Meeting report of the OECD conference on "Genome Editing: Applications in Agriculture-Implications for Health, Environment and Regulation"

The Potential of CRISPR/Cas9 to Circumvent the Risk Factor Neurotoxin β-N-oxalyl-L-α, β-diaminopropionic acid Limiting Wide Acceptance of the Underutilized Grass Pea (Lathyrus sativus L.)

Grass pea (Lathyrus sativus L.) is a protein-rich crop that is resilient to various abiotic stresses, including drought. However, it is not cultivated widely for human consumption due to the neurotoxin β-N-oxalyl-L-α, β-diaminopropionic acid (β-ODAP) and its association with neurolathyrism. Though some varieties with low β-ODAP have been developed through classical breeding, the β-ODAP content is increasing due to genotype x environment interactions. This review covers grass pea nutritional quality, β-ODAP biosynthesis, mechanism of paralysis, traditional ways to reduce β-ODAP, candidate genes for boosting sulfur-containing amino acids, and the potential and targets of gene editing to reduce β-ODAP content. Recently, two key enzymes (β-ODAP synthase and β-cyanoalanine synthase) have been identified in the biosynthetic pathway of β-ODAP. We proposed four strategies through which the genes encoding these enzymes can be targeted and suppressed using CRISPR/Cas9 gene editing. Compared to its homology in Medicago truncatula, the grass pea β-ODAP synthase gene sequence and β-cyanoalanine synthase showed 62.9% and 95% similarity, respectively. The β-ODAP synthase converts the final intermediate L-DAPA into toxic β-ODAP, whist β-cyanoalanine synthase converts O-Acetylserine into β-isoxazolin-5-on-2-yl-alanine. Since grass pea is low in methionine and cysteine amino acids, improvement of these amino acids is also needed to boost its protein content. This review contains useful resources for grass pea improvement while also offering potential gene editing strategies to lower β-ODAP levels.

Multi-faceted CRISPR-Cas9 strategy to reduce plant based food loss and waste for sustainable bio-economy - A review

Currently, international development requires innovative solutions to address imminent challenges like climate change, unsustainable food system, food waste, energy crisis, and environmental degradation. All the same, addressing these concerns with conventional technologies is time-consuming, causes harmful environmental impacts, and is not cost-effective. Thus, biotechnological tools become imperative for enhancing food and energy resilience through eco-friendly bio-based products by valorisation of plant and food waste to meet the goals of circular bioeconomy in conjunction with Sustainable Developmental Goals (SDGs). Genome editing can be accomplished using a revolutionary DNA modification tool, CRISPR-Cas9, through its uncomplicated guided mechanism, with great efficiency in various organisms targeting different traits. This review's main objective is to examine how the CRISPR-Cas system, which has positive features, could improve the bioeconomy by reducing food loss and waste with all-inclusive food supply chain both at on-farm and off-farm level; utilising food loss and waste by genome edited microorganisms through food valorisation; efficient microbial conversion of low-cost substrates as biofuel; valorisation of agro-industrial wastes; mitigating greenhouse gas emissions through forestry plantation crops; and protecting the ecosystem and environment. Finally, the ethical implications and regulatory issues that are related to CRISPR-Cas edited products in the international markets have also been taken into consideration.

Are null segregants new combinations of heritable material and should they be regulated?

Through genome editing and other techniques of gene technology, it is possible to create a class of organism called null segregants. These genetically modified organisms (GMOs) are products of gene technology but are argued to have no lingering vestige of the technology after the segregation of chromosomes or deletion of insertions. From that viewpoint regulations are redundant because any unique potential for the use of gene technology to cause harm has also been removed. We tackle this question of international interest by reviewing the early history of the purpose of gene technology regulation. The active ingredients of techniques used for guided mutagenesis, e.g., site-directed nucleases, such as CRISPR/Cas, are promoted for having a lower potential per reaction to create a hazard. However, others see this as a desirable industrial property of the reagents that will lead to genome editing being used more and nullifying the promised hazard mitigation. The contest between views revolves around whether regulations could alter the risks in the responsible use of gene technology. We conclude that gene technology, even when used to make null segregants, has characteristics that make regulation a reasonable option for mitigating potential harm. Those characteristics are that it allows people to create more harm faster, even if it creates benefits as well; the potential for harm increases with increased use of the technique, but safety does not; and regulations can control harm scaling.

