Transgenic and genome-edited fruits: background, constraints, benefits, and commercial opportunities

A rapid on-site visualization platform based on RPA coupled with CRISPR-Cas12a for the detection of genetically modified papaya 'Huanong No.1'

The Papaya ringspot virus (PRSV)-resistant genetically modified (GM) papaya 'Huanong No.1' has been certified as safe for consumption and widely planted in China for about 18 years. To protect consumers' rights and facilitate government supervision and monitoring, it is necessary to establish a simple, rapid, and specific detection method for 'Huanong No.1'. Herein, we developed a platform based on recombinase polymerase amplification (RPA) coupled with CRISPR-Cas12a for the detection of 'Huanong No.1'. The RPA-CRISPR-Cas12a platform was found to have high specificity, with amplification signals only present in 'Huanong No.1'. Additionally, the platform was highly sensitive, with a limit of detection (LOD) of approximately 20 copies. The detection process was fast and could be completed in less than 1 h. This novel platform enables the rapid on-site visualization detection of 'Huanong No.1', eliminating dependence on laboratory conditions and specialized instruments, and can serve as a technical reference for the rapid detection of other GM plants.

Pest risk assessment of Leucinodes orbonalis for the European Union

Following a request from the European Commission, the EFSA Panel on Plant Health performed a quantitative risk assessment of Leucinodes orbonalis (Lepidoptera: Crambidae), the eggplant fruit and shoot borer, for the EU. The assessment focused on potential pathways for entry, climatic conditions favouring establishment, spread and impact. Options for risk reduction are discussed but effectiveness was not quantified. L. orbonalis is a key pest of eggplant (aubergine/brinjal) in the Indian subcontinent and occurs throughout most of southern Asia with records mostly from India and Bangladesh. The main pathway of entry is fruit of solanaceous plants, primarily exotic varieties of eggplant, Solanum melongena and turkey berry, S. torvum. The trade in both commodities from Asia is small but nevertheless dwarfs the trade in other Solanum fruits from Asia (S. aethiopicum, S. anguivi, S. virginianum, S. aculeatissimum, S. undatum). Other Solanum fruits were therefore not further assessed as potential pathways. The trade in eggplant from Asia consists of special fruit types and caters mostly to niche markets in the EU, while most eggplant consumed in Europe is produced in southern European and northern African countries, where L. orbonalis does not occur. Using expert knowledge elicitation (EKE) and pathway modelling, the Panel estimated that approximately 3-670 infested fruit (90% certainty range, CR) of S. melongena or fruit bunches of S. torvum enter into regions of the EU that are suitable for L. orbonalis establishment each year. Based on CLIMEX modelling, and using two possible thresholds of ecoclimatic index (EI) to indicate uncertainty in establishment potential, climates favouring establishment occur mostly in southern Europe, where, based on human population, approximately 14% of the imported produce is distributed across NUTS2 regions where EI ≥ 30; or 23% of the produce is distributed where EI ≥ 15. Escape of adult moths occurs mostly from consumer waste. By analysing results of different scenarios for the proportion of S. melongena and S. torvum in the trade, and considering uncertainties in the climatic suitability of southern Europe, adult moth emergence in areas suitable for establishment is expected to vary between 84 individuals per year and one individual per 40 years (based on 90% CR in different scenarios). In the baseline scenario, 25% of the solanaceous fruit from Asia is S. torvum, 75% is S. melongena and EI ≥ 30 is required for establishment. After accounting for the chances of mating, host finding and establishment, the probability of a mated female establishing a founder population in the EU is less than 1 in 100,000 to about 1 event per 622 years (90% CR in baseline scenario). The waiting time until the first establishment is then 622 to more than 100,000 years (CR). If such a founder population were established, the moth is estimated to spread at a rate of 0.65-7.0 km per year after a lag phase of 5-92 years. The impact of the insect on the production of eggplant is estimated to be 0.67%-13% (CR) if growers take no specific action against the insect and 0.13%-1.9% if they do take targeted actions. Tomato (S. lycopersicum) and potato (S. tuberosum) are hosts of L. orbonalis, but the insect does not develop to maturity in tomato fruit, and it does not feed on potato tubers under field conditions; hence, damage to potato can only occur due to feeding on shoots. Tomato and potato are not preferred hosts; nevertheless, impact can occur if populations of L. orbonalis are high and preferred hosts are not available. The Panel did not assess this damage due to insufficient information.

