Feasibility of new breeding techniques for organic farming

Ecological restoration and rewilding: two approaches with complementary goals?

As we enter the UN Decade on Ecosystem Restoration (2021-2030) and address the urgent need to protect and restore ecosystems and their ecological functions at large scales, rewilding has been brought into the limelight. Interest in this discipline is thus increasing, with a large number of conceptual scientific papers published in recent years. Increasing enthusiasm has led to discussions and debates in the scientific community about the differences between ecological restoration and rewilding. The main goal of this review is to compare and clarify the position of each field. Our results show that despite some differences (e.g. top-down versus bottom-up and functional versus taxonomic approaches) and notably with distinct goals - recovery of a defined historically determined target ecosystem versus recovery of natural processes with often no target endpoint - ecological restoration and rewilding have a common scope: the recovery of ecosystems following anthropogenic degradation. The goals of ecological restoration and rewilding have expanded with the progress of each field. However, it is unclear whether there is a paradigm shift with ecological restoration moving towards rewilding or vice versa. We underline the complementarity in time and in space of ecological restoration and rewilding. To conclude, we argue that reconciliation of these two fields of nature conservation to ensure complementarity could create a synergy to achieve their common scope.

From concept to reality: Transforming agriculture through innovative rhizosphere engineering for plant health and productivity

The plant rhizosphere is regarded as a microbial hotspot due to a wide array of root exudates. These root exudates comprise diverse organic compounds such as phenolic, polysaccharides, flavonoids, fatty acids, and amino acids that showed chemotactic responses towards microbial communities and mediate significant roles in root colonization. The rhizospheric microbiome is a crucial driver of plant growth and productivity, contributing directly or indirectly by facilitating nutrient acquisition, phytohormone modulation, and phosphate solubilization under normal and stressful conditions. Moreover, these microbial candidates protect plants from pathogen invasion by secreting antimicrobial and volatile organic compounds. To enhance plant fitness and yield, rhizospheric microbes are frequently employed as microbial inoculants. However, recent developments have shifted towards targeted rhizosphere engineering or microbial recruitments as a practical approach to constructing desired plant rhizospheres for specific outcomes. The rhizosphere, composed of plants, microbes, and soil, can be modified in several ways to improve inoculant efficiency. Rhizosphere engineering is achieved through three essential mechanisms: a) plant-mediated modifications involving genetic engineering, transgenics, and gene editing of plants; b) microbe-mediated modifications involving genetic alterations of microbes through upstream or downstream methodologies; and c) soil amendments. These mechanisms shape the rhizospheric microbiome, making plants more productive and resilient under different stress conditions. This review paper comprehensively summarizes the various aspects of rhizosphere engineering and their potential applications in maintaining plant health and achieving optimum agricultural productivity.

Consumers' perceptions and acceptance of genome editing in agriculture: Insights from the United States of America and Switzerland

The terms "New Genomic Techniques" (NGTs) or "Genome Editing" refer to various methods that allow finding, cleaving, and repairing specific sequences in the genome. These techniques could contribute to managing various challenges in plant breeding and agriculture. Aside from regulatory uncertainties, the lack of consumer acceptance has frequently been cited as a significant barrier to the widespread use of NGTs in plant breeding and agriculture across the planet. This study was based on an anonymous online survey (N = 1202). It investigated what consumers from two countries that differ in gene technology regulation, namely the United States of America and Switzerland, thought about three specific applications of NGTs in plant breeding (i.e., blight-resistant potato, gluten-free wheat, cold-resistant soybean). The study highlights the importance of the affect heuristic for acceptance, as half of the participants in both countries expressed positive feelings regarding the three applications, a quarter of the participants expressed negative, and the remaining participants expressed torn or neutral emotions. Some evidence was provided that the regulatory context might have acted as a risk cue, as participants in Switzerland expressed more negative feelings, perceptions, and lower acceptance than participants from the United States of America. Lastly, our findings underscore the importance of a collaboration between the life sciences and social sciences in balancing technological innovations and public perceptions and acceptance, which have been shown in this study to be impacted by affect, values, and context.

Microbiome engineering for bioremediation of emerging pollutants

Axenic microbial applications in the open environment are unrealistic and may not be always practically viable. Therefore, it is important to use mixed microbial cultures and their interactions with the microbiome in the targeted ecosystem to perform robust functions towards their sustainability in harsh environmental conditions. Emerging pollutants like phthalates and hydrocarbons that are toxic to several aquatic and terrestrial life forms in the water bodies and lands are an alarming situation. The present review explores the possibility of devising an inclusive eco-friendly strategy like microbiome engineering which proves to be a unique and crucial technology involving the power of microbial communication through quorum sensing. This review discusses the interspecies and intra-species communications between different microbial groups with their respective environments. Moreover, this review also envisages the efforts for designing the next level of microbiome-host engineering concept (MHEC). The focus of the review also extended toward using omics and metabolic network analysis-based tools for effective microbiome engineering. These approaches might be quite helpful in the future to understand such microbial interactions but it will be challenging to implement in the real environment to get the desired functions. Finally, the review also discusses multiple approaches for the bioremediation of toxic chemicals from the soil environment.