Japanese Regulatory Framework and Approach for Genome-edited Foods Based on Latest Scientific Findings

The food supply system is facing important challenges and its sustainability has to be considered. Genome-editing technology, which accelerates the development of new variety, could be used to achieve sustainable development goals, thereby protecting the environment and ensuring the stable production of food for an increasing global population. The most widely used genome-editing tool, CRISPR/Cas9, is easy to use, affordable, and versatile. Foods produced by genome-editing technologies have been developed worldwide to create novel traits. In the first half of the review, the latest scientific findings on genome-editing technologies are summarized, and the technical challenge in genome sequence analysis are clarified. CRISPR/Cas9 has versatile alternative techniques, such as base editor and prime editor. Genome sequencing technology has developed rapidly in recent years. However, it is still difficult to detect large deletions and structural variations. Long-read sequencing technology would solve this challenge. In the second part, regulatory framework and approach for genome-edited foods is introduced. The four government ministries, including the Ministry of Environment, the Ministry of Agriculture, Forestry and Fisheries, and the Ministry of Health, Labour and Welfare (MHLW), started to discuss how the regulation should be implemented in 2019. The SDN-1 technique is excluded from the current genetically modified organism (GMO) regulation. The Japanese regulatory framework includes pre-submission consultation and submission of notification form. In the last part of this review, transparency of regulatory framework and consumer confidence were described. Since maintaining consumer trust is vital, transparency of regulatory framework is a key to consumers. The information of notification process on approved genome-edited foods is made public immediately. This review will help regulators build regulatory frameworks, and lead to harmonization of the framework between the countries.

Canadian Consumer Preferences Regarding Gene-Edited Food Products

Innovations in food production and processing have largely remained “behind the scenes” for decades. The current nature of social media and calls for increased transparency regarding food results in a new landscape where consumer product demands are more important than ever, but are increasingly based on limited, or incorrect, information. One area where consumer awareness is rapidly emerging is the area of gene-edited food products. This article uses a consumer survey to gather perceptions regarding food safety, gene editing and willingness to consume for three gene-edited food products. Four factors were found to strongly influence consumer perceptions: trust in the Canadian food safety system; food technology neophobia scores; knowledge of genetics; and self-knowledge of gene editing. The survey of 497 Canadians found that 15% identified as neophobics and 12% as neophilics. The majority of participants identified as neutral. When presented with various food values, participants indicated that nutrition, price, and taste were the three most important values. A participants’ willingness to consume gene-edited food products strongly correlated with neophobic and neophilic preferences, with neophobics unwilling to consume and neophilics being uncertain. The only food value that strongly affects consumer willingness to consume is the environmental impact of a products’ production. Canadian consumers have a moderate to high level of trust in Canada’s food safety system, but this level of trust fails to carry over to food products produced through innovative technologies; however, consumers express a higher level of trust in gene-edited technology than genetically modified technology.

Contributions of Genome Editing Technologies Towards Improved Nutrition, Environmental Sustainability and Poverty Reduction

The Sustainable Development Goals (SDGs) were launched in 2015, with the top three goals being poverty eradication, improved food security and increased human health. All 17 SDGs have a target achievement date of 2030. These are ambitious and inspirational goals that require substantial innovation and technology adoption for successful achievement. Innovations in plant breeding have substantially contributed to transforming the efficiency of food production since the mid 20th century, with innovations emerging in the current millennium demonstrating enhanced potential to improve crop yields, the nutritional values of food crops and environmental impacts. These outcomes underpin several SDGs, but in particular the first three. As climate change is expected to become increasingly variable, with greater impacts on agriculture, the ability to ensure increased food production is going to be increasingly important, as higher yields directly contribute to reducing poverty. This article reviews recent reports of potential contributions from genome editing technologies in terms of increased yield, enhanced nutrition and greater sustainability, highlighting their importance for achieving the leading three SDGs.

