Gene-edited Crops Research Articles

Gene Editing for Disease Resistance in Crops: Success Stories and Challenges

Gene editing has emerged as a transformative tool in modern agriculture, offering new avenues for enhancing disease resistance in crops. By precisely modifying the DNA of plants, scientists can develop varieties that are better equipped to withstand the onslaught of pathogens, which pose significant threats to global food security. This article delves into the success stories and challenges associated with gene editing for disease resistance in crops, with a focus on technologies like CRISPR-Cas9, TALENs, and ZFNs. One of the major success stories in this field is the development of disease-resistant varieties of wheat, rice, and tomatoes. For instance, researchers have used CRISPR-Cas9 to create wheat varieties resistant to powdery mildew, a devastating fungal disease. Similarly, gene editing has enabled the development of rice strains with enhanced resistance to bacterial blight, a disease that can lead to significant yield losses. In tomatoes, gene editing has been employed to confer resistance against the Tomato Yellow Leaf Curl Virus, which severely affects tomato production worldwide. These achievements underscore the potential of gene editing to create crops that are not only more resilient but also capable of maintaining high yields under disease pressure. However, the application of gene editing in crop disease resistance is not without challenges. One of the primary concerns is the regulatory landscape, which varies significantly across different countries. While some nations have embraced gene-edited crops, others have imposed strict regulations, treating them similarly to genetically modified organisms (GMOs). This inconsistency can hinder the global deployment of disease-resistant crops and create trade barriers. Additionally, there are concerns related to off-target effects, where unintended changes in the genome may occur, potentially leading to unintended consequences in the plant's growth or ecological interactions.

Environmental impacts of genetically modified crops.

Genetically modified (GM) crops have been adopted by some of the world's leading agricultural nations, but the full extent of their environmental impact remains largely unknown. Although concerns regarding the direct environmental effects of GM crops have declined, GM crops have led to indirect changes in agricultural practices, including pesticide use, agricultural expansion, and cropping patterns, with profound environmental implications. Recent studies paint a nuanced picture of these environmental impacts, with mixed effects of GM crop adoption on biodiversity, deforestation, and human health that vary with the GM trait and geographic scale. New GM or gene-edited crops with different traits would likely have different environmental and human health impacts.

Editing of SlWRKY29 by CRISPR-activation promotes somatic embryogenesis in Solanum lycopersicum cv. Micro-Tom.

At present, the development of plants with improved traits like superior quality, high yield, or stress resistance, are highly desirable in agriculture. Accelerated crop improvement, however, must capitalize on revolutionary new plant breeding technologies, like genetically modified and gene-edited crops, to heighten food crop traits. Genome editing still faces ineffective methods for the transformation and regeneration of different plant species and must surpass the genotype dependency of the transformation process. Tomato is considered an alternative plant model system to rice and Arabidopsis, and a model organism for fleshy-fruited plants. Furthermore, tomato cultivars like Micro-Tom are excellent models for tomato research due to its short life cycle, small size, and capacity to grow at high density. Therefore, we developed an indirect somatic embryo protocol from cotyledonary tomato explants and used this to generate epigenetically edited tomato plants for the SlWRKY29 gene via CRISPR-activation (CRISPRa). We found that epigenetic reprogramming for SlWRKY29 establishes a transcriptionally permissive chromatin state, as determined by an enrichment of the H3K4me3 mark. A whole transcriptome analysis of CRISPRa-edited pro-embryogenic masses and mature somatic embryos allowed us to characterize the mechanism driving somatic embryo induction in the edited tomato cv. Micro-Tom. Furthermore, we show that enhanced embryo induction and maturation are influenced by the transcriptional effector employed during CRISPRa, as well as by the medium composition and in vitro environmental conditions such as osmotic components, plant growth regulators, and light intensity.

