A tool for functional plant genomics: chimeric RNA/DNA oligonucleotides cause in vivo gene-specific mutations

Petunia dihydroflavonol 4-reductase is only a few amino acids away from producing orange pelargonidin-based anthocyanins

Anthocyanins are responsible for the color spectrum of both ornamental and natural flowers. However, not all plant species produce all colors. For example, roses are not blue because they do not naturally possess a hydroxylase that opens the pathway for delphinidin and its derivatives. It is more intriguing why some plants do not carry orange or scarlet red flowers with anthocyanins based on pelargonidin, because the precursor for these anthocyanins should be available if anthocyanins are made at all. The key to this is the substrate specificity of dihydroflavonol 4-reductase (DFR), an enzyme located at the branch point between flavonols and anthocyanins. The most common example is petunia, which does not bear orange flowers unless the enzyme is complemented by biotechnology. We changed a few amino acids in the active site of the enzyme and showed that the mutated petunia DFR started to favor dihydrokaempferol, the precursor to orange pelargonidin, in vitro. When transferred to petunia, it produced an orange hue and dramatically more pelargonidin-based anthocyanins in the flowers.

Unclasping potentials of genomics and gene editing in chickpea to fight climate change and global hunger threat

Genomics and genome editing promise enormous opportunities for crop improvement and elementary research. Precise modification in the specific targeted location of a genome has profited over the unplanned insertional events which are generally accomplished employing unadventurous means of genetic modifications. The advent of new genome editing procedures viz; zinc finger nucleases (ZFNs), homing endonucleases, transcription activator like effector nucleases (TALENs), Base Editors (BEs), and Primer Editors (PEs) enable molecular scientists to modulate gene expressions or create novel genes with high precision and efficiency. However, all these techniques are exorbitant and tedious since their prerequisites are difficult processes that necessitate protein engineering. Contrary to first generation genome modifying methods, CRISPR/Cas9 is simple to construct, and clones can hypothetically target several locations in the genome with different guide RNAs. Following the model of the application in crop with the help of the CRISPR/Cas9 module, various customized Cas9 cassettes have been cast off to advance mark discrimination and diminish random cuts. The present study discusses the progression in genome editing apparatuses, and their applications in chickpea crop development, scientific limitations, and future perspectives for biofortifying cytokinin dehydrogenase, nitrate reductase, superoxide dismutase to induce drought resistance, heat tolerance and higher yield in chickpea to encounter global climate change, hunger and nutritional threats.

Oligo-Not Only for Silencing: Overlooked Potential for Multidirectional Action in Plants

Oligo technology is a low-cost and easy-to-implement method for direct manipulation of gene activity. The major advantage of this method is that gene expression can be changed without requiring stable transformation. Oligo technology is mainly used for animal cells. However, the use of oligos in plants seems to be even easier. The oligo effect could be similar to that induced by endogenous miRNAs. In general, the action of exogenously introduced nucleic acids (Oligo) can be divided into a direct interaction with nucleic acids (genomic DNA, hnRNA, transcript) and an indirect interaction via the induction of processes regulating gene expression (at the transcriptional and translational levels) involving regulatory proteins using endogenous cellular mechanisms. Presumed mechanisms of oligonucleotides' action in plant cells (including differences from animal cells) are described in this review. Basic principles of oligo action in plants that allow bidirectional changes in gene activity and even those that lead to heritable epigenetic changes in gene expression are presented. The effect of oligos is related to the target sequence at which they are directed. This paper also compares different delivery methods and provides a quick guide to using IT tools to help design oligonucleotides.

The economics and policy of genome editing in crop improvement

In this review article we analyze the economics of genome editing and its potential long-term effect on crop improvement and agriculture. We describe the emergence of genome editing as a novel platform for crop improvement, distinct from the existing platforms of plant breeding and genetic engineering. We review key technical characteristics of genome editing and describe how it enables faster trait development, lower research and development costs, and the development of novel traits not possible through previous crop improvement methods. Given these fundamental technical and economic advantages, we describe how genome editing can greatly increase the productivity and broaden the scope of crop improvement with potential outsized economic effects. We further discuss how the global regulatory policy environment, which is still emerging, can shape the ultimate path of genome editing innovation, its effect on crop improvement, and its overall socioeconomic benefits to society.

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.

Viable protoplast formation of the coral endosymbiont alga Symbiodinium spp. in a microfluidics platform

Symbiodiniaceae is an important dinoflagellate family which lives in endosymbiosis with reef invertebrates, including coral polyps, making them central to the holobiont. With coral reefs currently under extreme threat from climate change, there is a pressing need to improve our understanding on the stress tolerance and stress avoidance mechanisms of Symbiodinium spp. Reactive oxygen species (ROS) such as singlet oxygen are central players in mediating various stress responses; however, the detection of ROS using specific dyes is still far from definitive in intact Symbiodinium cells due to the hindrance of uptake of certain fluorescent dyes because of the presence of the cell wall. Protoplast technology provides a promising platform for studying oxidative stress with the main advantage of removed cell wall, however the preparation of viable protoplasts remains a significant challenge. Previous studies have successfully applied cellulose-based protoplast preparation in Symbiodiniaceae; however, the protoplast formation and regeneration process was found to be suboptimal. Here, we present a microfluidics-based platform which allowed protoplast isolation from individually trapped Symbiodinium cells, by using a precisely adjusted flow of cell wall digestion enzymes (cellulase and macerozyme). Trapped single cells exhibited characteristic changes in their morphology, cessation of cell division and a slight decrease in photosynthetic activity during protoplast formation. Following digestion and transfer to regeneration medium, protoplasts remained photosynthetically active, regrew cell walls, regained motility, and entered exponential growth. Elevated flow rates in the microfluidic chambers resulted in somewhat faster protoplast formation; however, cell wall digestion at higher flow rates partially compromised photosynthetic activity. Physiologically competent protoplasts prepared from trapped cells in microfluidic chambers allowed for the first time the visualization of the intracellular localization of singlet oxygen (using Singlet Oxygen Sensor Green dye) in Symbiodiniaceae, potentially opening new avenues for studying oxidative stress.