Freedom of Choice—Organic Consumers’ Discourses on New Plant Breeding Techniques

In recent years, there have been significant developments in biotechnology, specifically regarding New Plant Breeding Techniques (NPBTs). Such advancements have been driven by the need to develop improved and more sustainable crops while reducing pesticides and fertilisers. NPBTs include a heterogeneous group of methods that allow performing plant mutations more precisely than in genetically modified (GM) technologies, saving time and effort. Although some experts consider NPBTs an opportunity for organic farming expansion, the European Court of Justice in 2018 pronounced against their use in organic farming since all plants obtained by NPBTs should follow the same regulations as Genetically Modified Organisms (GMOs). This study aims to understand consumers’ attitudes and viewpoints towards new breeding techniques. Focus groups and Q methodological approach were used to uncover consensus and divergence among organic consumers in seven selected European countries (Germany, Italy, Latvia, the Netherlands, Spain, Switzerland, United Kingdom). Results of qualitative studies suggest that organic consumers are generally hostile towards NPBTs in organic farming. Using Q methodology, three distinct factors were identified: the “Risk Averse”, the “Technological Optimists”, and the “Socially Concerned”. The results highlight that consumers’ subjective knowledge and understanding of NPBTs diverge from the discourse of NPBTs lobbyists and proponents.

Aligning Policy Design With Science to Achieve Food Security: The Contribution of Genome Editing to Sustainable Agriculture

The need to meet the food demands of the world's growing population is the main challenge to global agricultural policy and economy. Issues in food security require innovative solutions. Modern biotechnology has a significant potential to contribute to food security, wealth, and sustainable development. Genetic engineering offers tools to improve nutrition, increase yield, and enhance crop resilience. New techniques of genome editing provide ample means to overcome limitations inherent in conventional plant breeding, but their industrial applicability depends on regulatory environment, decision making, and public perception. An alignment of goals between science and policy can help realise the potential of modern biotechnology to contribute to food security, wealth, and sustainable development.

An integrated host-microbiome response to atrazine exposure mediates toxicity in Drosophila

The gut microbiome produces vitamins, nutrients, and neurotransmitters, and helps to modulate the host immune system-and also plays a major role in the metabolism of many exogenous compounds, including drugs and chemical toxicants. However, the extent to which specific microbial species or communities modulate hazard upon exposure to chemicals remains largely opaque. Focusing on the effects of collateral dietary exposure to the widely used herbicide atrazine, we applied integrated omics and phenotypic screening to assess the role of the gut microbiome in modulating host resilience in Drosophila melanogaster. Transcriptional and metabolic responses to these compounds are sex-specific and depend strongly on the presence of the commensal microbiome. Sequencing the genomes of all abundant microbes in the fly gut revealed an enzymatic pathway responsible for atrazine detoxification unique to Acetobacter tropicalis. We find that Acetobacter tropicalis alone, in gnotobiotic animals, is sufficient to rescue increased atrazine toxicity to wild-type, conventionally reared levels. This work points toward the derivation of biotic strategies to improve host resilience to environmental chemical exposures, and illustrates the power of integrative omics to identify pathways responsible for adverse health outcomes.

Beyond organic farming - harnessing biodiversity-friendly landscapes

We challenge the widespread appraisal that organic farming is the fundamental alternative to conventional farming for harnessing biodiversity in agricultural landscapes. Certification of organic production is largely restricted to banning synthetic agrochemicals, resulting in limited benefits for biodiversity but high yield losses despite ongoing intensification and specialisation. In contrast, successful agricultural measures to enhance biodiversity include diversifying cropland and reducing field size, which can multiply biodiversity while sustaining high yields in both conventional and organic systems. Achieving a landscape-level mosaic of natural habitat patches and fine-grained cropland diversification in both conventional and organic agriculture is key for promoting large-scale biodiversity. This needs to be urgently acknowledged by policy makers for an agricultural paradigm shift.

Organic farming: Does it contribute to contaminant-free produce and ensure food safety?