Fields of contestation and contamination: Maize seeds, agroecology and the (de)coloniality of agriculture in Malawi and South Africa

Farmer-managed seed systems and the conservation of agrobiodiversity are increasingly recognized as important components of food and seed sovereignty. In contrast, hybrid, genetically modified (GM), and, increasingly, gene-edited crops continue to be promoted by Green Revolution proponents as a “climate smart” package that includes fertilizers, pesticides, purchased seeds, and links to global markets. Influencing seed laws and policies to support the uptake of modern crop varieties has been a key entry point in many countries, facilitated by networks of foreign donors, philanthropists, governments, and multinational companies. Using the case of South Africa, where GM crops have been grown for several decades, we provide insights on implications for Malawi, which passed a Seed Act in 2022, implicitly supporting GM crops. Both countries have histories of colonial agriculture with strong policy support for modern, hybrid varieties of maize, and the replacement (and displacement) of local, open-pollinated maize varieties. In South Africa, several studies have revealed the contamination of smallholder fields and seed systems. Through a political ecology lens, we explore how maize and its cotechnologies were commodified in South Africa and Malawi, and what South African experiences of GM crop adoption in smallholder farming systems can tell us about the challenges to be faced by smallholder Malawian farmers. We reveal how colonial histories and ongoing colonialities of power, knowledge, being, and nature continue to shape the character and form of agriculture in both countries, running counter to the needs of agroecological smallholder farmers and their ways of knowing and being. We conclude by envisioning what reimagined, transformed and decolonial approaches for food and agriculture might look like on the African continent, and how they might contribute toward the attainment of food and seed sovereignty and an agroecological future.

CRISPR Variants for Gene Editing in Plants: Biosafety Risks and Future Directions.

The CRISPR genome editing technology is a crucial tool for enabling revolutionary advancements in plant genetic improvement. This review shows the latest developments in CRISPR/Cas9 genome editing system variants, discussing their benefits and limitations for plant improvement. While this technology presents immense opportunities for plant breeding, it also raises serious biosafety concerns that require careful consideration, including potential off-target effects and the unintended transfer of modified genes to other organisms. This paper highlights strategies to mitigate biosafety risks and explores innovative plant gene editing detection methods. Our review investigates the international biosafety guidelines for gene-edited crops, analyzing their broad implications for agricultural and biotechnology research and advancement. We hope to provide illuminating and refined perspectives for industry practitioners and policymakers by evaluating CRISPR genome enhancement in plants.

Qualitative and Quantitative Detection of CRISPR-Associated Cas Gene in Gene-Edited Foods.

Effective regulation of gene-edited products and resolution of public concerns are the prerequisites for the industrialization of gene-edited crops and their derived foods. CRISPR-associated protein, the core element of the CRISPR system, requires to be regulated. Thus, there is an urgent need to establish qualitative and quantitative detection methods for the Cas gene. In the present study, the primers and probes were designed and screened for Cas12a (Cpf1), which is the most commonly used target site in gene editing; we performed PCR system optimization, determined the optimal primer concentration and annealing temperature, and established qualitative PCR and quantitative PCR (qPCR) assays for detecting Cpf1 in gene editing by specificity and sensitivity tests. In specificity testing, qualitative PCR and qPCR methods could 100% detect samples containing Cpf1 DNA, while the detection rate of other samples without Cpf1 was 0%. In the assay sensitivity test, the limit of detection of qualitative PCR was 0.1% (approximately 44 copies), and the limit of detection of the qPCR method was 14 copies. In the stability test, both the qualitative PCR and qPCR methods were repeated 60 times at their corresponding lowest detection limit concentrations, and the results were positive. Thus, the qualitative and quantitative assays for Cpf1 are specific, sensitive, and stable. The method provides technical support for the effective monitoring of gene-edited products and their derived foods in the future.

Environmental Stimuli: A Major Challenge during Grain Filling in Cereals.

