Food and environmental safety assessment of new plant varieties after the European Court decision: Process-triggered or product-based?

Breeding crops for the future

Plant breeding techniques encompass all the processes aimed at improving the genetic characteristics of a crop. It helps in achieving desirable characteristics like resistance to diseases and pests, tolerance to environmental stresses, higher yield and improved quality of the crop. This review article aims to describe and evaluate the current plant breeding techniques and novel methods. This qualitative review employs a comparative approach in exploring the different plant breeding techniques. Conventional plant breeding techniques were compared with modern ones to understand the advancements in plant biotechnology. Backcross breeding, mass selection, and pure-line selection were all discussed in conventional plant breeding for self-pollination and recurrent selection and hybridisation were employed for cross-pollinated crops. Modern techniques comprise of CRISPR Cas-9, high-throughput phenotyping, marker-assisted selection and genomic selection. Further, novel techniques were reviewed to gain more insight. An in-depth analysis of conventional and modern plant breeding has helped gain insight on the advantages and disadvantages of the two. Modern breeding techniques have an upper hand as they are more reliable and less time consuming. It is also more accurate as it is a genotype-based method. However, conventional breeding techniques are cost effective and require less expertise. Modern plant breeding has an upper hand as it uses genomics techniques. Techniques like QTL mapping, marker assisted breeding aid in selection of superior plants right at the seedling stage, which is impossible with conventional breeding. Unlike the conventional method, modern methods are capable of selecting recessive alleles by using different markers. Modern plant breeding is a science and therefore more reliable and accurate.

The global demand for providing nutritious, sustainable, and safe diets for a 10 billion population by 2050 while preserving affordability, reducing environmental impacts, and adapting to climate change will require accelerating the transition to sustainable agri‐food systems. A plausible way to help tackle these challenges is by developing new plant varieties that have improved crop yield, plant nutritional quality, and sustainability (or resilience) traits. However, stakeholders, consumers, and citizens' concerns and appreciation of future‐proofing crops and the acceptability of new plant breeding strategies are not well‐established. These groups are actors in the agri‐food systems, and their views, values, needs, and expectations are crucial in helping to co‐design fair, ethical, acceptable, sustainable, and socially desirable policies on new plant breeding techniques (NPBTs) and the transition to sustainable agri‐food systems. In this study, we engaged with consumer experts and societal stakeholders to consider their perceptions, expectations, and acceptability of improving crops and NPBTs for future‐proofing the agri‐food systems. Our analysis points to a need for governments to take a proactive role in regulating NPBTs, ensure openness and transparency in breeding new crop varieties, and inform consumers about the effects of these breeding programmes and the risks and benefits of the new crop varieties developed. Consumer experts and societal stakeholders considered these strategies necessary to instil confidence in society about NPBTs and accelerate the transition to sustainable agri‐food systems.

National and international organizations have discussed current approaches to the safety assessment of complex (plant) food products in general and the safety assessment of GMO-derived food products in particular. One of the recommendations of different expert meetings was that the new analytical techniques, in particular the 'omics' approaches, need to be explored for their potential to improve the analysis and thereby the toxicological and nutritional assessment of complex (GMO-derived) plant products. This thesis aims to further explore this approach in general and, more specifically, has evaluated the potential added value of transcriptomics to assess unintended side effects in a newly bred (genetically modified) plant variety. As one of the first initiatives in this area a small food safety–related tomato-array was developed with pathway-selected cDNAs on the basis of two subtractive cDNA libraries. This tomato array was used to hybridise mRNA derived from tomatoes in five subsequent ripening stages from green, via breaker, turning, and light red, to red, to obtain a background library of gene expression profiles of different ripening stages for future comparisons. At the same time these initial series of experiments were aimed to assess the potential of the approach with respect to its sensitivity and specificity. In addition the tomato array was used to hybridise mRNA derived from GM tomato transformant lines and the traditionally bred parent line and the results were analysed for the presence of differential expression patterns in both transformant lines, that have incorporated the same genetic construct, compared to the parent line. A similar study was performed in Arabidopsis to assess the extent of unintended effects in GM lines that have incorporated different numbers of the introduced genetic construct. The resulting data show that the methodology of transcriptomics has the potential to detect large as well as small differences in gene expression. The first was primarily shown in the comparative study on the developmental stage, the latter in the comparison of transcriptomics profiles of the two transformant lines vs the parent variety. It was also shown that, for direct comparison, plants to be sampled need to be grown under very similar conditions and the sampling needs to be performed in a structured way taking into account the developmental stage of the selected plant organs and/or tissues. All experiments illustrated the necessity to establish the bandwidth of natural variation for comparative purposes in order to determine the biological as well as toxicological and/or nutritional significance of differences detected in GM lines or in lines resulting from other breeding procedures. Finally, the results of the international debate on the assessment of complex (GMO-derived) plant products, the knowledge on current breeding strategies, and the results of the first publications on experiments that aim to detect unintended effects in plant breeding strategies using 'omics' technologies, including the experiments described here, are combined to review current approaches. A new overall approach for the safety evaluation of complex plant products, including GMO-derived products, is proposed. This approach applies currently available tools, including the 'omics' technologies, to assess food safety aspects of newly developed plant varieties already during the plant breeding process. Undesired effects of the breeding procedures for the plant's physiology, can thus be traced at an early stage and this will help to further guarantee the safety of the final plant-derived food products. Observed differences in the final plant product will form part of the comparative safety assessment. It can be envisioned on the basis of the data presented in this thesis as well as in other studies described in the scientific literature that in general few differences will be observed between GM lines and the WT counterparts that fall outside of the bandwidth of natural variation of commercial counterparts. The toxicological and nutritional evaluation of the final plant products will need to focus on the limited number of differences that are outside of this bandwidth and may affect the product's food safety characteristics. To avoid inequalities in food safety assessment procedures that do not have a sound scientific basis, it is argued that these developments should have an impact on all novel plant varieties, not just on GMO-derived food plant products.