Organic farming for higher ecological and human health benefits has been adopted in about 186 countries, covering a total area of 71.5 Mha worldwide. Because of the associated practices, the flows of several environmental pollutants into the organic products threaten food safety and human health. The contaminants that occur at higher concentrations in organic produce include persistent organic pollutants (61.3-436.9 ng g^-1 lamb meat, and 0.28 pg g^-1-2.75 ng g^-1 bovine meat), heavy metals (0.5-33.0 mg kg^-1 lettuce), organochlorine pesticides (11-199 μg g^-1 carrots), cyclodienes, hexachlorocyclohexanes, hexabromocyclododecane (2-3 times higher than in conventionally produced porcine meat), hexachlorobenzene (1.38-14.49 ng g^-1 fat in milk), and non-brominated flame retardants (1.3-3.2 times higher than in conventional produce of greenhouse-grown tomato and cucumber). Moreover, some pollutants like per- and polyfluoroalkyl substances with a longer half-life (1.50-9.10 yrs) are reported to occur in several organic products. In fact, several legacy persistent organic pollutants are known for their significant trophic magnification in an urban terrestrial ecosystem. In addition, many plant functionalities are adversely affected in organic farming. Therefore, the long-term usage of organic products containing such pollutants poses a significant threat to human health. The major limitation in organic livestock production is the severe shortage of organic feed. Several variable standards and technical regulations set by the government and private agencies are the major obstacles in the global marketing of organic products. The present review critically addresses the impact of organic farming on hidden risks due to the use of composts as the amendment resources that enhance the phytoaccumulation and trophic transfer of pollutants, the functional diversity of the ecosystems, and poor harmonization among the policies and regulations in different countries for organic farming. The future directions of research have been suggested to mitigate unintended flows of pollutants into the organic products.

Emerging Molecular Tools for Engineering Phytomicrobiome

Microbial plant interaction plays a major role in the sustainability of plants. The understanding of phytomicrobiome interactions enables the gene-editing tools for the construction of the microbial consortia. In this interaction, microbes share several common secondary metabolites and terpenoid metabolic pathways with their host plants that ensure a direct connection between the microbiome and associated plant metabolome. In this way, the CRISPR-mediated gene-editing tool provides an attractive approach to accomplish the creation of microbial consortia. On the other hand, the genetic manipulation of the host plant with the help of CRISPR-Cas9 can facilitate the characterization and identification of the genetic determinants. It leads to the enhancement of microbial capacity for more trait improvement. Many plant characteristics like phytovolatilization, phytoextraction, phytodesalination and phytodegradation are targeted by these approaches. Alternatively, chemical communications by PGPB are accomplished by the exchange of different signal molecules. For example, quorum-sensing is the way of the cell to cell communication in bacteria that lead to the detection of metabolites produced by pathogens during adverse conditions and also helpful in devising some tactics towards understanding plant immunity. Along with quorum-sensing, different volatile organic compounds and N-acyl homoserine lactones play a significant role in cell to cell communication by microbe to plant and among the plants respectively. Therefore, it is necessary to get details of all the significant approaches that are useful in exploring cell to cell communications. In this review, we have described gene-editing tools and the cell to cell communication process by quorum-sensing based signaling. These signaling processes via CRISPR- Cas9 mediated gene editing can improve the microbe-plant community in adverse climatic conditions.

Precision Breeding Made Real with CRISPR: Illustration through Genetic Resistance to Pathogens

Since its discovery as a bacterial adaptive immune system and its development for genome editing in eukaryotes, the CRISPR technology has revolutionized plant research and precision crop breeding. The CRISPR toolbox holds great promise in the production of crops with genetic disease resistance to increase agriculture resilience and reduce chemical crop protection with a strong impact on the environment and public health. In this review, we provide an extensive overview on recent breakthroughs in CRISPR technology, including the newly developed prime editing system that allows precision gene editing in plants. We present how each CRISPR tool can be selected for optimal use in accordance with its specific strengths and limitations, and illustrate how the CRISPR toolbox can foster the development of genetically pathogen-resistant crops for sustainable agriculture.

Lay and scientific categorizations of new breeding techniques: Implications for food policy and genetically modified organism legislation

The rapid development of new genetic breeding techniques is accompanied by a polarized debate around their risks. Research on the public perception of these techniques lags behind scientific developments. This study tests a method for revealing laypeople's perceptions and attitudes about different genetic techniques. The objectives are to enable laypeople to understand the key principles of new genetic breeding techniques and to permit a comparison of their modes of classification with those of scientific experts. The combined method of a free sorting task and focus groups showed that the participants distinguished the techniques that did not induce any change in DNA sequence, and applied two different logics to classify the other breeding techniques: a Cartesian logic and a naturalistic logic with a distinct set of values. The lay categorization differed substantially from current scientific categorizations of genetic breeding techniques. These findings have implications for food innovation policy and genetically modified organism legislation.

Techniques for improving formulations of bioinoculants

Bioinoculants are eco-friendly microorganisms having a variety of products commonly utilized for improving the potential of soil and providing the nutrient requirements to the host plant. The usage of chemical fertilizers is not beneficial because it affects the soil microbial communities on large scale. The toxicity of chemical fertilizer decreases the fertility of soil and causes microbial disruption. Bioinoculants that are used as PGPR play an important role in the enhancement of crop production and beneficial for both producers and consumers economically by protecting the soil during unfavourable conditions. The utilization of PGPR in the bioinoculant form imparts successfully sustain agricultural yield production and such formulated products contain living microbial cells of bioinoculants that also helps in seed treatment and enhances the mobilization process of nutrients by the low-cost process. This review mainly focuses on different bioinoculant formulations related to its recent approaches such as metabolite formulations, liquid formulations, solid carrier-based formulations and synthetic polymer-based formulations. This review also gives an overview of some aspects of the bioinoculant efficiency and their appropriate formulation, production and storage condition of microbial cells.

