depending on the respective political, economic, and social circumstances, the respective legislator has the task of identifying these normative criteria and must find a suitable balance between them. To this end, a concept is developed on how the different interests can be related to each other and how to deal with conflicting and irreconcilable demands. Additionally, a legislator may have recourse to a number of further analyzed regulatory measures. An approval or notification procedure can be used for a risk assessment or a socio-economic evaluation. Coexistence measures and labeling provisions are able to reconcile interests that are at odds with each other and the precautionary principle can justify certain safeguard measures. As a result, the individual country-specific regulatory outcomes regarding genome edited plants are likely to be as manifold as the interests and regulatory measures at hand.

Isolation, characterization, and evaluation of three Citrus sinensis-derived constitutive gene promoters

Regulatory sequences from the citrus constitutive genes cyclophilin (CsCYP), glyceraldehyde-3-phosphate dehydrogenase C2 (CsGAPC2), and elongation factor 1-alpha (CsEF1) were isolated, fused to the uidA gene, and qualitatively and quantitatively evaluated in transgenic sweet orange plants. The 5' upstream region of a gene (the promoter) is the most important component for the initiation and regulation of gene transcription of both native genes and transgenes in plants. The isolation and characterization of gene regulatory sequences are essential to the development of intragenic or cisgenic genetic manipulation strategies, which imply the use of genetic material from the same species or from closely related species. We describe herein the isolation and evaluation of the promoter sequence from three constitutively expressed citrus genes: cyclophilin (CsCYP), glyceraldehyde-3-phosphate dehydrogenase C2 (CsGAPC2), and elongation factor 1-alpha (CsEF1). The functionality of the promoters was confirmed by a histochemical GUS assay in leaves, stems, and roots of stably transformed citrus plants expressing the promoter-uidA construct. Lower uidA mRNA levels were detected when the transgene was under the control of citrus promoters as compared to the expression under the control of the CaMV35S promoter. The association of the uidA gene with the citrus-derived promoters resulted in mRNA levels of up to 60-41.8% of the value obtained with the construct containing CaMV35S driving the uidA gene. Moreover, a lower inter-individual variability in transgene expression was observed amongst the different transgenic lines, where gene constructs containing citrus-derived promoters were used. In silico analysis of the citrus-derived promoter sequences revealed that their activity may be controlled by several putative cis-regulatory elements. These citrus promoters will expand the availability of regulatory sequences for driving gene expression in citrus gene-modification programs.

Regulation and Evolution of NLR Genes: A Close Interconnection for Plant Immunity

NLR (NOD-like receptor) genes belong to one of the largest gene families in plants. Their role in plants' resistance to pathogens has been clearly described for many members of this gene family, and dysregulation or overexpression of some of these genes has been shown to induce an autoimmunity state that strongly affects plant growth and yield. For this reason, these genes have to be tightly regulated in their expression and activity, and several regulatory mechanisms are described here that tune their gene expression and protein levels. This gene family is subjected to rapid evolution, and to maintain diversity at NLRs, a plethora of genetic mechanisms have been identified as sources of variation. Interestingly, regulation of gene expression and evolution of this gene family are two strictly interconnected aspects. Indeed, some examples have been reported in which mechanisms of gene expression regulation have roles in promotion of the evolution of this gene family. Moreover, co-evolution of the NLR gene family and other gene families devoted to their control has been recently demonstrated, as in the case of miRNAs.