Climate change poses significant challenges to global food security and agricultural productivity, necessitating the development of climate-resilient crop varieties. This review explores current and future plant breeding strategies aimed at coping with climate change. Various approaches, including traditional and cutting-edge techniques, wild relatives, and climate-informed strategies, have been employed to develop climate-resilient crop varieties. Traits such as heat and drought tolerance, early flowering, and maturation have been bred into varieties to mitigate the impact of changing climate conditions. Genetic mapping has identified genomic regions and candidate genes associated with stress tolerance, enabling the incorporation of stress tolerance alleles into high-yielding genetic backgrounds. Furthermore, advanced techniques such as gene editing, genomic selection, high-throughput phenotyping, and omics technologies have revolutionized plant breeding for climate adaptation, offering precise and efficient means of introducing desired traits. The integration of these cutting-edge techniques holds immense potential for developing climate-resilient crop varieties. However, challenges related to regulatory frameworks, intellectual property rights, and public acceptance must be addressed for responsible and sustainable adoption. A holistic, multidisciplinary approach that links breeding and climate science is crucial to strengthen adaptation and ensure food security in the face of accelerated climate change. Continued advancements in gene editing, genomic selection, high-throughput phenotyping, and omics technologies will further enhance breeding efficiency and precision. The future of plant breeding lies in the development of "climate-smart" varieties and cultivation systems resilient to future conditions with a focus on addressing farmer needs and global food security.

In addition to obviating the use of synthetic agrochemicals and emphasizing farming in accordance with agro-ecological guidelines, organic farming acknowledges the integrity of plants as an essential element of its natural approaches to crop production. For cultivated plants, integrity refers to their inherent nature, wholeness, completeness, species-specific characteristics, and their being in balance with their (organically farmed) environment, while accomplishing their “natural aim.” We argue that this integrity of plants has ethical value, distinguishing integrity of life, plant-typic integrity, genotypic integrity, and phenotypic integrity. We have developed qualitative criteria to ethically evaluate existing practices and have applied these criteria to assess whether current plant breeding and propagation techniques violate the integrity of crop plants. This process has resulted in a design of a holistic, scientific approach of organic plant breeding and seed production. Our evaluation has met considerable criticism from mainstream (crop) scientists. We respond to the following questions: (1). Can ethics be incorporated into objective crop sciences? (2). What is the nature of the intrinsic value of plants in organic farming? We argue that criteria to take integrity into account can only be assessed from a holistic perspective and we show that a holistic approach is needed to design such ethical notions in a consistent way. The ethical notions have been further elaborated by formulating human responsibility and respect towards crop plants. Responsibility and respect can only be shown by providing crop plants the right to be nurtured and to express natural behavior at all levels of integrity.

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.

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

Genome editing with engineered nucleases (“GEEN”) has emerged as an effective genetic engineering method that uses ‘molecular scissors’—artificially engineered nucleases—to digest DNA at targeted locations in the genome of various organisms including plant species. The DNA binding domains of zinc finger (ZF) proteins were first used as plant genome editing tools via the use of designed ZF nucleases (ZFNs), with TAL-effectors (TALE) and the RNA-DNA recognition system CRISPR/Cas9 now being used as powerful genome editing tools to create targeted gene modifications, not only in model plants but also in crop species. The key to genome editing is the introduction of targeted gene-specific double-stranded DNA breaks (DSBs) using the designed endonucleases, then allowing site-directed mutagenesis via nonhomologous end joining (NHEJ) repair and/or gene targeting via homologous recombination (HR), to occur efficiently at specific sites in the genome. This chapter provides an overview of recent advances in genome editing technologies, giving an insight into current plant molecular biology and breeding techniques.