Dissecting the complex genetic basis of pre- and post-harvest traits in Vitis vinifera L. using genome-wide association studies

Addressing the pressing challenges in agriculture necessitates swift advancements in breeding programs, particularly for perennial crops like grapevines. Moving beyond the traditional biparental quantitative trait loci (QTL) mapping, we conducted a genome-wide association study (GWAS) encompassing 588 Vitis vinifera L. cultivars from a Chilean breeding program, spanning three seasons and testing 13 key yield-related traits. A strong candidate gene, Vitvi11g000454, located on chromosome 11 and related to plant response to biotic and abiotic stresses through jasmonic acid signaling, was associated with berry width and holds potential for enhancing berry size in grape breeding. We also mapped novel QTL associated with post-harvest traits across chromosomes 2, 4, 9, 11, 15, 18, and 19, broadening our grasp on the genetic intricacies dictating fruit post-harvest behavior, including decay, shriveling, and weight loss. Leveraging gene ontology annotations, we drew parallels between traits and scrutinized candidate genes, laying a robust groundwork for future trait-feature identification endeavors in plant breeding. We also highlighted the importance of carefully considering the choice of the response variable in GWAS analyses, as the use of best linear unbiased estimators (BLUEs) corrections in our study may have led to the suppression of some common QTL in grapevine traits. Our results underscore the imperative of pioneering non-destructive evaluation techniques for long-term conservation traits, offering grape breeders and cultivators insights to improve post-harvest table grape quality and minimize waste.

Advancing tree genomics to future proof next generation orchard production

The challenges facing tree orchard production in the coming years will be largely driven by changes in the climate affecting the sustainability of farming practices in specific geographical regions. Identifying key traits that enable tree crops to modify their growth to varying environmental conditions and taking advantage of new crop improvement opportunities and technologies will ensure the tree crop industry remains viable and profitable into the future. In this review article we 1) outline climate and sustainability challenges relevant to horticultural tree crop industries, 2) describe key tree crop traits targeted for improvement in agroecosystem productivity and resilience to environmental change, and 3) discuss existing and emerging genomic technologies that provide opportunities for industries to future proof the next generation of orchards.

Hybrid Fruits for Improving Health-A Comprehensive Review

Several species of hybrid fruits, such as citrus, grapes, blueberries, apples, tomatoes, and lingonberries among others, have attracted scientific attention in recent years, especially due to their reported antioxidant and anti-inflammatory properties. The bagasse, leaves, bark, and seeds of these hybrid fruits have large amounts of polyphenols, such as flavonoids, which act as potent antioxidants. Several studies have been carried out in cellular models of neurotoxicity of the extract of these fruits, to document the beneficial effects for human health, as well as to prove its antiproliferative effect in cancer cells. In the present review, through a synthesis of existing information in the scientific literature, we demonstrate that hybrid fruits are a source of antioxidant and bioactive compounds, which act in the inhibition of diseases such as cancer, diabetes, and inflammatory and neurodegenerative diseases, and consequently improving human health.

CRISPR technology towards genome editing of the perennial and semi-perennial crops citrus, coffee and sugarcane

Gene editing technologies have opened up the possibility of manipulating the genome of any organism in a predicted way. CRISPR technology is the most used genome editing tool and, in agriculture, it has allowed the expansion of possibilities in plant biotechnology, such as gene knockout or knock-in, transcriptional regulation, epigenetic modification, base editing, RNA editing, prime editing, and nucleic acid probing or detection. This technology mostly depends on in vitro tissue culture and genetic transformation/transfection protocols, which sometimes become the major challenges for its application in different crops. Agrobacterium-mediated transformation, biolistics, plasmid or RNP (ribonucleoprotein) transfection of protoplasts are some of the commonly used CRISPR delivery methods, but they depend on the genotype and target gene for efficient editing. The choice of the CRISPR system (Cas9, Cas12), CRISPR mechanism (plasmid or RNP) and transfection technique (Agrobacterium spp., PEG solution, lipofection) directly impacts the transformation efficiency and/or editing rate. Besides, CRISPR/Cas technology has made countries rethink regulatory frameworks concerning genetically modified organisms and flexibilize regulatory obstacles for edited plants. Here we present an overview of the state-of-the-art of CRISPR technology applied to three important crops worldwide (citrus, coffee and sugarcane), considering the biological, methodological, and regulatory aspects of its application. In addition, we provide perspectives on recently developed CRISPR tools and promising applications for each of these crops, thus highlighting the usefulness of gene editing to develop novel cultivars.