Light, temperature, water, and fertilizer are arguably the most important environmental factors regulating crop growth and productivity. Environmental stimuli, including low light, extreme temperatures, and water stresses caused by climate change, affect crop growth and production and pose a growing threat to sustainable agriculture. Furthermore, soil salinity is another major environmental constraint affecting crop growth and threatening global food security. The grain filling stage is the final stage of growth and is also the most important stage in cereals, directly determining the grain weight and final yield. However, the grain filling process is extremely vulnerable to different environmental stimuli, especially for inferior spikelets. Given the importance of grain filling in cereals and the deterioration of environmental problems, understanding environmental stimuli and their effects on grain filling constitutes a major focus of crop research. In recent years, significant advances made in this field have led to a good description of the intricate mechanisms by which different environmental stimuli regulate grain filling, as well as approaches to adapt cereals to changing climate conditions and to give them better grain filling. In this review, the current environmental stimuli, their dose-response effect on grain filling, and the physiological and molecular mechanisms involved are discussed. Furthermore, what we can do to help cereal crops adapt to environmental stimuli is elaborated. Overall, we call for future research to delve deeper into the gene function-related research and the commercialization of gene-edited crops. Meanwhile, smart agriculture is the development trend of the future agriculture under environmental stimuli.

Review of CRISPR/Cas Systems on Detection of Nucleotide Sequences.

Nowadays, with the rapid development of biotechnology, the CRISPR/Cas technology in particular has produced many new traits and products. Therefore, rapid and high-resolution detection methods for biotechnology products are urgently needed, which is extremely important for safety regulation. Recently, in addition to being gene editing tools, CRISPR/Cas systems have also been used in detection of various targets. CRISPR/Cas systems can be successfully used to detect nucleic acids, proteins, metal ions and others in combination with a variety of technologies, with great application prospects in the future. However, there are still some challenges need to be addressed. In this review, we will list some detection methods of genetically modified (GM) crops, gene-edited crops and single-nucleotide polymorphisms (SNPs) based on CRISPR/Cas systems, hoping to bring some inspiration or ideas to readers.

Bibliometric Analysis of Functional Crops and Nutritional Quality: Identification of Gene Resources to Improve Crop Nutritional Quality through Gene Editing Technology.

Food security and hidden hunger are two worldwide serious and complex challenges nowadays. As one of the newly emerged technologies, gene editing technology and its application to crop improvement offers the possibility to relieve the pressure of food security and nutrient needs. In this paper, we analyzed the research status of quality improvement based on gene editing using four major crops, including rice, soybean, maize, and wheat, through a bibliometric analysis. The research hotspots now focus on the regulatory network of related traits, quite different from the technical improvements to gene editing in the early stage, while the trends in deregulation in gene-edited crops have accelerated related research. Then, we mined quality-related genes that can be edited to develop functional crops, including 16 genes related to starch, 15 to lipids, 14 to proteins, and 15 to other functional components. These findings will provide useful reference information and gene resources for the improvement of functional crops and nutritional quality based on gene editing technology.

Governing gene-edited crops: risks, regulations, and responsibilities as perceived by agricultural genomics experts in Canada

ABSTRACT This paper explores the role and responsibilities of agricultural genomics experts in governing gene editing (GE) for food and agriculture, engaging with the frameworks of technological determinism and Responsible Research and Innovation (RRI). We interview agricultural genomics experts in Canada to study expert views on risks, benefits, and regulatory challenges of GE crops and the extent to which agricultural genomics experts exercise the RRI principles of anticipation, reflexivity, deliberative inclusion, and responsiveness. Agricultural genomics experts wield power in food systems both in shaping the applications of technology and as advisers influencing policy and governance. Their resistance to RRI principles, especially deliberative inclusion and responsiveness, and exercises of discursive closure are challenges for responsible governance of GE crops. The study offers empirical and theoretical contributions, working across Science and Technology Studies and food systems research.

The evolution of China's regulation of agricultural biotechnology.