ABSTRACTNew breeding techniques in plant agriculture exploded upon the scene about two years ago, in 2014. While these innovative plant breeding techniques, soon to be led by CRISPR/Cas9, initially appear to hold tremendous promise for plant breeding, if not a revolution for the industry, the question of how the products of these technologies will be regulated is rapidly becoming a key aspect of the technology's future potential. Regulation of innovative technologies and products has always lagged that of the science, but in the past decade, regulatory systems in many jurisdictions have become gridlocked as they try to regulate genetically modified (GM) crops. This regulatory incapability to efficiently assess and approve innovative new agricultural products is particularly important for new plant breeding techniques as if these techniques are classified as genetically modified breeding techniques, then their acceptance and future will diminish considerably as they will be rejected by the European Union. Conversely, if the techniques are accepted as conventional plant breeding, then the future is blindingly bright. This article examines the international debate about the regulation of new plant breeding techniques and then assesses how the Canadian regulatory system has approached the regulation of these technologies through two more public product approvals, GM apples and GM potatoes, then discusses other crop variety approval and those in the regulatory pipeline.

New plant breeding technologies (NPBTs) are increasingly used for developing new plants with novel traits. The science tells us that those plants in general are as safe as than those once developed using “conventional” plant breeding methods. The knowledge about the induced changes and properties of the new plants by using NPBTs is more precise. This should lead to the conclusion that plants developed using NPBTs should not be regulated differently than those developed using “conventional” plant breeding methods. This contribution discusses the economics of regulating new plant breeding technologies. We first develop the theoretical model and elaborate on the different regulatory approaches being used and compare their advantages and disadvantages. Then we provide a perspectives on EU regulation around mutagenesis-based New Plant Breeding Techniques (NPBT), formed by new insights from a survey among Dutch plant breeding companies. The survey measures the attitude of breeding companies towards the ruling of the EU Court of Justice that subjected the use of CRISPR-Cas in the development of new plant varieties under the general EU regulations around GMOs. The results show that plant breeders experience a financial barrier because of the ruling, with perceived negative impact on competitiveness and investments in CRISPR-Cas as a result. The degree of negative impact differs however significantly among seed-sectors and company sizes. One of the most striking results was the relative optimism of companies in the sector about more lenient legislation in the next five years, despite the stated negative effects.

Plant breeding facilitates the selection of plant populations with the desired trait from the genetic pool. A set of expressed or non-expressed genetic combinations are generally evolved due to spontaneous or induced mutations in the genetic pool of particular plant species. Genetic modification is the basis of diversity that allows domestication alongside adaptation in changing environmental conditions, i.e., from wild to cultivated species. Plant phenotype-based selective breeding has been an efficient way used in the past. Also, induction of random mutations by physical or chemical agents and further selection for desired traits from the mutant library has produced several plant varieties. However, conventional mutagenesis combined with selective breeding has some drawbacks. It makes the random mutations; the process is laborious and slower; it comes with the risk of losing beneficial traits during breeding. In recent times, genome-editing (GE) tools comprising molecular genetic scissors are tailored to precisely target the desired location in the plant genome. The most used GE tool is the clustered regularly interspaced short palindromic repeat-associated (CRISPR/Cas) endonuclease system. The CRISPR-based tools are part of a new technology called new plant breeding techniques (NBTs) that accelerate plant breeding. Diverse CRISPR-based tools have been optimized to achieve expected goals in NBTs like higher yield, tolerance to biotic and abiotic stresses, prevention of post-harvest losses, value addition, and novel traits-in-demand by farmers and consumers. This chapter summarizes an overview of the CRISPR/Cas system, CRISPR-based tools for plant breeding, and recent applications of CRISPR technology in agriculture.

Chapter 9 - CRISPR-Cas technologies for food and nutritional security

Plant breeding is one way to confront the challenge of bridging the widening gap between the demand and supply of food. Despite the importance, however, plant breeding has its own negative side effects. The replacement of landraces with a few genetically uniform varieties depletes genetic diversity and provides ideal conditions for diseases and insect pests that called genetic vulnerability. The increasingly growing human population and the subsequently rising demands for more food, on the one hand, and the success of such efforts like the “Green Revolution” from adoption of genetically uniform varieties in many parts of the world, on the other, are the main driving force towards this narrow genetic base. It is, therefore, important to understand the phenomena and plan to minimize the risks from genetic vulnerability. Under marginal conditions where resource-poor farmers dominate, the current plant breeding strategies, variety release, registration and certification procedures leading to genetic uniformity should be reconsidered and some level of genetic diversity should deliberately be maintained in variety development programs. Genetic diversity can be introduced at different levels and in different ways which may include intra-varietal, inter-varietal, inter-parental and inter-specific diversities. Breeding for specific adaptation instead of wide adaptation, systematic spatial and temporal gene deployment, use of inter-specific varietal mixtures and integration of horizontal and vertical resistances have been suggested as solutions.

Genetic techniques for plant breeding