CRISPR/Cas as a Genome-Editing Technique in Fruit Tree Breeding

CRISPR (short for "Clustered Regularly Interspaced Short Palindromic Repeats") is a technology that research scientists use to selectively modify the DNA of living organisms. CRISPR was adapted for use in the laboratory from the naturally occurring genome-editing systems found in bacteria. In this work, we reviewed the methods used to introduce CRISPR/Cas-mediated genome editing into fruit species, as well as the impacts of the application of this technology to activate and knock out target genes in different fruit tree species, including on tree development, yield, fruit quality, and tolerance to biotic and abiotic stresses. The application of this gene-editing technology could allow the development of new generations of fruit crops with improved traits by targeting different genetic segments or even could facilitate the introduction of traits into elite cultivars without changing other traits. However, currently, the scarcity of efficient regeneration and transformation protocols in some species, the fact that many of those procedures are genotype-dependent, and the convenience of segregating the transgenic parts of the CRISPR system represent the main handicaps limiting the potential of genetic editing techniques for fruit trees. Finally, the latest news on the legislation and regulations about the use of plants modified using CRISPR/Cas systems has been also discussed.

Biotechnological and Biocontrol Approaches for Mitigating Postharvest Diseases Caused by Fungal Pathogens and Their Mycotoxins in Fruits: A Review

Postharvest diseases caused by fungal pathogens are significant contributors to the postharvest losses of fruits. Moreover, some fungal pathogens produce mycotoxins, which further compromise the safety and quality of fruits. In this review, the potential of biotechnological and biocontrol approaches for mitigating postharvest diseases and mycotoxins in fruits is explored. The review begins by discussing the impact of postharvest diseases on fruit quality and postharvest losses. Next, it provides an overview of major postharvest diseases caused by fungal pathogens. Subsequently, it delves into the role of biotechnological approaches in controlling these diseases. The review also explored the application of biocontrol agents, such as antagonistic yeasts, bacteria, and fungi, which can suppress pathogen growth. Furthermore, future trends and challenges in these two approaches are discussed in detail. Overall, this review can provide insights into promising biotechnological and biocontrol strategies for managing postharvest diseases and mycotoxins in fruits.

Apple CRISPR-Cas9-A Recipe for Successful Targeting of AGAMOUS-like Genes in Domestic Apple

Fruit trees and other fruiting hardwood perennials are economically valuable, and there is interest in developing improved varieties. Both conventional breeding and biotechnology approaches are being utilized towards the goal of developing advanced cultivars. Increased knowledge of the effectiveness and efficiency of biotechnology approaches can help guide use of the CRISPR gene-editing technology. Here, we examined CRISPR-Cas9-directed genome editing in the valuable commodity fruit tree Malus x domestica (domestic apple). We transformed two cultivars with dual CRISPR-Cas9 constructs designed to target two AGAMOUS-like genes simultaneously. The main goal was to determine the effectiveness of this approach for achieving target gene changes. We obtained 6 Cas9 control and 38 independent CRISPR-Cas9 events. Of the 38 CRISPR-Cas9 events, 34 (89%) had gene edits and 14 (37%) showed changes to all alleles of both target genes. The most common change was large deletions, which were present in 59% of all changed alleles, followed by small deletions (21%), small insertions (12%), and a combination of small insertions and deletions (8%). Overall, a high rate of successful gene alterations was found. Many of these changes are predicted to cause frameshifts and alterations to the predicted peptides. Future work will include monitoring the floral development and floral form.

Bio-based solutions for reducing loss and waste of fresh fruits and vegetables: an industry perspective

Reducing loss and waste of fresh produce requires a systems-wide approach, where supply chain, logistical, and cold chain considerations are balanced with plant breeding, biotechnological, biochemical, and bioinspired solutions. Even though bioengineered specialty crops got off to a rocky start, genetically modified nonbrowning apples and potatoes have been on the market for almost a decade, with bioengineered pineapples, tomatoes, and gene-edited leafy greens with novel taste and nutritional profiles entering the market this year. Traditional and modern breeding expand the toolset of solutions for alleviating labor concerns, extending shelf life, and developing a generally tastier product less likely to be wasted by consumers. Critical to the systems approach is ensuring shelf-life extensions are not 'swallowed' into the supply chain and passed on to consumers.