Isolation and identification of five cold-inducible promoters from Oryza sativa

Five promoters of the cold-inducible rice genes were isolated. The quantitative and qualitative expression analyses in the high generation transgenic rice suggest that the genes are stably induced by low temperature. Cold-inducible promoters are highly desirable for stress-inducible gene expression in crop genetic engineering. In this study, five rice genes, including OsABA8ox1, OsMYB1R35, OsERF104, OsCYP19-4, and OsABCB5, were found to be transcriptionally induced by cold stress. The promoters of these five genes were isolated, and their activities were identified in various tissues of transgenic rice plants at different growth stages both before and after cold stress. Histochemical staining, quantitative fluorescence assays, and GUSplus gene expression assays in corresponding promoter-GUSplus transgenic rice plants confirmed that the five promoters were cold-inducible with different expression patterns and strengths. The OsABA8ox1 and OsERF104 promoters had very low background expression; in contrast, the OsMYB1R35 promoter had higher basal activity in the roots, and OsCYP19-4 promoter activity was preferentially high in leaves and flowers of untreated transgenic lines. The OsABCB5 promoter had the highest basal activity among the five promoters. After cold induction, the activities of the OsABA8ox1, OsMYB1R35, and OsABCB5 promoters were high in both roots and leaves, slightly lower than that of the constitutively expressed OsActin1 promoter but comparable to that of the AtRD29A promoter. During the cold treatment time course, the activities of OsABA8ox1 and OsABCB5 promoters were quickly up-regulated in the early period and peaked at 24 h, after which the induction level gradually decreased until 48 h. The activities of the OsMYB1R35 and OsCYP19-4 promoters increased under stress in a time-dependent manner, while OsERF104 promoter activity began to increase at 4 h and then decreased strongly. Furthermore, activities' analysis in T₃, T₄, and T₅ homozygous progeny of single-copy plants revealed that five promoters maintained their activities at comparable levels with no evidence of silencing under cold stress. Overall, the five cold-inducible rice promoters described herein could potentially be used in crop biotechnology.

Genome Editing Tools in Plants

Genome editing tools have the potential to change the genomic architecture of a genome at precise locations, with desired accuracy. These tools have been efficiently used for trait discovery and for the generation of plants with high crop yields and resistance to biotic and abiotic stresses. Due to complex genomic architecture, it is challenging to edit all of the genes/genomes using a particular genome editing tool. Therefore, to overcome this challenging task, several genome editing tools have been developed to facilitate efficient genome editing. Some of the major genome editing tools used to edit plant genomes are: Homologous recombination (HR), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), pentatricopeptide repeat proteins (PPRs), the CRISPR/Cas9 system, RNA interference (RNAi), cisgenesis, and intragenesis. In addition, site-directed sequence editing and oligonucleotide-directed mutagenesis have the potential to edit the genome at the single-nucleotide level. Recently, adenine base editors (ABEs) have been developed to mutate A-T base pairs to G-C base pairs. ABEs use deoxyadeninedeaminase (TadA) with catalytically impaired Cas9 nickase to mutate A-T base pairs to G-C base pairs.

Breeding next generation tree fruits: technical and legal challenges

The new plant breeding technologies (NPBTs) have recently emerged as powerful tools in the context of 'green' biotechnologies. They have wide potential compared to classical genetic engineering and they are attracting the interest of politicians, stakeholders and citizens due to the revolutionary impact they may have on agriculture. Cisgenesis and genome editing potentially allow to obtain pathogen-resistant plants or plants with enhanced qualitative traits by introducing or disrupting specific genes in shorter times compared to traditional breeding programs and by means of minimal modifications in the plant genome. Grapevine, the most important fruit crop in the world from an economical point of view, is a peculiar case for NPBTs because of the load of cultural aspects, varietal traditions and consumer demands, which hinder the use of classical breeding techniques and, furthermore, the application of genetic engineering to wine grape cultivars. Here we explore the technical challenges which may hamper the application of cisgenesis and genome editing to this perennial plant, in particular focusing on the bottlenecks of the Agrobacterium-mediated gene transfer. In addition, strategies to eliminate undesired sequences from the genome and to choose proper target sites are discussed in light of peculiar features of this species. Furthermore is reported an update of the international legislative frameworks regulating NPBT products which shows conflicting positions and, in the case of the European Union, a prolonged lack of regulation.