Advances in S gene targeted genome-editing and its applicability to disease resistance breeding in selected Solanaceae crop plants

Genome-editing tools for the development of traits to tolerate abiotic and biotic adversaries are the recently devised breeding techniques revolutionizing molecular breeding by addressing the issues of rapidness and precision. To that end, disease resistance development by disrupting disease susceptibility genes (S genes) to intervene in the biological mechanism of pathogenicity has significantly improved the techniques of molecular breeding. Despite the achievements in genome-editing aimed at the intervention of the function of susceptibility determinants or gene regulatory elements, off-target effects associated with yield-related traits are still the main setbacks. The challenges are attributed to the complexity of the inheritance of traits controlled by pleiotropic genes. Therefore, a more rigorous genome-editing tool with ultra-precision and efficiency for the development of broad-spectrum and durable disease resistance applied to staple crop plants is of critical importance in molecular breeding programs. The main objective of this article is to review the most impressive progresses achieved in resistance breeding against the main diseases of three Solanaceae crops (potato, Solanum tuberosum; tomato, Solanum lycopersicum and pepper, Capsicum annuum) using genome-editing by disrupting the sequences of S genes, their promoters, or pathogen genes. In this paper, we discussed the complexity and applicability of genome-editing tools, summarized the main disease of Solanaceae crops, and compiled the recent reports on disease resistance developed by S-gene silencing and their off-target effects. Moreover, GO count and gene annotation were made for pooled S-genes from biological databases. Achievements and prospects of S-gene-based next-generation breeding technologies are also discussed.

Most S genes are membrane –anchored and are involved in infection and pre-penetration process

S gene-editing is less likely to cause an off-target effect

Gene-editing has been considered a more acceptable engineering tool

Editing S genes either from the pathogen or host ends has opened new possibilities

Enhancing HR Frequency for Precise Genome Editing in Plants

Gene-editing tools, such as Zinc-fingers, TALENs, and CRISPR-Cas, have fostered a new frontier in the genetic improvement of plants across the tree of life. In eukaryotes, genome editing occurs primarily through two DNA repair pathways: non-homologous end joining (NHEJ) and homologous recombination (HR). NHEJ is the primary mechanism in higher plants, but it is unpredictable and often results in undesired mutations, frameshift insertions, and deletions. Homology-directed repair (HDR), which proceeds through HR, is typically the preferred editing method by genetic engineers. HR-mediated gene editing can enable error-free editing by incorporating a sequence provided by a donor template. However, the low frequency of native HR in plants is a barrier to attaining efficient plant genome engineering. This review summarizes various strategies implemented to increase the frequency of HDR in plant cells. Such strategies include methods for targeting double-strand DNA breaks, optimizing donor sequences, altering plant DNA repair machinery, and environmental factors shown to influence HR frequency in plants. Through the use and further refinement of these methods, HR-based gene editing may one day be commonplace in plants, as it is in other systems.

Autopolyploidization affects transcript patterns and gene targeting frequencies in Physcomitrella

In Physcomitrella, whole-genome duplications affected the expression of about 3.7% of the protein-encoding genes, some of them relevant for DNA repair, resulting in a massively reduced gene-targeting frequency. Qualitative changes in gene expression after an autopolyploidization event, a pure duplication of the whole genome (WGD), might be relevant for a different regulation of molecular mechanisms between angiosperms growing in a life cycle with a dominant diploid sporophytic stage and the haploid-dominant mosses. Whereas angiosperms repair DNA double-strand breaks (DSB) preferentially via non-homologous end joining (NHEJ), in the moss Physcomitrella homologous recombination (HR) is the main DNA-DSB repair pathway. HR facilitates the precise integration of foreign DNA into the genome via gene targeting (GT). Here, we studied the influence of ploidy on gene expression patterns and GT efficiency in Physcomitrella using haploid plants and autodiploid plants, generated via an artificial WGD. Single cells (protoplasts) were transfected with a GT construct and material from different time-points after transfection was analysed by microarrays and SuperSAGE sequencing. In the SuperSAGE data, we detected 3.7% of the Physcomitrella genes as differentially expressed in response to the WGD event. Among the differentially expressed genes involved in DNA-DSB repair was an upregulated gene encoding the X-ray repair cross-complementing protein 4 (XRCC4), a key player in NHEJ. Analysing the GT efficiency, we observed that autodiploid plants were significantly GT suppressed (p < 0.001) attaining only one third of the expected GT rates. Hence, an alteration of global transcript patterns, including genes related to DNA repair, in autodiploid Physcomitrella plants correlated with a drastic suppression of HR.

Application of Genome Editing in Tomato Breeding: Mechanisms, Advances, and Prospects

Plants regularly face the changing climatic conditions that cause biotic and abiotic stress responses. The abiotic stresses are the primary constraints affecting crop yield and nutritional quality in many crop plants. The advances in genome sequencing and high-throughput approaches have enabled the researchers to use genome editing tools for the functional characterization of many genes useful for crop improvement. The present review focuses on the genome editing tools for improving many traits such as disease resistance, abiotic stress tolerance, yield, quality, and nutritional aspects of tomato. Many candidate genes conferring tolerance to abiotic stresses such as heat, cold, drought, and salinity stress have been successfully manipulated by gene modification and editing techniques such as RNA interference, insertional mutagenesis, and clustered regularly interspaced short palindromic repeat (CRISPR/Cas9). In this regard, the genome editing tools such as CRISPR/Cas9, which is a fast and efficient technology that can be exploited to explore the genetic resources for the improvement of tomato and other crop plants in terms of stress tolerance and nutritional quality. The review presents examples of gene editing responsible for conferring both biotic and abiotic stresses in tomato simultaneously. The literature on using this powerful technology to improve fruit quality, yield, and nutritional aspects in tomato is highlighted. Finally, the prospects and challenges of genome editing, public and political acceptance in tomato are discussed.