CRISPR/Cas9-mediated BoaAOP2s editing alters aliphatic glucosinolate side-chain metabolic flux and increases the glucoraphanin content in Chinese kale

Glucoraphanin (GRA) is an aliphatic glucosinolate (GSL), and its hydrolysis product has powerful anticancer activity. ALKENYL HYDROXALKYL PRODUCING 2 (AOP2) gene, encodes a 2-oxoglutarate-dependent dioxygenase, which can catalyze GRA to form gluconapin (GNA). However, GRA only present in trace amounts in Chinese kale. To increase the content of GRA in Chinese kale, three copies of BoaAOP2 were isolated and edited using CRISPR/Cas9 system. The content of GRA was 11.71- to 41.29-fold (0.082-0.289 μmol g^-1 FW) higher in T1 generation of boaaop2 mutants than in wild-type plants, and this was accompanied by an increase in the GRA/GNA ratio and reductions in the content of GNA and total aliphatic GSLs. BoaAOP2.1 is an effective gene for the alkenylation of aliphatic GSLs in Chinese kale. Overall, targeted editing of CRISPR/Cas9-mediated BoaAOP2s altered aliphatic GSL side-chain metabolic flux and enhanced the GRA content in Chinese kale, suggesting that metabolic engineering of BoaAOP2s has huge potential in improving nutritional quality of Chinese kale.

Microsatellite diversity in four cultivated species of Actinidiaceae and Rutaceae

Microsatellites or Simple Sequence Repeats (SSRs) are short iterations of 1-6 bp in the genomes of almost all living organisms. Our study aimed to explore the microsatellite diversity in four cultivated species, namely Actinidia chinensis, Actinidia eriantha, Citrus maxima, and Citrus sinensis of the Actinidiaceae and Rutaceae families. We present a comprehensive analysis of microsatellite abundance, distribution, and motif composition in the genomes of these species. The association of microsatellite abundance with genomic features such as genome size, GC content, number of microsatellites, relative abundance, and relative density was also examined. The results revealed significant variations in the frequency and distribution of microsatellites across the genomes of these four species. Notably, a positive correlation was observed between genome size and microsatellite number as well as with GC content, indicating that larger genomes provide more opportunities for the accumulation of microsatellites. Furthermore, a negative correlation of genome size with relative microsatellite abundance and relative density was observed. These findings provide new insights into the microsatellite landscape of Actinidiaceae and Rutaceae, which could be explored for the development of microsatellite markers for diverse applications in the characterization of genetic diversity, molecular plant breeding, and phylogenetic analysis.

Integration of Metabolome and Transcriptome Profiling Reveals the Effect of Modified Atmosphere Packaging (MAP) on the Browning of Fresh-Cut Lanzhou Lily (Lilium davidii var. unicolor) Bulbs during Storage

The fresh-cut bulbs of the Lanzhou lily (Lilium davidii var. unicolor) experience browning problems during storage. To solve the problem of browning in the preservation of Lanzhou lily bulbs, we first investigated the optimal storage temperature and gas ratio of modified atmosphere packaging (MAP) of Lanzhou lily bulbs. Then, we tested the browning index (BD), activity of phenylalanine ammonia lyase (PAL), polyphenol oxidase (PPO) and peroxidase (POD), the content of malonaldehyde (MDA) and other physiological activity indicators related to browning. The results showed that the storage conditions of 10% O₂ + 5% CO₂ + 85% N₂ and 4 °C were the best. To further explore the anti-browning mechanism of MAP in fresh-cut Lanzhou lily bulbs, the integration of metabolome and transcriptome analyses showed that MAP mainly retarded the unsaturated fatty acid/saturated fatty acid ratio in the cell membrane, inhibited the lipid peroxidation of the membrane and thus maintained the integrity of the cell membrane of Lanzhou lily bulbs. In addition, MAP inhibited the oxidation of phenolic substances and provided an anti-tanning effect. This study provided a preservation scheme to solve the problem of the browning of freshly cut Lanzhou lily bulbs, and discussed the mechanism of MAP in preventing browning during the storage of the bulbs.