To ensure safe use of genetically modified organisms (GMOs), since 1993, China has made great efforts to establish and improve the safety regulatory system for GMOs. Here, we summarize and analyze the regulatory framework of agricultural GMOs, and the progress in regulatory approval of GM crops in China. In general, the development of GMO safety regulations underwent four stages: exploration (1993-2000), development (2001-2010), improvement (2011-2020) and current (2021-present) stage. The first formal regulation was promulgated in 1993, which provided a basis for further development of the regulations, during the exploration stage, when insect-resistant GM cotton, expressing genes from Bacillus thuringiensis (Bt), was approved for cultivation. During the development stage, the Chinese government issued a series of administrative measures, which covered almost all the fields relative to GMO safety when the basic regulatory system was established. Along with the controversy over GMO safety, the regulations have been further, and greatly improved, during improvement stage. From 2021, a few additional revisions have been made, and meanwhile, the new regulation on gene-edited crops was introduced with the development of biotechnology, forming a relative complete regulation and law system for China. The well-developed GMO regulations establishes a firm basis for safe use of GM crops in China. Currently, GM cotton and GM papaya have been widely grown on a large scale in China that have brought great economic and ecological benefits. In addition, 12 corn events, 3 soybean events, and 2 rice events have also obtained biosafety certification, but presently, these lines have yet to enter commercial production. However, several GM soybean and corn events have entered pilot industrialization, and can soon be expected to be commercially grown in China. In addition to planting, six GM crops, including soybean, corn, cotton, canola, papaya and sugar beet, with a total of 64 events, have been approved for import as processing material in China.

Managers’ attitudes toward gene-editing technology and companies’ R&D investment in gene-editing: the case of Chinese seed companies

ABSTRACT The Chinese government has issued a series of new policies to make it easier to industrialize gene-edited crops. However, whether technological advantages will eventually translate into industrial advantages and whether farmers will soon have access to gene-edited varieties partly depends on seed companies’ willingness to produce and sell gene-edited varieties to farmers and to invest in developing their own gene-edited varieties. This study utilizes data from a survey of 111 seed companies collected in 2019 before the implementation of new regulations. This study provides empirical evidence on whether gene-edited crops will be available to farmers. The results show that the number of companies conducting research on gene-edited crops is limited, mostly to large companies. Approximately 55% of seed company managers would consider developing and selling gene-edited crops modified by SDN-1 and SDN-2 site-directed nuclease genome editing without external genetic material, whereas 46% support crops modified by SDN-3, which require gene replacement or foreign deoxyribonucleic acid (DNA) insertion and are regulated as genetically modified organisms (GMOs). The regression results show that large companies and companies with well-educated researchers are more likely to support and develop gene-editing technology. Past GM investment experience and collaboration with public institutions in gene-editing research increases the probability of company investment in gene editing R&D. These results suggest that gene-edited cultivars are more likely to be produced and sold to farmers in the future than GMOs, and that gene-edited agricultural products could have a significant market share of the seed market in the future.

Editing the genome of common cereals (Rice and Wheat): techniques, applications, and industrial aspects.

Gene editing techniques have made a significant contribution to the development of better crops. Gene editing enables precise changes in the genome of crops, which can introduce new possibilities for altering the crops' traits. Since the last three decades, various gene editing techniques such as meganucleases, zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and clustered regularly interspersed short palindromic repeats (CRISPR)/Cas (CRISPR-associated proteins) have been discovered. In this review, we discuss various gene editing techniques and their applications to common cereals. Further, we elucidate the future of gene-edited crops, their regulatory features, and industrial aspects globally. To achieve this, we perform a comprehensive literature survey using databases such as PubMed, Web of Science, SCOPUS, Google Scholar etc. For the literature search, we used keywords such as gene editing, crop genome modification, CRISPR/Cas, ZFN, TALEN, meganucleases etc. With the advent of the CRISPR/Cas technology in the last decade, the future of gene editing has transitioned into a new dimension. The functionality of CRISPR/Cas in both DNA and RNA has increased through the use of various Cas enzymes and their orthologs. Constant research efforts in this direction have improved the gene editing process for crops by minimizing its off-target effects. Scientists also use computational tools, which help them to design experiments and analyze the results of gene editing experiments in advance. Gene editing has diverse potential applications. In the future, gene editing will open new avenues for solving more agricultural issues and boosting crop production, which may have great industrial prospects.