Challenges and Perspectives in Homology-Directed Gene Targeting in Monocot Plants

Continuing crop domestication/redomestication and modification is a key determinant of the adaptation and fulfillment of the food requirements of an exploding global population under increasingly challenging conditions such as climate change and the reduction in arable lands. Monocotyledonous crops are not only responsible for approximately 70% of total global crop production, indicating their important roles in human life, but also the first crops to be challenged with the abovementioned hurdles; hence, monocot crops should be the first to be engineered and/or de novo domesticated/redomesticated. A long time has passed since the first green revolution; the world is again facing the challenge of feeding a predicted 9.7 billion people in 2050, since the decline in world hunger was reversed in 2015. One of the major lessons learned from the first green revolution is the importance of novel and advanced trait-carrying crop varieties that are ideally adapted to new agricultural practices. New plant breeding techniques (NPBTs), such as genome editing, could help us succeed in this mission to create novel and advanced crops. Considering the importance of NPBTs in crop genetic improvement, we attempt to summarize and discuss the latest progress with major approaches, such as site-directed mutagenesis using molecular scissors, base editors and especially homology-directed gene targeting (HGT), a very challenging but potentially highly precise genome modification approach in plants. We therefore suggest potential approaches for the improvement of practical HGT, focusing on monocots, and discuss a potential approach for the regulation of genome-edited products.

Genome Editing in Agriculture: Technical and Practical Considerations

The advent of precise genome-editing tools has revolutionized the way we create new plant varieties. Three groups of tools are now available, classified according to their mechanism of action: Programmable sequence-specific nucleases, base-editing enzymes, and oligonucleotides. The corresponding techniques not only lead to different outcomes, but also have implications for the public acceptance and regulatory approval of genome-edited plants. Despite the high efficiency and precision of the tools, there are still major bottlenecks in the generation of new and improved varieties, including the efficient delivery of the genome-editing reagents, the selection of desired events, and the regeneration of intact plants. In this review, we evaluate current delivery and regeneration methods, discuss their suitability for important crop species, and consider the practical aspects of applying the different genome-editing techniques in agriculture.

Roads Forward for European GMO Policy-Uncertainties in Wake of ECJ Judgment Have to be Mitigated by Regulatory Reform

This article gives an overview of legal and procedural uncertainties regarding genome edited organisms and possible ways forward for European GMO policy. After a recent judgment by the European Court of Justice (ECJ judgment of 25 July 2018, C-528/16), organisms obtained by techniques of genome editing are GMOs and subject to the same obligations as transgenic organisms. Uncertainties emerge if genome edited organisms cannot be distinguished from organisms bred by conventional techniques, such as crossing or random mutagenesis. In this case, identical organisms can be subject to either GMO law or exempt from regulation because of the use of a technique that cannot be identified. Regulatory agencies might not be able to enforce GMO law for such cases in the long term. As other jurisdictions do not regulate such organisms as GMOs, accidental imports might occur and undermine European GMO regulation. In the near future, the EU Commission as well as European and national regulatory agencies will decide on how to apply the updated interpretation of the law. In order to mitigate current legal and procedural uncertainties, a first step forward lies in updating all guidance documents to specifically address genome editing specifically address genome editing, including a solution for providing a unique identifier. In part, the authorization procedure for GMO release can be tailored to different types of organisms by making use of existing flexibilities in GMO law. However, only an amendment to the regulations that govern the process of authorization for GMO release can substantially lower the burden for innovators. In a second step, any way forward has to aim at amending, supplementing or replacing the European GMO Directive (2001/18/EC). The policy options presented in this article presuppose political readiness for reform. This may not be realistic in the current political situation. However, if the problems of current GMO law are just ignored, European competitiveness and research in green biotechnology will suffer.

Risk Assessment and Regulation of Plants Modified by Modern Biotechniques: Current Status and Future Challenges

This review describes the current status and future challenges of risk assessment and regulation of plants modified by modern biotechniques, namely genetic engineering and genome editing. It provides a general overview of the biosafety and regulation of genetically modified plants and details different regulatory frameworks with a focus on the European situation. The environmental risk and safety assessment of genetically modified plants is explained, and aspects of toxicological assessments are discussed, especially the controversial debate in Europe on the added scientific value of untargeted animal feeding studies. Because RNA interference (RNAi) is increasingly explored for commercial applications, the risk and safety assessment of RNAi-based genetically modified plants is also elucidated. The production, detection, and identification of genome-edited plants are described. Recent applications of modern biotechniques, namely synthetic biology and gene drives, are discussed, and a short outlook on the future follows.

CRISPR/Cas9-mediated homologous recombination in tobacco

KEY MESSAGE

Co-transformation of multiple T-DNA in a binary vector enabled CRISPR/Cas9-mediated HR in tobacco. HR occurred in a limited region around the gRNA target site. In this study, CRISPR/Cas9-mediated homologous recombination (HR) in tobacco (Nicotiana tabacum L. 'SR-1') was achieved using binary vectors comprising two (T1-T2) or three (T1-T2-T3) independent T-DNA regions. For HR donor with the tobacco acetolactate synthase gene, SuRB, T-DNA1 contained ΔSuRBW568L, which lacked the N-terminus region of SuRB and was created by three nucleotide substitutions (ATG to GCT; W568L), leading to herbicide chlorsulfuron (Cs) resistance, flanked by the hygromycin (Hm)-resistant gene. T-DNA2 consisted of the hSpCas9 gene and two gRNA inserts targeting SuRB and An2. For the 2nd HR donor with the tobacco An2 gene encoding a MYB transcription factor involved in anthocyanin biosynthesis, T-DNA3 had a 35S promoter-driven An2 gene lacking the 3rd exon resulting in anthocyanin accumulation after successful HR. After selecting for Hm and Cs resistance from among the 7462 Agrobacterium-inoculated explants, 77 independent lines were obtained. Among them, the ATG to GCT substitution of endogenous SuRB was detected in eight T1-T2-derived lines and two T1-T2-T3-derived lines. Of these mutations, four T1-T2-derived lines were bi-allelic. All the HR events occurred across the endogenous SuRB and 5' homology arm of the randomly integrated T-DNA1. HR of the SuRB paralog, SuRA, was also found in one of the T1-T2-derived lines. Sequence analysis of its SuRA-targeted region indicated that the HR occurred in a limited (< 153 bp) region around the gRNA target site. Even though some T1-T2-T3-derived lines introduced three different T-DNAs and modified the An2 gRNA target site, no signs of HR in the endogenous An2 could be observed.