Nutritional quality and health risks of wheat grains from organic and conventional cropping systems

The influence of cropping systems on nutrition and food safety is controversial. This study aimed to evaluate the effects of an organic cropping system (OCS) on wheat nutrition and food safety at the molecular level by using a comprehensive research method. Nutrient deviation in samples from an OCS and a conventional cropping system (CCS) were detected, and 58 biomarkers were selected through multivariate statistical analysis and were further qualitatively and quantitatively analyzed. The health risk of heavy metal(loid)s (HMs) for different populations was assessed based on the estimated average daily dose and recommended ingestion reference dose, which indicated that populations ingesting grains from OCSs had higher non-carcinogenic and carcinogenic risks. Additionally, HMs posed greater non-carcinogenic risks to children under five years old and greater carcinogenic risks to adults.This study highlights the need to consider the potential risk from HMs and nutritive ingredient differences in organic food.

Quantitative Trait Loci (QTL) Analysis of Fruit and Agronomic Traits of Tropical Pumpkin (Cucurbita moschata) in an Organic Production System

Interest in the development of organically grown vegetable crops has risen over the past decades due to consumer preferences. However, most crops that have desirable consumer traits have been bred in conventional growing conditions, and their transfer to an organic setting is challenging. Here, the organically grown Hawaiian pumpkin (Cucurbita moschata) accession ‘Shima’ was crossed with the conventionally grown Puerto Rican variety ‘Taina Dorada’ to develop a backcross (BC1) population, where ‘Shima’ was the recurrent parent. A total of 202 BC1 (‘Shima’ X F1) progenies were planted in a certified organic field, and twelve traits were evaluated. We used genotype-by-sequencing (GBS) to identify the Quantitative Trait Loci (QTL) associated with insect tolerance along with commercially desirable traits. A total of 1582 single nucleotide polymorphisms (SNPs) were identified, from which 711 SNPs were used to develop a genetic map and perform QTL mapping. Reads associated with significant QTLs were aligned to the publicly available Cucurbita moschata genome and identified several markers linked to genes that have been previously reported to be associated with that trait in other crop systems, such as melon (Cucumis melo L.). This research provides a resource for marker-assisted selection (MAS) efforts in Cucurbita moschata, as well as serving as a model study to improve cultivars that are transitioning from a conventional to an organic setting.

Evolution of Abscisic Acid Signaling for Stress Responses to Toxic Metals and Metalloids

Toxic heavy metals and metalloids in agricultural ecosystems are crucial factors that limit global crop productivity and food safety. Industrial toxic heavy metals and metalloids such as cadmium, lead, and arsenic have contaminated large areas of arable land in the world and their accumulation in the edible parts of crops is causing serious health risks to humans and animals. Plants have co-evolved with various concentrations of these toxic metals and metalloids in soil and water. Some green plant species have significant innovations in key genes for the adaptation of abiotic stress tolerance pathways that are able to tolerate heavy metals and metalloids. Increasing evidence has demonstrated that phytohormone abscisic acid (ABA) plays a vital role in the alleviation of heavy metal and metalloid stresses in plants. Here, we trace the evolutionary origins of the key gene families connecting ABA signaling with tolerance to heavy metals and metalloids in green plants. We also summarize the molecular and physiological aspects of ABA in the uptake, root-to-shoot translocation, chelation, sequestration, reutilization, and accumulation of key heavy metals and metalloids in plants. The molecular evolution and interaction between the ABA signaling pathway and mechanisms for heavy metal and metalloid tolerance are highlighted in this review. Therefore, we propose that it is promising to manipulate ABA signaling in plant tissues to reduce the uptake and accumulation of toxic heavy metals and metalloids in crops through the application of ABA-producing bacteria or ABA analogues. This may lead to improvements in tolerance of major crops to heavy metals and metalloids.

A complex eIF4E locus impacts the durability of va resistance to Potato virus Y in tobacco

Many recessive resistances against potyviruses are mediated by eukaryotic translation initiation factor 4E (eIF4E). In tobacco, the va resistance gene commonly used to control Potato virus Y (PVY) corresponds to a large deletion affecting the eIF4E-1 gene on chromosome 21. Here, we compared the resistance durability conferred by various types of mutations affecting eIF4E-1 (deletions of various sizes, frameshift or nonsense mutations). The 'large deletion' genotypes displayed the broadest and most durable resistance, whereas frameshift and nonsense mutants displayed a less durable resistance, with rapid and frequent apparition of resistance-breaking variants. In addition, genetic and transcriptomic analyses revealed that resistance durability is strongly impacted by a complex genetic locus on chromosome 14, which contains three other eIF4E genes. One of these, eIF4E-3, is rearranged as a hybrid gene between eIF4E-2 and eIF4E-3 (eIF4E-2-3 ) in the genotypes showing the most durable resistance, while eIF4E-2 is differentially expressed between the tested varieties. RNA-seq and quantitative reverse transcriptase-polymerase chain reaction experiments demonstrated that eIF4E-2 expression level is positively correlated with resistance durability. These results suggest that besides the nature of the mutation affecting eIF4E-1, three factors linked with a complex locus may potentially impact va durability: loss of an integral eIF4E-3, presence of eIF4E-2-3 and overexpression of eIF4E-2. This latter gene might act as a decoy in a non-productive virus-plant interaction, limiting the ability of PVY to evolve towards resistance breaking. Taken together, these results show that va resistance durability can in large part be explained by complex redundancy effects in the eIF4E gene family.