Public Perceptions of Risks and Benefits of Gene-edited Food Crops: An International Comparative Study between the US, Japan, and Germany

This study statistically explored public perceptions of the risks and benefits of the agricultural application of gene editing to food crops using online surveys in the US ( n = 2,050), Japan ( n = 1,842), and Germany ( n = 1,962). US participants exhibited the most positive attitudes toward this emerging technology. Japanese participants demonstrated similar attitudes to German participants regarding risk perceptions and demonstrated closer attitudes to US participants regarding benefit perceptions. Further, US participants did not highly differentiate between gene-edited and conventionally bred foods when compared to German and Japanese participants. Presentation of information using either animal or plant illustrations did not have any impact on risk perceptions toward gene-edited crops in the three countries, but the German and Japanese people who were given information with plant illustrations showed higher perceptions of benefit than those who were given the same information but with animal illustrations. The study results empirically indicate that despite receiving the same information under the same experimental conditions, perceptions can vary among countries. Our survey and provision of contrasting information illustrations, as well as including participants from an Asian country—Japan—in addition to Americans and Germans broadens the framework of civic epistemology.

Governance of Gene-edited Plants: Insights from the History of Biotechnology Oversight and Policy Process Theory

The history of US biotechnology oversight for genetically modified plants is analyzed in the context of policy process theories to derive insights for contemporary governance of gene-edited plants. The Advocacy Coalition Framework sheds light on how opposing coalitions with different policy beliefs struggled to influence oversight, along with coalition disputes over the scope of issues that should be considered in regulatory policy-making. The Multiple Streams Approach and Punctuated Equilibrium Theory explain how focusing events arising from these struggles opened “windows of opportunity” to put issues on the public policy agenda and force changes to oversight over time. For example, nongovernmental organizations had a prominent role in bringing legal challenges through federal courts or in raising attention to risk issues in the media—efforts that prompted advancements in federal regulations, guidance documents, or risk-mitigation practices for biotechnology oversight. These policy dynamics depended on public information to bring controversies to light and elicit a policy response. However, recent biotech regulations allow for gene-edited crops to enter the marketplace without requirements for public disclosure or tracking. Lack of transparency jeopardizes the public legitimacy of gene-edited crops, venues for public participation in biotechnology oversight, and ultimately responsiveness to adapt oversight to future biotech products and emerging risks.

Gene Editing in Plants

Gene editing has the potential to become a transformative tool of plant breeding. Modern plant breeding programs are built on a rich history of crossing and selection of desirable varieties, made more efficient in recent decades with the application of genomics. The additional precision of gene editing techniques such as CRISPR is poised to enable better identification and advancement of beneficial traits such as disease resistance that appeals to farmers or enhanced flavor that appeals to consumers. It is important to recognize, however, that gene-edited crops are coming to market in the wake of debates surrounding genetically modified organisms. Although uses of gene editing under discussion do not typically center on transferring DNA into a plant from an unrelated species, the regulatory and societal lenses though which consumers and the scientific community view gene-edited plants will be a major influence on what traits reach farms and who is able to develop them. Health professionals have a frontline role in discussing food safety and nutrition with their clients and are encouraged to consult regulatory and scientific experts to stay abreast of introduction of new breeding techniques, as well as their use and safety.

De-novo Domestication for Improving Salt Tolerance in Crops.