Certain new plant breeding techniques and their marketability in the context of EU GMO legislation - recent developments

The comparatively low adoption rate of GMO products in the European Union (EU) market seems to be connected with the strictness of authorization regulations and inefficiency of the authorization process itself. These problems will apply to any product deemed to be a GMO that could potentially be marketable in the EU. Since modern methods of plant breeding involving oligonucleotide-directed mutagenesis (ODMs) or site-directed nucleases (SDNs), including Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), are becoming ever more popular, it is crucial to establish whether the products of such new breeding techniques (NBTs), in particular those which involve precise methods of mutagenesis, are exempted from the EU legislation on GMOs or not. Legal uncertainty as to their status may result in reluctance to invest in such methods and develop them further. Here, developments are presented in the legal classification of certain NBTs products in the context of recent decisions and jurisprudence. The socioeconomic aspects of GMO adoption in both global and European contexts are discussed. The legal and practical landscape of GMO regulation in the EU is presented and how it may pose an obstacle to investment and the development of new products. The latest jurisprudence (e.g., Case C-528/16) [1] on the interpretation of the legal concept of GMOs and the scope of the legislation are analyzed, with the conclusion that the strict regulations will probably also apply to products of the NBTs involving precise methods of mutagenesis. This in turn will probably result in the restriction of their application in the development of new plant varieties in the EU.

DNA Break Repair in Plants and Its Application for Genome Engineering

Genome engineering is a biotechnological approach to precisely modify the genetic code of a given organism in order to change the context of an existing sequence or to create new genetic resources, e.g., for obtaining improved traits or performance. Efficient targeted genome alterations are mainly based on the induction of DNA double-strand breaks (DSBs) or adjacent single-strand breaks (SSBs). Naturally, all organisms continuously have to deal with DNA-damaging factors challenging the genetic integrity, and therefore a wide range of DNA repair mechanisms have evolved. A profound understanding of the different repair pathways is a prerequisite to control and enhance targeted gene modifications. DSB repair can take place by nonhomologous end joining (NHEJ) or homology-dependent repair (HDR). As the main outcome of NHEJ-mediated repair is accompanied by small insertions and deletions, it is applicable to specifically knock out genes or to rearrange linkage groups or whole chromosomes. The basic requirement for HDR is the presence of a homologous template; thus this process can be exploited for targeted integration of ectopic sequences into the plant genome. The development of different types of artificial site-specific nucleases allows for targeted DSB induction in the plant genome. Such synthetic nucleases have been used for both qualitatively studying DSB repair in vivo with respect to mechanistic differences and quantitatively in order to determine the role of key factors for NHEJ and HR, respectively. The conclusions drawn from these studies allow for a better understanding of genome evolution and help identifying synergistic or antagonistic genetic interactions while supporting biotechnological applications for transiently modifying the plant DNA repair machinery in favor of targeted genome engineering.

Pod Shattering: A Homologous Series of Variation Underlying Domestication and an Avenue for Crop Improvement

In wild habitats, fruit dehiscence is a critical strategy for seed dispersal; however, in cultivated crops it is one of the major sources of yield loss. Therefore, indehiscence of fruits, pods, etc., was likely to be one of the first traits strongly selected in crop domestication. Even with the historical selection against dehiscence in early domesticates, it is a trait still targeted in many breeding programs, particularly in minor or underutilized crops. Here, we review dehiscence in pulse (grain legume) crops, which are of growing importance as a source of protein in human and livestock diets, and which have received less attention than cereal crops and the model plant Arabidopsis thaliana. We specifically focus on the (i) history of indehiscence in domestication across legumes, (ii) structures and the mechanisms involved in shattering, (iii) the molecular pathways underlying this important trait, (iv) an overview of the extent of crop losses due to shattering, and the effects of environmental factors on shattering, and, (v) efforts to reduce shattering in crops. While our focus is mainly pulse crops, we also included comparisons to crucifers and cereals because there is extensive research on shattering in these taxa.

Editing the Genome Without Double-Stranded DNA Breaks

Genome editing methods have commonly relied on the initial introduction of double-stranded DNA breaks (DSBs), resulting in stochastic insertions, deletions, and translocations at the target genomic locus. To achieve gene correction, these methods typically require the introduction of exogenous DNA repair templates and low-efficiency homologous recombination processes. In this review, we describe alternative, mechanistically motivated strategies to perform chemistry on the genome of unmodified cells without introducing DSBs. One such strategy, base editing, uses chemical and biological insights to directly and permanently convert one target base pair to another. Despite its recent introduction, base editing has already enabled a number of new capabilities and applications in the genome editing community. We summarize these advances here and discuss the new possibilities that this method has unveiled, concluding with a brief analysis of future prospects for genome and transcriptome editing without double-stranded DNA cleavage.

Relaxed chromatin induced by histone deacetylase inhibitors improves the oligonucleotide-directed gene editing in plant cells

Improving efficiency of oligonucleotide-directed mutagenesis (ODM) is a prerequisite for wide application of this gene-editing approach in plant science and breeding. Here we have tested histone deacetylase inhibitor treatments for induction of relaxed chromatin and for increasing the efficiency of ODM in cultured maize cells. For phenotypic assay we produced transgenic maize cell lines expressing the non-functional Green Fluorescent Protein (mGFP) gene carrying a TAG stop codon. These transgenic cells were bombarded with corrective oligonucleotide as editing reagent to recover GFP expression. Repair of green fluorescent protein function was monitored by confocal fluorescence microscopy and flow cytometry was used for quantification of correction events. Sequencing PCR fragments of the GFP gene from corrected cells indicated a nucleotide exchange in the stop codon (TAG) from T to G nucleotide that resulted in the restoration of GFP function. We show that pretreatment of maize cells with sodium butyrate (5-10 mM) and nicotinamide (1-5 mM) as known inhibitors of histone deacetylases can cause elevated chromatin sensitivity to DNase I that was visualized in agarose gels and confirmed by the reduced presence of intact PCR template for the inserted exogenous mGFP gene. Maize cells with more relaxed chromatin could serve as an improved recipient for targeted nucleotide exchange as indicated by an average of 2.67- to 3.62-fold increase in GFP-positive cells. Our results stimulate further studies on the role of the condition of the recipient cells in ODM and testing the application of chromatin modifying agents in other, programmable nuclease-based genome-editing techniques in higher plants.