Advances in Understanding and Harnessing the Molecular Regulatory Mechanisms of Vegetable Quality

The quality of vegetables is facing new demands in terms of diversity and nutritional health. Given the improvements in living standards and the quality of consumed products, consumers are looking for vegetable products that maintain their nutrition, taste, and visual qualities. These requirements are directing scientists to focus on vegetable quality in breeding research. Thus, in recent years, research on vegetable quality has been widely carried out, and many applications have been developed via gene manipulation. In general, vegetable quality traits can be divided into three parts. First, commodity quality, which is most related to the commerciality of plants, refers to the appearance of the product. The second is flavor quality, which usually represents the texture and flavor of vegetables. Third, nutritional quality mainly refers to the contents of nutrients and health ingredients such as soluble solids (sugar), vitamin C, and minerals needed by humans. With biotechnological development, researchers can use gene manipulation technologies, such as molecular markers, transgenes and gene editing to improve the quality of vegetables. This review attempts to summarize recent studies on major vegetable crops species, with Brassicaceae, Solanaceae, and Cucurbitaceae as examples, to analyze the present situation of vegetable quality with the development of modern agriculture.

Regulatory and Policy Considerations Around Genome Editing in Agriculture

The increasingly widespread use of genome editing brought with it a fierce debate about the most adequate regulation of this latest innovation in modern biotechnology and the products resulting from it. In almost all cases, this debate has become a repetition or continuation of the deliberations concerning genetically modified organisms (GMOs) of the 1990s and early 2000s.This chapter aims to untangle the historically influenced and often biased arguments of the debates by addressing the complex question of the correct interpretation of relevant underlying law and its applicability. In doing so, the chapter considers 25 countries and regions that have published results or ongoing investigations and discussions pertaining to the governance of genome editing in their jurisdictions: 16 have published policies or signed statements that exempt gene edited plants from GMO-regulations, as long as no foreign DNA or transgene remained in the final product. Such exemptions are based on the widely supported acceptance that the products of the underlying genome editing processes resemble those of "conventional breeding" techniques. These policies and statements often refer to the important role that modern precision biotechnologies, of which genome editing is one, play in addressing some of the world's overarching challenges, such as the loss of biodiversity, pest and disease control, and climate change; they are furthermore shown to exhibit an adherence to the four universal principles of good regulation: (a) proportionality, (b) non-discrimination, (c) predictability, and (d) enforceability. And while it is the right of jurisdictions to develop their own regulations independent from that of their neighbors, it is specifically the principle of "enforceability" that may become the ultimate litmus test of those regulations that do not grant exemptions from GMO-regulations.

Regulatory Barriers to Innovative Plant Breeding in Canada

The regulation of plant breeding is gaining increasing scrutiny, particularly as it pertains to the regulation of gene editing and other new breeding technologies. Genome editing is used worldwide in both public and private plant breeding laboratories and there is considerable uncertainty about the ability of regulatory agencies to match the rapid scientific pace being set. This research focuses on Canada, where advances in plant breeding technology are constrained by the boundaries of the regulatory system established in the early 1990's. This research presents the results of a survey of 93 public and private plant breeders and their views on the existing Canadian regulatory framework regarding conventional breeding and genome editing techniques for plants with novel traits (PNTs). The results contribute to the ongoing debate regarding how, or whether, to regulate products of genome-edited plant breeding, beyond the existing agronomic and safety requirements. Plant breeders identify the level of Canadian crop research competitiveness and quantify the impacts of novelty within Canada's regulatory system for PNTs. One significant finding is that PNT regulations in Canada have created an innovation barrier in terms of applying genome editing technologies to the development of new varieties, particularly in public sector research.