Global agriculture production is under serious threat from rapidly increasing population and adverse climate changes. Food security is currently a huge challenge to feed 10 billion people by 2050. Crop domestication through conventional approaches is not good enough to meet the food demands and unable to fast-track the crop yields. Also, intensive breeding and rigorous selection of superior traits causes genetic erosion and eliminates stress-responsive genes, which makes crops more prone to abiotic stresses. Salt stress is one of the most prevailing abiotic stresses that poses severe damages to crop yield around the globe. Recent innovations in state-of-the-art genomics and transcriptomics technologies have paved the way to develop salinity tolerant crops. De novo domestication is one of the promising strategies to produce superior new crop genotypes through exploiting the genetic diversity of crop wild relatives (CWRs). Next-generation sequencing (NGS) technologies open new avenues to identifying the unique salt-tolerant genes from the CWRs. It has also led to the assembly of highly annotated crop pan-genomes to snapshot the full landscape of genetic diversity and recapture the huge gene repertoire of a species. The identification of novel genes alongside the emergence of cutting-edge genome editing tools for targeted manipulation renders de novo domestication a way forward for developing salt-tolerance crops. However, some risk associated with gene-edited crops causes hurdles for its adoption worldwide. Halophytes-led breeding for salinity tolerance provides an alternative strategy to identify extremely salt tolerant varieties that can be used to develop new crops to mitigate salinity stress.

Socio-Economic Considerations and Potential Implications for Gene-Edited Crops

Regulatory clarity and efficiency are increasingly important for the successful commercialization of technologies resulting from public and private R&D investments. This article examines recent developments in the movement away from mostly science-based risk assessment regulatory and variety approval systems focusing on human and animal health and environmental safety to hybrid systems that include assessment of socio-economic considerations allowed for under the auspices of the Cartagena Protocol on Biosafety. We propose that socio-economic consideration assessments can be grouped into three methodological categories: empirically based, legally grounded and consensus approaches. Our exploration of developments in the three categories reveals gaps in data, consistency and methodology rigor, that must be addressed for efficient and reliable socio-economic consideration assessment. We assess the potential impacts of these gaps on the regulation of gene-edited crop varieties, concluding that if gene-edited crops are regulated as genetically modified crops, they will endure the same fate, that is, lengthy regulatory approval processes and failure to be commercialized. The end result being that the regulatory burdens in potential adopting and food insecure countries will prevent important new crop varieties from reaching farmers and producers for their use. https://doi.org/10.21423/jrs-v09i2ludlow

CRISPR-Cas9-Mediated Gene Editing of MYB28 Genes Impair Glucoraphanin Accumulation of Brassica oleracea in the Field.

Discoveries in model plants grown under optimal conditions can provide important directions for crop improvement. However, it is important to verify whether results can be translated to crop plants grown in the field. In this study, we sought to study the role of MYB28 in the regulation of aliphatic glucosinolate (A-GSL) biosynthesis and associated sulfur metabolism in field-grown Brassica oleracea with the use of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 gene-editing technology. We describe the first myb28 knockout mutant in B. oleracea, and the first CRISPR field trial in the United Kingdom approved and regulated by the UK Department for Environment, Food & Rural Affairs after the reclassification of gene-edited crops as genetically modified organisms by the European Court of Justice on July 25, 2018. We report that knocking out myb28 results in downregulation of A-GSL biosynthesis genes and reduction in accumulation of the methionine-derived glucosinolate, glucoraphanin, in leaves and florets of field-grown myb28 mutant broccoli plants, whereas accumulation of sulfate, S-methyl cysteine sulfoxide, and indole glucosinolate in leaf and floret tissues remained unchanged. These results demonstrate the potential of gene-editing approaches to translate discoveries in fundamental biological processes for improved crop performance.

U.K. set to loosen rules for gene-edited crops and animals

U.K. set to loosen rules for gene-edited crops and animals