Risk associated with off-target plant genome editing and methods for its limitation

Assessment for potential adverse effects of plant genome editing logically focuses on the specific characteristics of the derived phenotype and its release environment. Genome-edited crops, depending on the editing objective, can be classified as either indistinguishable from crops developed through conventional plant breeding or as crops which are transgenic. Therefore, existing regulatory regimes and risk assessment procedures accommodate genome-edited crops. The ability for regulators and the public to accept a product focus in the evaluation of genome-edited crops will depend on research which clarifies the precision of the genome-editing process and evaluates unanticipated off-target edits from the process. Interpretation of genome-wide effects of genome editing should adhere to existing frameworks for comparative risk assessment where the nature and degree of effects are considered relative to a baseline of genome-wide mutations as found in crop varieties developed through conventional breeding methods. Research addressing current uncertainties regarding unintended changes from plant genome editing, and adopting procedures that clearly avoid the potential for gene drive initiation, will help to clarify anticipated public and regulatory questions regarding risk of crops derived through genome editing.

A Standard Methodology to Examine On-site Mutagenicity As a Function of Point Mutation Repair Catalyzed by CRISPR/Cas9 and SsODN in Human Cells

Combinatorial gene editing using CRISPR/Cas9 and single-stranded oligonucleotides is an effective strategy for the correction of single-base point mutations, which often are responsible for a variety of human inherited disorders. Using a well-established cell-based model system, the point mutation of a single-copy mutant eGFP gene integrated into HCT116 cells has been repaired using this combinatorial approach. The analysis of corrected and uncorrected cells reveals both the precision of gene editing and the development of genetic lesions, when indels are created in uncorrected cells in the DNA sequence surrounding the target site. Here, the specific methodology used to analyze this combinatorial approach to the gene editing of a point mutation, coupled with a detailed experimental strategy to measuring indel formation at the target site, is outlined. This protocol outlines a foundational approach and workflow for investigations aimed at developing CRISPR/Cas9-based gene editing for human therapy. The conclusion of this work is that on-site mutagenesis takes place as a result of CRISPR/Cas9 activity during the process of point mutation repair. This work puts in place a standardized methodology to identify the degree of mutagenesis, which should be an important and critical aspect of any approach destined for clinical implementation.

Gene Editing in Polyploid Crops: Wheat, Camelina, Canola, Potato, Cotton, Peanut, Sugar Cane, and Citrus

Polyploid crops make up a significant portion of the major food and fiber crops of the world and include wheat, potato, cotton, apple, peanut, citrus, and brassica oilseeds such as rape, canola, and Camelina. The presence of three sets of chromosomes in triploids, four sets in tetraploids, and six sets in hexaploids present significant challenges to conventional plant breeding and, potentially, to efficient use of rapidly emerging gene and genome-editing systems such as zinc finger nucleases, single-stranded oligonucleotides, TALE effector nucleases, and clustered regularly interspaced short palindromic repeats (CRISPR/Cas9). However, recent studies with each of these techniques in several polyploid crops have demonstrated facile editing of some or all of the genes targeted for modification on homeologous chromosomes. These modifications have allowed improvements in food nutrition, seed oil composition, disease resistance, weed protection, plant breeding procedures, and food safety. Plants and plant products exhibiting useful new traits created through gene editing but lacking foreign DNA may face reduced regulatory restrictions. Such plants can be obtained either by simply selecting for null segregants that have lost their editing transgenes during plant breeding or, even more attractively, by delivery of biodegradable Cas9/sgRNA ribonucleoprotein complexes (i.e., no DNA) into plant cells where they are expressed only transiently but allow for efficient gene editing-a system that has been recently demonstrated in at least two polyploid crops. Such systems that create precise mutations but leave no transgene footprint hold potential promise for assisting with the elimination or great diminution of regulatory processes that presently burden approvals of conventional transgenic crops.

Current and future editing reagent delivery systems for plant genome editing

Many genome editing tools have been developed and new ones are anticipated; some have been extensively applied in plant genetics, biotechnology and breeding, especially the CRISPR/Cas9 system. These technologies have opened up a new era for crop improvement due to their precise editing of user-specified sequences related to agronomic traits. In this review, we will focus on an update of recent developments in the methodologies of editing reagent delivery, and consider the pros and cons of current delivery systems. Finally, we will reflect on possible future directions.

From classical mutagenesis to nuclease-based breeding - directing natural DNA repair for a natural end-product

Production of mutants of crop plants by the use of chemical or physical genotoxins has a long tradition. These factors induce the natural DNA repair machinery to repair damage in an error-prone way. In the case of radiation, multiple double-strand breaks (DSBs) are induced randomly in the genome, leading in very rare cases to a desirable phenotype. In recent years the use of synthetic, site-directed nucleases (SDNs) - also referred to as sequence-specific nucleases - like the CRISPR/Cas system has enabled scientists to use exactly the same naturally occurring DNA repair mechanisms for the controlled induction of genomic changes at pre-defined sites in plant genomes. As these changes are not necessarily associated with the permanent integration of foreign DNA, the obtained organisms per se cannot be regarded as genetically modified as there is no way to distinguish them from natural variants. This applies to changes induced by DSBs as well as single-strand breaks, and involves repair by non-homologous end-joining and homologous recombination. The recent development of SDN-based 'DNA-free' approaches makes mutagenesis strategies in classical breeding indistinguishable from SDN-derived targeted genome modifications, even in regard to current regulatory rules. With the advent of new SDN technologies, much faster and more precise genome editing becomes available at reasonable cost, and potentially without requiring time-consuming deregulation of newly created phenotypes. This review will focus on classical mutagenesis breeding and the application of newly developed SDNs in order to emphasize similarities in the context of the regulatory situation for genetically modified crop plants.