Targeting ripening regulators to develop fruit with high quality and extended shelf life

Fruit quality directly impacts fruit marketability and consumer acceptance. Breeders have focused on fruit quality traits to extend shelf life, primarily through fruit texture, but, in some cases, have neglected other qualities such as flavor and nutrition. In recent years, integrative biotechnology and consumer-minded approaches have surfaced, aiding in the development of flavorful, long-lasting fruit. Here, we discussed how specific transcription factors and hormones involved in fruit ripening can be targeted to generate high-quality fruit through traditional breeding and bioengineering. We highlight regulators that can be used to generate novel-colored fruit or biofortify fresh produce with health-promoting nutrients, such as vitamin C. Overall, we argue that addressing grower and industry needs must be balanced with consumer-based traits.

Biotechnological interventions in reducing losses of tropical fruits and vegetables

Tropical fruits and vegetables are predominantly cultivated in warm climate zones, resulting in cultivar diversity in terms of structure, features, and physiology. These constitute a variety of bioactive ingredients such as vitamins, minerals, phenolic acids, anthocyanins, flavonoids, fatty acids, fiber, and their distinctive appearances attract customers across the world. The global production of fruit and vegetables has been attained a tremendous increase for the last few decades. However, huge losses at pre- and postharvest levels are major constraints in their judicious use. Traditional breeding strategies were used to minimize these losses, but their functionality is limited due to their time and labor intensiveness. Recent biotechnological, computational, and multiomics approaches not only address the losses concern but also aid in boosting crop productivity and nutritional values. This article emphasizes molecular tools that have been used to reduce losses of tropical fruits and vegetables at pre- and postharvest levels.

Improving nutrition through biofortification-A systematic review

Nutritious foods are essential for human health and development. However, malnutrition and hidden hunger continue to be a challenge globally. In most developing countries, access to adequate and nutritious food continues to be a challenge. Although hidden hunger is less prevalent in developed countries compared to developing countries where iron (Fe) and zinc (Zn) deficiencies are common. The United Nations (UN) 2nd Sustainable Development Goal was set to eradicate malnutrition and hidden hunger. Hidden hunger has led to numerous cases of infant and maternal mortalities, and has greatly impacted growth, development, cognitive ability, and physical working capacity. This has influenced several countries to develop interventions that could help combat malnutrition and hidden hunger. Interventions such as dietary diversification and food supplementation are being adopted. However, fortification but mainly biofortification has been projected to be the most sustainable solution to malnutrition and hidden hunger. Plant-based foods (PBFs) form a greater proportion of diets in certain populations; hence, fortification of PBFs is relevant in combating malnutrition and hidden hunger. Agronomic biofortification, plant breeding, and transgenic approaches are some currently used strategies in food crops. Crops such as cereals, legumes, oilseeds, vegetables, and fruits have been biofortified through all these three strategies. The transgenic approach is sustainable, efficient, and rapid, making it suitable for biofortification programs. Omics technology has also been introduced to improve the efficiency of the transgenic approach.

Biotechnological approaches for reducing fruit losses caused by pathogenic infection

Fruit loss due to disease occurs in both the field and postharvest. Knowledge of host immune responses and pathogen virulence is enabling the formulation of increasingly sophisticated strategies for disease control. Traditional genetic modification, typically involving overexpression of genes involved in pathogen perception and defence responses, is beginning to be superseded by CRISPR-Cas9 manipulation of host susceptibility targets. Moreover, the refinement of RNA interference (RNAi) strategies, including spray-induced gene silencing (SIGS), is allowing more nuanced control options. These latter approaches have the advantage over earlier technologies in that either they do not result in the generation of genetically modified organisms (RNAi-based SIGS), or the genetic manipulation used leaves no trace of introduced genetic material (gene editing). Thus, these strategies may be more widely acceptable for deployment for future disease control.

A review on urban agriculture: technology, socio-economy, and policy

It has been a challenge to support the expansion of urban agriculture (UA) in cities due to its poor economic profitability. However, it is also hard to deny the increasing benefits of UA in improving the socio-environmental dimension of cities. Hence, in this review, different aspects of UA were examined to highlight its value beyond profitability such as social, health and well-being, disaster risk reduction, and environmental perspectives. A case study and relevant policies were analyzed to determine how policy makers can bridge the gap between current and future UA practices and sustainable development. Bridging these policy gaps can help the UA sector to sustainably grow and become successfully integrated in cities. Moreover, advancements in UA technologies and plant biotechnology were presented as potential solutions in increasing the future profitability of commercial UA. Consequently, as new UA-related technologies evolve, the multidisciplinary nature of UA and its changing identity from agriculture to digital technology, similarly require adaptive policies. These policies should maximize the potential of UA in contributing to resiliency and sustainability and incentivize the organic integration of UA in cities, while equally serving social justice.