Ideal Cereals With Lower Arsenic and Cadmium by Accurately Enhancing Vacuolar Sequestration Capacity

Cereals are a staple food for many people around the world; however, they are also a major dietary source of toxic metal(loid)s. Many agricultural regions throughout the world are contaminated with toxic metal(loid)s, which can accumulate to high levels in the grains of cereals cultivated in these regions, posing serious health risks to consumers. Arsenic (As) and cadmium (Cd) are efficiently accumulated in cereals through metal transport pathways. Therefore, there is an urgent need to develop crops that contain greatly reduced levels of toxic metal(loid)s. Vacuolar sequestration of toxic metal(loid)s is a primary strategy for reducing toxic metal(loid)s in grains. However, until recently, detailed strategies and mechanisms for reducing toxic metal(loid)s in grain were limited by the lack of experimental data. New strategies to reduce As and Cd in grain by enhancing vacuolar sequestration in specific tissues are critical to develop crops that lower the daily intake of As and Cd, potentially improving human health. This review provides insights and strategies for developing crops with strongly reduced amounts of toxic metal(loid)s without jeopardizing agronomic traits.

New frontiers in agriculture productivity: Optimised microbial inoculants and in situ microbiome engineering

Increasing agricultural productivity is critical to feed the ever-growing human population. Being linked intimately to plant health, growth and productivity, harnessing the plant microbiome is considered a potentially viable approach for the next green revolution, in an environmentally sustainable way. In recent years, our understanding of drivers, roles, mechanisms, along with knowledge to manipulate the plant microbiome, have significantly advanced. Yet, translating this knowledge to expand farm productivity and sustainability requires the development of solutions for a number of technological and logistic challenges. In this article, we propose new and emerging strategies to improve the survival and activity of microbial inoculants, including using selected indigenous microbes and optimising microbial delivery methods, as well as modern gene editing tools to engineer microbial inoculants. In addition, we identify multiple biochemical and molecular mechanisms and/approaches which can be exploited for microbiome engineering in situ to optimise plant-microbiome interactions for improved farm yields. These novel biotechnological approaches can provide effective tools to attract and maintain activities of crop beneficial microbiota that increase crop performance in terms of nutrient acquisition, and resistance to biotic and abiotic stresses, resulting in an increased agricultural productivity and sustainability.

Are current EU policies on GMOs justified?

The European Court of Justice's recent ruling that the new techniques for crop development are to be considered as genetically modified organisms under the European Union's regulations exacerbates the need for a critical evaluation of those regulations. The paper analyzes the regulation from the perspective of moral and political philosophy. It considers whether influential arguments for restrictions of genetically modified organisms provide cogent justifications for the policies that are in place, in particular a pre-release authorization requirement, mandatory labelling, and de facto bans (in the form of withholding or opting out of authorizations). It is argued that arguments pertaining to risk can justify some form of pre-release authorization scheme, although not necessarily the current one, but that neither de facto bans nor mandatory labelling can be justified by reference to common arguments concerning naturalness, agricultural policy (in particular the promotion of organic farming), socio-economic effects, or consumers' right to choose.

Handling Tensions between Natural and Utility Purpose of Farm Animals and Crop Plants

We analyze the extent to which humans respect farm animals and crop plants and whether humans provide them adequate care. Concerns are justified, since many farm animals and crop plants have become completely dependent on humans for their survival. We explore whether the concept of ‘telos’ can be useful. From a biocentric and ecocentric custodian position, an animal or a plant possesses a telos, a nature of its own and a natural, species-specific purpose, but also a telos through its destination imposed by humanity because of its usefulness and service to human beings. Based on both forms of telos farm animals and crop plants deserve respect and have a moral value. Both forms of telos seem to oppose each other: the more humans domesticate the animal or plant, the more it must sacrifice its ‘natural telos’ to serve its ‘utility telos’. Humans should enable the animal or the plant to realize its natural telos in harmony with its utility telos. Both forms of telos could be reconciled if humans fulfil their moral duty to support farm animals and crops in completing their production cycle in a respectful manner. We formulate some guidelines to operationalize, and give meaning to, the concept of telos.