Safety, Security, and Policy Considerations for Plant Genome Editing

Genome editing with engineered nucleases (GEEN) is increasingly used as a tool for gene discovery and trait development in crops through generation of targeted changes in endogenous genes. The development of the CRISPR-Cas9 system (clustered regularly interspaced short palindromic repeats with associated Cas9 protein), in particular, has enabled widespread use of genome editing. Research to date has not comprehensively addressed genome-editing specificity and off-target mismatches that may result in unintended changes within plant genomes or the potential for gene drive initiation. Governance and regulatory considerations for bioengineered crops derived from using GEEN will require greater clarity as to target specificity, the potential for mismatched edits, unanticipated downstream effects of off-target mutations, and assurance that genome reagents do not occur in finished products. Since governance and regulatory decision making involves robust standards of evidence extending from the laboratory to the postcommercial marketplace, developers of genome-edited crops must anticipate significant engagement and investment to address questions of regulators and civil society.

Targeted modification of plant genomes for precision crop breeding

The development of gene targeting and gene editing techniques based on programmable site-directed nucleases (SDNs) has increased the precision of genome modification and made the outcomes more predictable and controllable. These approaches have achieved rapid advances in plant biotechnology, particularly the development of improved crop varieties. Here, we review the range of alterations which have already been implemented in plant genomes, and summarize the reported efficiencies of precise genome modification. Many crop varieties are being developed using SDN technologies and although their regulatory status in the USA is clear there is still a decision pending in the EU. DNA-free genome editing strategies are briefly discussed because they also present a unique regulatory challenge. The potential applications of genome editing in plant breeding and crop improvement are highlighted by drawing examples from the recent literature.

Homology-based double-strand break-induced genome engineering in plants

This review summarises the recent progress in DSB-induced gene targeting by homologous recombination in plants. We are getting closer to efficiently inserting genes or precisely exchanging single amino acids. Although the basic features of double-strand break (DSB)-induced genome engineering were established more than 20 years ago, only in recent years has the technique come into the focus of plant biologists. Today, most scientists apply the recently discovered CRISPR/Cas system for inducing site-specific DSBs in genes of interest to obtain mutations by non-homologous end joining (NHEJ), which is the prevailing and often imprecise mechanism of DSB repair in somatic plant cells. However, predefined changes like the site-specific insertion of foreign genes or an exchange of single amino acids can be achieved by DSB-induced homologous recombination (HR). Although DSB induction drastically enhances the efficiency of HR, the efficiency is still about two orders of magnitude lower than that of NHEJ. Therefore, significant effort have been put forth to improve DSB-induced HR based technologies. This review summarises the previous studies as well as discusses the most recent developments in using the CRISPR/Cas system to improve these processes for plants.

Progress of targeted genome modification approaches in higher plants

Transgene integration in plants is based on illegitimate recombination between non-homologous sequences. The low control of integration site and number of (trans/cis)gene copies might have negative consequences on the expression of transferred genes and their insertion within endogenous coding sequences. The first experiments conducted to use precise homologous recombination for gene integration commenced soon after the first demonstration that transgenic plants could be produced. Modern transgene targeting categories used in plant biology are: (a) homologous recombination-dependent gene targeting; (b) recombinase-mediated site-specific gene integration; (c) oligonucleotide-directed mutagenesis; (d) nuclease-mediated site-specific genome modifications. New tools enable precise gene replacement or stacking with exogenous sequences and targeted mutagenesis of endogeneous sequences. The possibility to engineer chimeric designer nucleases, which are able to target virtually any genomic site, and use them for inducing double-strand breaks in host DNA create new opportunities for both applied plant breeding and functional genomics. CRISPR is the most recent technology available for precise genome editing. Its rapid adoption in biological research is based on its inherent simplicity and efficacy. Its utilization, however, depends on available sequence information, especially for genome-wide analysis. We will review the approaches used for genome modification, specifically those for affecting gene integration and modification in higher plants. For each approach, the advantages and limitations will be noted. We also will speculate on how their actual commercial development and implementation in plant breeding will be affected by governmental regulations.

Oligonucleotide-Mediated Genome Editing Provides Precision and Function to Engineered Nucleases and Antibiotics in Plants

Here, we report a form of oligonucleotide-directed mutagenesis for precision genome editing in plants that uses single-stranded oligonucleotides (ssODNs) to precisely and efficiently generate genome edits at DNA strand lesions made by DNA double strand break reagents. Employing a transgene model in Arabidopsis (Arabidopsis thaliana), we obtained a high frequency of precise targeted genome edits when ssODNs were introduced into protoplasts that were pretreated with the glycopeptide antibiotic phleomycin, a nonspecific DNA double strand breaker. Simultaneous delivery of ssODN and a site-specific DNA double strand breaker, either transcription activator-like effector nucleases (TALENs) or clustered, regularly interspaced, short palindromic repeats (CRISPR/Cas9), resulted in a much greater targeted genome-editing frequency compared with treatment with DNA double strand-breaking reagents alone. Using this site-specific approach, we applied the combination of ssODN and CRISPR/Cas9 to develop an herbicide tolerance trait in flax (Linum usitatissimum) by precisely editing the 5'-ENOLPYRUVYLSHIKIMATE-3-PHOSPHATE SYNTHASE (EPSPS) genes. EPSPS edits occurred at sufficient frequency that we could regenerate whole plants from edited protoplasts without employing selection. These plants were subsequently determined to be tolerant to the herbicide glyphosate in greenhouse spray tests. Progeny (C1) of these plants showed the expected Mendelian segregation of EPSPS edits. Our findings show the enormous potential of using a genome-editing platform for precise, reliable trait development in crop plants.

The Regulatory Status of Genome-edited Crops

Genome editing with engineered nucleases (GEEN) represents a highly specific and efficient tool for crop improvement with the potential to rapidly generate useful novel phenotypes/traits. Genome editing techniques initiate specifically targeted double strand breaks facilitating DNA-repair pathways that lead to base additions or deletions by non-homologous end joining as well as targeted gene replacements or transgene insertions involving homology-directed repair mechanisms. Many of these techniques and the ancillary processes they employ generate phenotypic variation that is indistinguishable from that obtained through natural means or conventional mutagenesis; and therefore, they do not readily fit current definitions of genetically engineered or genetically modified used within most regulatory regimes. Addressing ambiguities regarding the regulatory status of genome editing techniques is critical to their application for development of economically useful crop traits. Continued regulatory focus on the process used, rather than the nature of the novel phenotype developed, results in confusion on the part of regulators, product developers, and the public alike and creates uncertainty as of the use of genome engineering tools for crop improvement.