Genome Editing for Sustainable Crop Improvement and Mitigation of Biotic and Abiotic Stresses

Climate change poses a serious threat to global agricultural activity and food production. Plant genome editing technologies have been widely used to develop crop varieties with superior qualities or can tolerate adverse environmental conditions. Unlike conventional breeding techniques (e.g., selective breeding and mutation breeding), modern genome editing tools offer more targeted and specific alterations of the plant genome and could significantly speed up the progress of developing crops with desired traits, such as higher yield and/or stronger resilience to the changing environment. In this review, we discuss the current development and future applications of genome editing technologies in mitigating the impacts of biotic and abiotic stresses on agriculture. We focus specifically on the CRISPR/Cas system, which has been the center of attention in the last few years as a revolutionary genome-editing tool in various species. We also conducted a bibliographic analysis on CRISPR-related papers published from 2012 to 2021 (10 years) to identify trends and potential in the CRISPR/Cas-related plant research. In addition, this review article outlines the current shortcomings and challenges of employing genome editing technologies in agriculture with notes on future prospective. We believe combining conventional and more innovative technologies in agriculture would be the key to optimizing crop improvement beyond the limitations of traditional agricultural practices.

Genome Editing for Sustainable Crop Improvement and Mitigation of Biotic and Abiotic Stresses

Climate change poses a serious threat to global agricultural activity and food production. Plant genome editing technologies have been widely used to develop crop varieties with superior qualities or can tolerate adverse environmental conditions. Unlike conventional breeding techniques (e.g., selective breeding and mutation breeding), modern genome editing tools offer more targeted and specific alterations of the plant genome and could significantly speed up the progress of developing crops with desired traits, such as higher yield and/or stronger resilience to the changing environment. In this review, we discuss the current development and future applications of genome editing technologies in mitigating the impacts of biotic and abiotic stresses on agriculture. We focus specifically on the CRISPR/Cas system, which has been the center of attention in the last few years as a revolutionary genome-editing tool in various species. We also conducted a bibliographic analysis on CRISPR-related papers published from 2012 to 2021 (10 years) to identify trends and potential in the CRISPR/Cas-related plant research. In addition, this review article outlines the current shortcomings and challenges of employing genome editing technologies in agriculture with notes on future prospective. We believe combining conventional and more innovative technologies in agriculture would be the key to optimizing crop improvement beyond the limitations of traditional agricultural practices.

A whiff of the future: functions of phenylalanine-derived aroma compounds and advances in their industrial production

Plants produce myriad aroma compounds-odorous molecules that are key factors in countless aspects of the plant's life cycle, including pollinator attraction and communication within and between plants. For humans, aroma compounds convey accurate information on food type, and are vital for assessing the environment. The phenylpropanoid pathway is the origin of notable aroma compounds, such as raspberry ketone and vanillin. In the last decade, great strides have been made in elucidating this pathway with the identification of numerous aroma-related biosynthetic enzymes and factors regulating metabolic shunts. These scientific achievements, together with public acknowledgment of aroma compounds' medicinal benefits and growing consumer demand for natural products, are driving the development of novel biological sources for wide-scale, eco-friendly, and inexpensive production. Microbes and plants that are readily amenable to metabolic engineering are garnering attention as suitable platforms for achieving this goal. In this review, we discuss the importance of aroma compounds from the perspectives of humans, pollinators and plant-plant interactions. Focusing on vanillin and raspberry ketone, which are of high interest to the industry, we present key knowledge on the biosynthesis and regulation of phenylalanine-derived aroma compounds, describe advances in the adoption of microbes and plants as platforms for their production, and propose routes for improvement.