Genome editing for resistance against plant pests and pathogens

The conventional breeding of crops struggles to keep up with increasing food needs and ever-adapting pests and pathogens. Global climate changes have imposed another layer of complexity to biological systems, increasing the challenge to obtain improved crop cultivars. These dictate the development and application of novel technologies, like genome editing (GE), that assist targeted and fast breeding programs in crops, with enhanced resistance to pests and pathogens. GE does not require crossings, hence avoiding the introduction of undesirable traits through linkage in elite varieties, speeding up the whole breeding process. Additionally, GE technologies can improve plant protection by directly targeting plant susceptibility (S) genes or virulence factors of pests and pathogens, either through the direct edition of the pest genome or by adding the GE machinery to the plant genome or to microorganisms functioning as biocontrol agents (BCAs). Over the years, GE technology has been continuously evolving and more so with the development of CRISPR/Cas. Here we review the latest advancements of GE to improve plant protection, focusing on CRISPR/Cas-based genome edition of crops and pests and pathogens. We discuss how other technologies, such as host-induced gene silencing (HIGS) and the use of BCAs could benefit from CRISPR/Cas to accelerate the development of green strategies to promote a sustainable agriculture in the future.

CRISPR-Cas9 Application in Canadian Public and Private Plant Breeding

Plant-breeding technologies have expanded, accelerating breeding research beyond the confines of current regulations. The application of genome editing, such as CRISPR-Cas9, do not neatly fit into existing regulatory frameworks, creating uncertainty as to whether they can be regarded as conventionally developed varieties without further regulation. This research presents the current views of Canadian plant breeders based on a national survey of plant breeders. There is evidence that a review of existing regulations is required, as >60% anticipate the use of genome-editing technologies in the next few years. This paper reviews plant-breeding practices under the context of present plants with novel trait (PNT) regulations and where plant breeders place the use of CRISPR-Cas9 within the suite of available genome-editing options. This paper establishes when and why, or why not, breeders choose to introduce CRISPR-Cas9 into their research over other plant-breeding applications.

CRISPR/Cas systems: opportunities and challenges for crop breeding

Increasing crop production to meet the demands of a growing population depends largely on crop improvement through new plant-breeding techniques (NPBT) such as genome editing. CRISPR/Cas systems are NPBTs that enable efficient target-specific gene editing in crops, which is supposed to accelerate crop breeding in a way that is different from genetically modified (GM) technology. Herein, we review the applications of CRISPR/Cas systems in crop breeding focusing on crop domestication, heterosis, haploid induction, and synthetic biology, and summarize the screening methods of CRISPR/Cas-induced mutations in crops. We highlight the importance of molecular characterization of CRISPR/Cas-edited crops, and pay special attentions to emerging highly specific genome-editing tools such as base editors and prime editors. We also discuss future improvements of CRISPR/Cas systems for crop improvement.

Biotechnology and Biosafety Policy at OECD: Future Trends

The OECD Council Recommendation on Recombinant DNA Safety Considerations is a legal instrument which has been in force since 1986. It outlines the safety assessment practices that countries should have in place for agricultural and environmental biotechnology. This article suggests possible updates to make it suitable for the modern era.

Designing future crops: challenges and strategies for sustainable agriculture

Crop production is facing unprecedented challenges. Despite the fact that the food supply has significantly increased over the past half-century, ~8.9 and 14.3% people are still suffering from hunger and malnutrition, respectively. Agricultural environments are continuously threatened by a booming world population, a shortage of arable land, and rapid changes in climate. To ensure food and ecosystem security, there is a need to design future crops for sustainable agriculture development by maximizing net production and minimalizing undesirable effects on the environment. The future crops design projects, recently launched by the National Natural Science Foundation of China and Chinese Academy of Sciences (CAS), aim to develop a roadmap for rapid design of customized future crops using cutting-edge technologies in the Breeding 4.0 era. In this perspective, we first introduce the background and missions of these projects. We then outline strategies to design future crops, such as improvement of current well-cultivated crops, de novo domestication of wild species and redomestication of current cultivated crops. We further discuss how these ambitious goals can be achieved by the recent development of new integrative omics tools, advanced genome-editing tools and synthetic biology approaches. Finally, we summarize related opportunities and challenges in these projects.