Oligonucleotide-directed mutagenesis for precision gene editing

Differences in gene sequences, many of which are single nucleotide polymorphisms, underlie some of the most important traits in plants. With humanity facing significant challenges to increase global agricultural productivity, there is an urgent need to accelerate the development of these traits in plants. oligonucleotide-directed mutagenesis (ODM), one of the many tools of Cibus' Rapid Trait Development System (RTDS(™) ) technology, offers a rapid, precise and non-transgenic breeding alternative for trait improvement in agriculture to address this urgent need. This review explores the application of ODM as a precision genome editing technology, with emphasis on using oligonucleotides to make targeted edits in plasmid, episomal and chromosomal DNA of bacterial, fungal, mammalian and plant systems. The process of employing ODM by way of RTDS technology has been improved in many ways by utilizing a fluorescence conversion system wherein a blue fluorescent protein (BFP) can be changed to a green fluorescent protein (GFP) by editing a single nucleotide of the BFP gene (CAC→TAC; H66 to Y66). For example, dependent on oligonucleotide length, applying oligonucleotide-mediated technology to target the BFP transgene in Arabidopsis thaliana protoplasts resulted in up to 0.05% precisely edited GFP loci. Here, the development of traits in commercially relevant plant varieties to improve crop performance by genome editing technologies such as ODM, and by extension RTDS, is reviewed.

Genetic spell-checking: gene editing using single-stranded DNA oligonucleotides

Single-stranded oligonucleotides (ssODNs) can be used to direct the exchange of a single nucleotide or the repair of a single base within the coding region of a gene in a process that is known, generically, as gene editing. These molecules are composed of either all DNA residues or a mixture of RNA and DNA bases and utilize inherent metabolic functions to execute the genetic alteration within the context of a chromosome. The mechanism of action of gene editing is now being elucidated as well as an understanding of its regulatory circuitry, work that has been particularly important in establishing a foundation for designing effective gene editing strategies in plants. Double-strand DNA breakage and the activation of the DNA damage response pathway play key roles in determining the frequency with which gene editing activity takes place. Cellular regulators respond to such damage and their action impacts the success or failure of a particular nucleotide exchange reaction. A consequence of such activation is the natural slowing of replication fork progression, which naturally creates a more open chromatin configuration, thereby increasing access of the oligonucleotide to the DNA template. Herein, how critical reaction parameters influence the effectiveness of gene editing is discussed. Functional interrelationships between DNA damage, the activation of DNA response pathways and the stalling of replication forks are presented in detail as potential targets for increasing the frequency of gene editing by ssODNs in plants and plant cells.

Precise Genome Modification via Sequence-Specific Nucleases-Mediated Gene Targeting for Crop Improvement

Genome editing technologies enable precise modifications of DNA sequences in vivo and offer a great promise for harnessing plant genes in crop improvement. The precise manipulation of plant genomes relies on the induction of DNA double-strand breaks by sequence-specific nucleases (SSNs) to initiate DNA repair reactions that are based on either non-homologous end joining (NHEJ) or homology-directed repair (HDR). While complete knock-outs and loss-of-function mutations generated by NHEJ are very valuable in defining gene functions, their applications in crop improvement are somewhat limited because many agriculturally important traits are conferred by random point mutations or indels at specific loci in either the genes' encoding or promoter regions. Therefore, genome modification through SSNs-mediated HDR for gene targeting (GT) that enables either gene replacement or knock-in will provide an unprecedented ability to facilitate plant breeding by allowing introduction of precise point mutations and new gene functions, or integration of foreign genes at specific and desired "safe" harbor in a predefined manner. The emergence of three programmable SSNs, such as zinc finger nucleases, transcriptional activator-like effector nucleases, and the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems has revolutionized genome modification in plants in a more controlled manner. However, while targeted mutagenesis is becoming routine in plants, the potential of GT technology has not been well realized for traits improvement in crops, mainly due to the fact that NHEJ predominates DNA repair process in somatic cells and competes with the HDR pathway, and thus HDR-mediated GT is a relative rare event in plants. Here, we review recent research findings mainly focusing on development and applications of precise GT in plants using three SSNs systems described above, and the potential mechanisms underlying HDR events in plant cells. We then address the challenges and propose future perspectives in order to facilitate the implementation of precise genome modification through SSNs-mediated GT for crop improvement in a global context.

Gene editing by co-transformation of TALEN and chimeric RNA/DNA oligonucleotides on the rice OsEPSPS gene and the inheritance of mutations

Although several site-specific nucleases (SSNs), such as zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas, have emerged as powerful tools for targeted gene editing in many organisms, to date, gene targeting (GT) in plants remains a formidable challenge. In the present study, we attempted to substitute a single base in situ on the rice OsEPSPS gene by co-transformation of TALEN with chimeric RNA/DNA oligonucleotides (COs), including different strand composition such as RNA/DNA (C1) or DNA/RNA (C2) but contained the same target base to be substituted. In contrast to zero GT event obtained by the co-transformation of TALEN with homologous recombination plasmid (HRP), we obtained one mutant showing target base substitution although accompanied by undesired deletion of 12 bases downstream the target site from the co-transformation of TALEN and C1. In addition to this typical event, we also obtained 16 mutants with different length of base deletions around the target site among 105 calli lines derived from transformation of TALEN alone (4/19) as well as co-transformation of TELAN with either HRP (5/30) or C1 (2/25) or C2 (5/31). Further analysis demonstrated that the homozygous gene-edited mutants without foreign gene insertion could be obtained in one generation. The induced mutations in transgenic generation were also capable to pass to the next generation stably. However, the genotypes of mutants did not segregate normally in T1 population, probably due to lethal mutations. Phenotypic assessments in T1 generation showed that the heterozygous plants with either one or three bases deletion on target sequence, called d1 and d3, were more sensitive to glyphosate and the heterozygous d1 plants had significantly lower seed-setting rate than wild-type.