Plant immunity in natural populations and agricultural fields: Low presence of pathogenesis-related proteins in Solanum leaves

Plant immunity has mainly been studied under controlled conditions, limiting our knowledge regarding the regulation of immunity under natural conditions where plants grow in association with multiple microorganisms. Plant pathology theory, based on laboratory data, predicts complex biochemical plant-pathogen interactions leading to coevolution of pathogen infectivity vs. plant recognition of microbes in multiple layers over time. However, plant immunity is currently not evaluated in relation to ecological time-scales and field conditions. Here we report status of immunity in plants without visible disease symptoms in wild populations of nightshades, Solanum dulcamara and Solanum nigrum, and in agricultural fields of potato, Solanum tuberosum. We analysed presence of pathogenesis-related proteins in over 500 asymptomatic leaf samples collected in the field in June, July and August over three years. Pathogenesis-related proteins were present in only one-third of the collected samples, suggesting low activity of the immune system. We could also detect an increase in pathogenesis-related proteins later in the growing season, particularly in S. tuberosum. Our findings, based on pathogenesis-related protein markers, indicate major gaps in our knowledge regarding the status and regulation of plant immunity under field conditions.

Development of Wheat With Hypoimmunogenic Gluten Obstructed by the Gene Editing Policy in Europe

Coeliac Disease (CD) is an auto-immune reaction to gluten in 1-2% of the human population. A gluten-free (GF) diet, excluding wheat, barley, and rye, is the only remedy. This diet is difficult to adhere to, partly because wheat gluten is added to many processed products for their viscoelastic properties. In addition, GF products are less healthy and expensive. Wheat products containing only hypoimmunogenic gluten proteins would be a desirable option. Various gluten peptides that trigger CD have been characterized. A single wheat variety contains around hundred gluten genes, producing proteins with varying numbers of epitopes. Gene editing using CRISPR/Cas9 can precisely remove or modify the DNA sequences coding for immunogenic peptides. Wheat with hypoimmunogenic gluten thus exemplifies the potential of gene editing for improving crops for human consumption where conventional breeding cannot succeed. We describe here, in relation to breeding hypoimmunogenic wheat varieties, the inconsistencies of applying GM regulation in Europe for gene-edited plants while mutation breeding-derived plants are exempted. We explain that healthy products derived from this new technology may become available in the United States, Canada, Argentina and other countries but not in Europe, because of strict regulation of unintended GM risk at the expense of reduction the existing immunogenicity risks of patients. We argue that regulation of gene-edited plants should be based on scientific evidence. Therefore, we strongly recommend implementing the innovation principle. Responsible Research and Innovation, involving stakeholders including CD patient societies in the development of gene-editing products, will enable progress toward healthy products and encourage public acceptance.

Opportunities for genome editing in vegetable crops

Vegetables include high-value crops with health-promoting effects and reduced environmental impact. The availability of genomic and biotechnological tools in certain species, coupled with the recent development of new breeding techniques based on precise editing of DNA, provides unique opportunities to finally take advantage of the past decades of detailed genetic analyses, thus making improvement of traits related to quality and stress tolerance achievable in a reasonable time frame. Recent reports of such approaches in vegetables illustrate the feasibility of obtaining multiple homozygous mutations in a single generation, heritable by the progeny, using stable or transient transformation approaches, which may not rely on the integration of unwanted foreign DNA. Application of these approaches to currently non-sequenced/tissue culture recalcitrant crops will contribute to meet the challenges posed by the increase in population and climate change.

Challenges towards Revitalizing Hemp: A Multifaceted Crop

Hemp has been an important crop throughout human history for food, fiber, and medicine. Despite significant progress made by the international research community, the basic biology of hemp plants remains insufficiently understood. Clear objectives are needed to guide future research. As a semi-domesticated plant, hemp has many desirable traits that require improvement, including eliminating seed shattering, enhancing the quantity and quality of stem fiber, and increasing the accumulation of phytocannabinoids. Methods to manipulate the sex of hemp plants will also be important for optimizing yields of seed, fiber, and cannabinoids. Currently, research into trait improvement is hindered by the lack of molecular techniques adapted to hemp. Here we review how addressing these limitations will help advance our knowledge of plant biology and enable us to fully domesticate and maximize the agronomic potential of this promising crop.

Is biotechnology (more) acceptable when it enables a reduction in phytosanitary treatments? A European comparison of the acceptability of transgenesis and cisgenesis

Reduced pesticide use is one of the reasons given by Europeans for accepting new genetic engineering techniques. According to the advocates of these techniques, consumers are likely to embrace the application of cisgenesis to apple trees. In order to verify the acceptability of these techniques, we estimate a Bayesian multilevel structural equation model, which takes into account the multidimensional nature of acceptability and individual, national, and European effects, using data from the Eurobarometer 2010 73.1 on science. The results underline the persistence of clear differences between European countries and whilst showing considerable defiance, a relatively wider acceptability of vertical gene transfer as a means of reducing phytosanitary treatments, compared to horizontal transfer.