N-acylhomoserine lactonase-based hybrid nanoflowers: a novel and practical strategy to control plant bacterial diseases

BACKGROUND

The disease caused by plant pathogenic bacteria in the production, transportation, and storage of many crops has brought huge losses to agricultural production. N-acylhomoserine lactonases (AHLases) can quench quorum-sensing (QS) by hydrolyzing acylhomoserine lactones (AHLs), which makes them the promising candidates for controlling infections of QS-dependent pathogenic bacteria. Although many AHLases have been isolated and considered as a potentially effective preventive and therapeutic agents for bacterial diseases, the intrinsically poor ambient stability has seriously restricted its application.

RESULTS

Herein, we showed that a spheroid enzyme-based hybrid nanoflower (EHNF), AhlX@Ni₃(PO₄)₂, can be easily synthesized, and it exhibited 10 times AHL (3OC8-HSL) degradation activity than that with free AhlX (a thermostable AHL lactonase). In addition, it showed intriguing stability even at the working concentration, and retained ~ 100% activity after incubation at room temperature (25 °C) for 40 days and approximately 80% activity after incubation at 60 °C for 48 h. Furthermore, it exhibited better organic solvent tolerance and long-term stability in a complicated ecological environment than that of AhlX. To reduce the cost and streamline production processes, CSA@Ni₃(PO₄)₂, which was assembled from the crude supernatants of AhlX and Ni₃(PO₄)₂, was synthesized. Both AhlX@Ni₃(PO₄)₂ and CSA@Ni₃(PO₄)₂ efficiently attenuated pathogenic bacterial infection.

CONCLUSIONS

In this study, we have developed N-acylhomoserine lactonase-based hybrid nanoflowers as a novel and efficient biocontrol reagent with significant control effect, outstanding environmental adaptability and tolerance. It was expected to overcome the bottlenecks of poor stability and limited environmental tolerance that have existed for over two decades and pioneered the practical application of EHNFs in the field of biological control.

Research Progress on Genetic Basis of Fruit Quality Traits in Apple (Malus × domestica)

Identifying the genetic variation characteristics of phenotypic traits is important for fruit tree breeding. During the long-term evolution of fruit trees, gene recombination and natural mutation have resulted in a high degree of heterozygosity. Apple (Malus × domestica Borkh.) shows strong ecological adaptability and is widely cultivated, and is among the most economically important fruit crops worldwide. However, the high level of heterozygosity and large genome of apple, in combination with its perennial life history and long juvenile phase, complicate investigation of the genetic basis of fruit quality traits. With continuing augmentation in the apple genomic resources available, in recent years important progress has been achieved in research on the genetic variation of fruit quality traits. This review focuses on summarizing recent genetic studies on apple fruit quality traits, including appearance, flavor, nutritional, ripening, and storage qualities. In addition, we discuss the mapping of quantitative trait loci, screening of molecular markers, and mining of major genes associated with fruit quality traits. The overall aim of this review is to provide valuable insights into the mechanisms of genetic variation and molecular breeding of important fruit quality traits in apple.

Genetics Matters: Voyaging from the Past into the Future of Humanity and Sustainability

The understanding of how genetic information may be inherited through generations was established by Gregor Mendel in the 1860s when he developed the fundamental principles of inheritance. The science of genetics, however, began to flourish only during the mid-1940s when DNA was identified as the carrier of genetic information. The world has since then witnessed rapid development of genetic technologies, with the latest being genome-editing tools, which have revolutionized fields from medicine to agriculture. This review walks through the historical timeline of genetics research and deliberates how this discipline might furnish a sustainable future for humanity.

Physiological, biochemical, and molecular aspects of grafting in fruit trees

Grafting is a widely used practice for asexual propagation of fruit trees. Many physiological, biochemical, and molecular changes occur upon grafting that can influence important horticultural traits. This technology has many advantages, including avoidance of juvenility, modifying the scion architecture, improving productivity, adapting scion cultivars to unfavourable environmental conditions, and developing traits in resistance to insect pests, bacterial and fungal diseases. A limitation of grafting is scion-rootstock incompatibility. It may be caused by many factors, including insufficient genetic proximity, physiological or biochemical factors, lignification at the graft union, poor graft architecture, insufficient cell recognition between union tissues, and metabolic differences in the scion and the rootstock. Plant hormones, like auxin, ethylene (ET), cytokinin (CK), gibberellin (GA), abscisic acid (ABA), and jasmonic acid (JA) orchestrate several crucial physiological and biochemical processes happening at the site of the graft union. Additionally, epigenetic changes at the union affect chromatin architecture by DNA methylation, histone modification, and the action of small RNA molecules. The mechanism triggering these effects likely is affected by hormonal crosstalk, protein and small molecules movement, nutrients uptake, and transport in the grafted trees. This review provides an overview of the basis of physiological, biochemical, and molecular aspects of fruit tree grafting between scion and rootstock.