Regulatory barriers to improving global food security

Crop agriculture and food production constantly face climactic challenges to the supply of safe, nutritious food. These challenges highlight the importance of innovation resulting in improved crop technologies, capable of providing consistently increasing yields in the face of abiotic and biotic stresses. This article addresses the challenge that regulatory barriers are, and can, have on the adoption of innovative crop and food technologies that improve food security. Evidence of increased crop yield and the potential for increased yields, are presented from innovative plant breeding technologies, especially gene editing. Recent advances from the use of gene editing in the pharmaceutical field may offer opportunities to reduce regulatory burdens.

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The EU regulatory framework for GM crops is in gridlock with no signs of ending.

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The CJEU 2018 gene editing ruling has resulted in a decline in EU R&D investment.

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Gene editing regulation in the EU will have spillover effects in Africa and Asia.

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Covid-19 vaccines may require regulation as equivalent to GMOs, delaying approval.

How should we regulate products of new breeding techniques? Opinion of surveyed experts in plant biotechnology

The adoption of genome editing depends among others, on a clear and navigable regulatory framework that renders consistent decisions. Some countries like the United States decided to deregulate specific transgene-free genome edited products that could be created through traditional breeding and are not considered to be plant pests, while others are still challenged to fit emerging technologies in their regulatory system. Here we poll international experts in plant biotechnology on what approach should nations agree upon to accommodate current and future new breeding technologies and derived products. A key finding is product-based models or dual-product/process systems are viewed as potential appropriate frameworks to regulate outcomes of genome editing. As regulation of novel products of biotechnology is expected to impact research and trade, we test the impact of experts' worldviews on these issues. Results show that region influences worldviews of trade but not of agricultural innovation. In contrast, there was no effect of experts' worldviews on how products of novel biotechnologies should be regulated.

Principles, Applications, and Biosafety of Plant Genome Editing Using CRISPR-Cas9

The terms genome engineering, genome editing, and gene editing, refer to modifications (insertions, deletions, substitutions) in the genome of a living organism. The most widely used approach to genome editing nowadays is based on Clustered Regularly Interspaced Short Palindromic Repeats and associated protein 9 (CRISPR-Cas9). In prokaryotes, CRISPR-Cas9 is an adaptive immune system that naturally protects cells from DNA virus infections. CRISPR-Cas9 has been modified to create a versatile genome editing technology that has a wide diversity of applications in medicine, agriculture, and basic studies of gene functions. CRISPR-Cas9 has been used in a growing number of monocot and dicot plant species to enhance yield, quality, and nutritional value, to introduce or enhance tolerance to biotic and abiotic stresses, among other applications. Although biosafety concerns remain, genome editing is a promising technology with potential to contribute to food production for the benefit of the growing human population. Here, we review the principles, current advances and applications of CRISPR-Cas9-based gene editing in crop improvement. We also address biosafety concerns and show that humans have been exposed to Cas9 protein homologues long before the use of CRISPR-Cas9 in genome editing.

Improving Nutritional and Functional Quality by Genome Editing of Crops: Status and Perspectives

Genome-editing tools including meganucleases, zinc finger nucleases, transcription activator-like effector nucleases and clustered regularly interspaced short palindromic repeats (CRISPR) system have been applied to improve the quality of staple, oilseed, and horticultural crops with great accuracy and efficiency compared to conventional breeding. In particular, the CRISPR method has proven to be a feasible, cost-effective and versatile tool allowing precise and efficient editing of plant genomes in recent years, showing great potential in crop improvement. Until now, various genome-edited crops with enhanced commercial value have been developed by not only global companies but also small laboratories in universities, suggesting low entry barriers with respect to manpower and capital. In this study, we review the current applications of genome editing technologies to improve the nutritional and functional quality and preferred traits of various crops. Combining this rapidly advancing genome-editing technology and conventional breeding will greatly extend the potential of genome-edited crops and their commercialization.

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.