A Conceptual Framework for Integrated Pest Management

The concept of integrated pest management (IPM) has been accepted and incorporated in public policies and regulations in the European Union and elsewhere, but a holistic science of IPM has not yet been developed. Hence, current IPM programs may often be considerably less efficient than the sum of separately applied individual crop protection actions. Thus, there is a clear need to formulate general principles for synergistically combining traditional and novel IPM actions to improve efforts to optimize plant protection solutions. This paper addresses this need by presenting a conceptual framework for a modern science of IPM. The framework may assist attempts to realize the full potential of IPM and reduce risks of deficiencies in the implementation of new policies and regulations.

Use of Natural Diversity and Biotechnology to Increase the Quality and Nutritional Content of Tomato and Grape

Improving fruit quality has become a major goal in plant breeding. Direct approaches to tackling fruit quality traits specifically linked to consumer preferences and environmental friendliness, such as improved flavor, nutraceutical compounds, and sustainability, have slowly been added to a breeder priority list that already includes traits like productivity, efficiency, and, especially, pest and disease control. Breeders already use molecular genetic tools to improve fruit quality although most advances have been made in producer and industrial quality standards. Furthermore, progress has largely been limited to simple agronomic traits easy-to-observe, whereas the vast majority of quality attributes, specifically those relating to flavor and nutrition, are complex and have mostly been neglected. Fortunately, wild germplasm, which is used for resistance against/tolerance of environmental stresses (including pathogens), is still available and harbors significant genetic variation for taste and health-promoting traits. Similarly, heirloom/traditional varieties could be used to identify which genes contribute to flavor and health quality and, at the same time, serve as a good source of the best alleles for organoleptic quality improvement. Grape (Vitis vinifera L.) and tomato (Solanum lycopersicum L.) produce fleshy, berry-type fruits, among the most consumed in the world. Both have undergone important domestication and selection processes, that have dramatically reduced their genetic variability, and strongly standardized fruit traits. Moreover, more and more consumers are asking for sustainable production, incompatible with the wide range of chemical inputs. In the present paper, we review the genetic resources available to tomato/grape breeders, and the recent technological progresses that facilitate the identification of genes/alleles of interest within the natural or generated variability gene pool. These technologies include omics, high-throughput phenotyping/phenomics, and biotech approaches. Our review also covers a range of technologies used to transfer to tomato and grape those alleles considered of interest for fruit quality. These include traditional breeding, TILLING (Targeting Induced Local Lesions in Genomes), genetic engineering, or NPBT (New Plant Breeding Technologies). Altogether, the combined exploitation of genetic variability and innovative biotechnological tools may facilitate breeders to improve fruit quality tacking more into account the consumer standards and the needs to move forward into more sustainable farming practices.

Accelerating the Domestication of New Crops: Feasibility and Approaches

The domestication of new crops would promote agricultural diversity and could provide a solution to many of the problems associated with intensive agriculture. We suggest here that genome editing can be used as a new tool by breeders to accelerate the domestication of semi-domesticated or even wild plants, building a more varied foundation for the sustainable provision of food and fodder in the future. We examine the feasibility of such plants from biological, social, ethical, economic, and legal perspectives.

Direct and Pollinator-Mediated Effects of Herbivory on Strawberry and the Potential for Improved Resistance

The global decline in pollinators has partly been blamed on pesticides, leading some to propose pesticide-free farming as an option to improve pollination. However, herbivores are likely to be more prevalent in pesticide-free environments, requiring knowledge of their effects on pollinators, and alternative crop protection strategies to mitigate any potential pollination reduction. Strawberry leaf beetles (SLB) Galerucella spp. are important strawberry pests in Northern Europe and Russia. Given that SLB attack both leaf and flower tissue, we hypothesized pollinators would discriminate against SLB-damaged strawberry plants (Fragaria vesca, cultivar 'Rügen'), leading to lower pollination success and yield. In addition we screened the most common commercial cultivar 'Rügen' and wild Swedish F. vesca genotypes for SLB resistance to assess the potential for inverse breeding to restore high SLB resistance in cultivated strawberry. Behavioral observations in a controlled experiment revealed that the local pollinator fauna avoided strawberry flowers with SLB-damaged petals. Low pollination, in turn, resulted in smaller more deformed fruits. Furthermore, SLB-damaged flowers produced smaller fruits even when they were hand pollinated, showing herbivore damage also had direct effects on yield, independent of indirect effects on pollination. We found variable resistance in wild woodland strawberry to SLB and more resistant plant genotypes than the cultivar 'Rügen' were identified. Efficient integrated pest management strategies should be employed to mitigate both direct and indirect effects of herbivory for cultivated strawberry, including high intrinsic plant resistance.