DNA/RNA chimera templates improve the emission intensity and target the accessibility of silver nanocluster-based sensors for human microRNA detection

In recent years microRNAs (miRNAs) have been established as important biomarkers in a variety of diseases including cancer, diabetes, cardiovascular disease, aging, Alzheimer's disease, asthma, autoimmune disease and liver diseases. As a consequence, a variety of monitoring methods for miRNAs have been developed, including a fast and simple method for miRNA detection by exploitation of the unique photoluminescence of DNA-templated silver nanoclusters (DNA/AgNCs). To increase the versatility of the AgNC-based method, we have adopted DNA/RNA chimera templates for AgNC-based probes, allowing response from several human miRNAs which are hardly detectable with DNA-based probes. Here, we demonstrate in detail the power of DNA/RNA chimera/AgNC probes in detecting two human miRNAs, let-7a and miR-200c. The DNA/RNA chimera-based probes are highly efficient to determine the level of miRNAs in several human cell lines.

Precise plant breeding using new genome editing techniques: opportunities, safety and regulation in the EU

Several new plant breeding techniques (NPBTs) have been developed during the last decade, and make it possible to precisely perform genome modifications in plants. The major problem, other than technical aspects, is the vagueness of regulation concerning these new techniques. Since the definition of eight NPBTs by a European expert group in 2007, there has been an ongoing debate on whether the resulting plants and their products are covered by GMO legislation. Obviously, cover by GMO legislation would severely hamper the use of NPBT, because genetically modified plants must pass a costly and time-consuming GMO approval procedure in the EU. In this review, we compare some of the NPBTs defined by the EU expert group with classical breeding techniques and conventional transgenic plants. The list of NPBTs may be shortened (or extended) during the international discussion process initiated by the Organization for Economic Co-operation and Development. From the scientific point of view, it may be argued that plants developed by NPBTs are often indistinguishable from classically bred plants and are not expected to possess higher risks for health and the environment. In light of the debate on the future regulation of NPBTs and the accumulated evidence on the biosafety of genetically modified plants that have been commercialized and risk-assessed worldwide, it may be suggested that plants modified by crop genetic improvement technologies, including genetic modification, NPBTs or other future techniques, should be evaluated according to the new trait and the resulting end product rather than the technique used to create the new plant variety.

Emerging gene editing strategies for Duchenne muscular dystrophy targeting stem cells

The progressive loss of muscle mass characteristic of many muscular dystrophies impairs the efficacy of most of the gene and molecular therapies currently being pursued for the treatment of those disorders. It is becoming increasingly evident that a therapeutic application, to be effective, needs to target not only mature myofibers, but also muscle progenitors cells or muscle stem cells able to form new muscle tissue and to restore myofibers lost as the result of the diseases or during normal homeostasis so as to guarantee effective and lost lasting effects. Correction of the genetic defect using oligodeoxynucleotides (ODNs) or engineered nucleases holds great potential for the treatment of many of the musculoskeletal disorders. The encouraging results obtained by studying in vitro systems and model organisms have set the groundwork for what is likely to become an emerging field in the area of molecular and regenerative medicine. Furthermore, the ability to isolate and expand from patients various types of muscle progenitor cells capable of committing to the myogenic lineage provides the opportunity to establish cell lines that can be used for transplantation following ex vivo manipulation and expansion. The purpose of this article is to provide a perspective on approaches aimed at correcting the genetic defect using gene editing strategies and currently under development for the treatment of Duchenne muscular dystrophy (DMD), the most sever of the neuromuscular disorders. Emphasis will be placed on describing the potential of using the patient own stem cell as source of transplantation and the challenges that gene editing technologies face in the field of regenerative biology.

An attempt to detect siRNA-mediated genomic DNA modification by artificially induced mismatch siRNA in Arabidopsis

Although tremendous progress has been made in recent years in identifying molecular mechanisms of small interfering RNA (siRNA) functions in higher plants, the possibility of direct interaction between genomic DNA and siRNA remains an enigma. Such an interaction was proposed in the ‘RNA cache’ hypothesis, in which a mutant allele is restored based on template-directed gene conversion. To test this hypothesis, we generated transgenic Arabidopsis thaliana plants conditionally expressing a hairpin dsRNA construct of a mutated acetolactate synthase (mALS) gene coding sequence, which confers chlorsulfuron resistance, in the presence of dexamethasone (DEX). In the transgenic plants, suppression of the endogenous ALS mRNA expression as well as 21-nt mALS siRNA expression was detected after DEX treatment. After screening >100,000 progeny of the mALS siRNA-induced plants, no chlorsulfuron-resistant progeny were obtained. Further experiments using transgenic calli also showed that DEX-induced expression of mALS siRNA did not affect the number of chlorsulfuron-resistant calli. No trace of cytosine methylation of the genomic ALS region corresponding to the dsRNA region was observed in the DEX-treated calli. These results do not necessarily disprove the ‘RNA cache’ hypothesis, but indicate that an RNAi machinery for ALS mRNA suppression does not alter the ALS locus, either genetically or epigenetically.

Deployment of new biotechnologies in plant breeding

The first crops obtained through new plant breeding techniques are close to commercialization. Regulatory issues will determine the adoption of the techniques by breeders.

Modified bases enable high-efficiency oligonucleotide-mediated allelic replacement via mismatch repair evasion

Genome engineering using single-stranded oligonucleotides is an efficient method for generating small chromosomal and episomal modifications in a variety of host organisms. The efficiency of this allelic replacement strategy is highly dependent on avoidance of the endogenous mismatch repair (MMR) machinery. However, global MMR inactivation generally results in significant accumulation of undesired background mutations. Here, we present a novel strategy using oligos containing chemically modified bases (2′-Fluoro-Uridine, 5-Methyl-deoxyCytidine, 2,6-Diaminopurine or Iso-deoxyGuanosine) in place of the standard T, C, A or G to avoid mismatch detection and repair, which we tested in Escherichia coli. This strategy increases transient allelic-replacement efficiencies by up to 20-fold, while maintaining a 100-fold lower background mutation level. We further show that the mismatched bases between the full length oligo and the chromosome are often not incorporated at the target site, probably due to nuclease activity at the 5′ and 3′ termini of the oligo. These results further elucidate the mechanism of oligo-mediated allelic replacement (OMAR) and enable improved methodologies for efficient, large-scale engineering of genomes.