A new eIF4E1 allele characterized by RNAseq data mining is associated with resistance to potato virus Y in tomato albeit with a low durability

Allele mining on susceptibility factors offers opportunities to find new sources of resistance among crop wild relatives for breeding purposes. As a proof of concept, we used available RNAseq data to investigate polymorphisms among the four tomato genes encoding translation initiation factors [eIF4E1 and eIF4E2, eIFiso4E and the related gene new cap-binding protein(nCBP)] to look for new potential resistance alleles to potyviruses. By analysing polymorphism among RNAseq data obtained for 20 tomato accessions, 10 belonging to the cultivated type Solanum lycopersicum and 10 belonging to the closest related wild species Solanum pimpinellifolium, we isolated one new eIF4E1 allele, in the S. pimpinellifolium LA0411 accession, which encodes a potential new resistance allele, mainly due to a polymorphism associated with an amino acid change within eIF4E1 region II. We confirmed that this new allele, pot12, is indeed associated with resistance to potato virus Y, although with a restricted resistance spectrum and a very low durability potential. This suggests that mutations occurring in eIF4E region II only may not be sufficient to provide efficient and durable resistance in plants. However, our study emphasizes the opportunity brought by RNAseq data to mine for new resistance alleles. Moreover, this approach could be extended to seek for putative new resistance alleles by screening for variant forms of susceptibility genes encoding plant host proteins known to interact with viral proteins.

A TILLING approach to generate broad-spectrum resistance to potyviruses in tomato is hampered by eIF4E gene redundancy

Genetic resistance to pathogens is important for sustainable maintenance of crop yields. Recent biotechnologies offer alternative approaches to generate resistant plants by compensating for the lack of natural resistance. Tomato (Solanum lycopersicum) and related species offer a model in which natural and TILLING-induced potyvirus resistance alleles may be compared. For resistance based on translation initiation factor eIF4E1, we confirm that the natural allele Sh-eIF4E1(PI24)-pot1, isolated from the wild tomato species Solanum habrochaites, is associated with a wide spectrum of resistance to both potato virus Y and tobacco etch virus isolates. In contrast, a null allele of the same gene, isolated through a TILLING strategy in cultivated tomato S. lycopersicum, is associated with a much narrower resistance spectrum. Introgressing the null allele into S. habrochaites did not extend its resistance spectrum, indicating that the genetic background is not responsible for the broad resistance. Instead, the different types of eIF4E1 mutations affect the levels of eIF4E2 differently, suggesting that eIF4E2 is also involved in potyvirus resistance. Indeed, combining two null mutations affecting eIF4E1 and eIF4E2 re-establishes a wide resistance spectrum in cultivated tomato, but to the detriment of plant development. These results highlight redundancy effects within the eIF4E gene family, where regulation of expression alters susceptibility or resistance to potyviruses. For crop improvement, using loss-of-function alleles to generate resistance may be counter-productive if they narrow the resistance spectrum and limit growth. It may be more effective to use alleles encoding functional variants similar to those found in natural diversity.

Uneven HAK/KUP/KT Protein Diversity Among Angiosperms: Species Distribution and Perspectives

HAK/KUP/KT K(+) transporters have been widely associated with K(+) transport across membranes in bacteria, fungi, and plants. Indeed some members of the plant HAK/KUP/KT family contribute to root K(+) uptake, notably at low external concentrations. Besides such role in acquisition, several studies carried out in Arabidopsis have shown that other members are also involved in developmental processes. With the publication of new plant genomes, a growing interest on plant species other than Arabidopsis has become evident. In order to understand HAK/KUP/KT diversity in these new plant genomes, we discuss the evolutionary trends of 913 HAK/KUP/KT sequences identified in 46 genomes revealing five major groups with an uneven distribution among angiosperms, notably between dicotyledonous and monocotyledonous species. This information evidenced the richness of crop genomes in HAK/KUP/KT transporters and supports their study for unraveling novel physiological roles of such transporters in plants.

Optimizing Crops for Biocontrol of Pests and Disease

Volatile compounds and extrafloral nectar are common defenses of wild plants; however, in crops they bear an as-yet underused potential for biological control of pests and diseases. Odor emission and nectar secretion are multigene traits in wild plants, and thus form difficult targets for breeding. Furthermore, domestication has changed the capacity of crops to express these traits. We propose that breeding crops for an enhanced capacity for tritrophic interactions and volatile-mediated direct resistance to herbivores and pathogens can contribute to environmentally-friendly and sustainable agriculture. Natural plant volatiles with antifungal or repellent properties can serve as direct resistance agents. In addition, volatiles mediating tritrophic interactions can be combined with nectar-based food rewards for carnivores to boost indirect plant defense.

CRISPR Critters and CRISPR Cracks

This essay focuses on possible nonhuman applications of CRISPR/Cas9 that are likely to be widely overlooked because they are unexpected and, in some cases, perhaps even "frivolous." We look at five uses for "CRISPR Critters": wild de-extinction, domestic de-extinction, personal whim, art, and novel forms of disease prevention. We then discuss the current regulatory framework and its possible limitations in those contexts. We end with questions about some deeper issues raised by the increased human control over life on earth offered by genome editing.