Transgenic Model Systems Have Revolutionized the Study of Disease

The current pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected most of the world in a profound way. As an indirect consequence, the general public has been put into direct contact with the research process, almost in real time. Justifiably, a lot of this focus has been targeted toward research directly linked to coronavirus disease 2019 (COVID-19). In this opinion article, we want to highlight to a general audience the value of having a diverse “portfolio” of research approaches for society as a whole. In this study, we will focus on our field of research, namely the study of gene regulation through the use of transgenesis. We will highlight how this type of research can also be used to provide a better understanding as well as tools to fight SARS-CoV-2 and other future challenges.

Genomic Approaches for Improvement of Tropical Fruits: Fruit Quality, Shelf Life and Nutrient Content

The breeding of tropical fruit trees for improving fruit traits is complicated, due to the long juvenile phase, generation cycle, parthenocarpy, polyploidy, polyembryony, heterozygosity and biotic and abiotic factors, as well as a lack of good genomic resources. Many molecular techniques have recently evolved to assist and hasten conventional breeding efforts. Molecular markers linked to fruit development and fruit quality traits such as fruit shape, size, texture, aroma, peel and pulp colour were identified in tropical fruit crops, facilitating Marker-assisted breeding (MAB). An increase in the availability of genome sequences of tropical fruits further aided in the discovery of SNP variants/Indels, QTLs and genes that can ascertain the genetic determinants of fruit characters. Through multi-omics approaches such as genomics, transcriptomics, metabolomics and proteomics, the identification and quantification of transcripts, including non-coding RNAs, involved in sugar metabolism, fruit development and ripening, shelf life, and the biotic and abiotic stress that impacts fruit quality were made possible. Utilizing genomic assisted breeding methods such as genome wide association (GWAS), genomic selection (GS) and genetic modifications using CRISPR/Cas9 and transgenics has paved the way to studying gene function and developing cultivars with desirable fruit traits by overcoming long breeding cycles. Such comprehensive multi-omics approaches related to fruit characters in tropical fruits and their applications in breeding strategies and crop improvement are reviewed, discussed and presented here.

Development and Adoption of Genetically Engineered Plants for Virus Resistance: Advances, Opportunities and Challenges

Plant viruses cause yield losses to crops of agronomic and economic significance and are a challenge to the achievement of global food security. Although conventional plant breeding has played an important role in managing plant viral diseases, it will unlikely meet the challenges posed by the frequent emergence of novel and more virulent viral species or viral strains. Hence there is an urgent need to seek alternative strategies of virus control that can be more readily deployed to contain viral diseases. The discovery in the late 1980s that viral genes can be introduced into plants to engineer resistance to the cognate virus provided a new avenue for virus disease control. Subsequent advances in genomics and biotechnology have led to the refinement and expansion of genetic engineering (GE) strategies in crop improvement. Importantly, many of the drawbacks of conventional breeding, such as long lead times, inability or difficulty to cross fertilize, loss of desirable plant traits, are overcome by GE. Unfortunately, public skepticism towards genetically modified (GM) crops and other factors have dampened the early promise of GE efforts. These concerns are principally about the possible negative effects of transgenes to humans and animals, as well as to the environment. However, with regards to engineering for virus resistance, these risks are overstated given that most virus resistance engineering strategies involve transfer of viral genes or genomic segments to plants. These viral genomes are found in infected plant cells and have not been associated with any adverse effects in humans or animals. Thus, integrating antiviral genes of virus origin into plant genomes is hardly unnatural as suggested by GM crop skeptics. Moreover, advances in deep sequencing have resulted in the sequencing of large numbers of plant genomes and the revelation of widespread endogenization of viral genomes into plant genomes. This has raised the possibility that viral genome endogenization is part of an antiviral defense mechanism deployed by the plant during its evolutionary past. Thus, GM crops engineered for viral resistance would likely be acceptable to the public if regulatory policies were product-based (the North America regulatory model), as opposed to process-based. This review discusses some of the benefits to be gained from adopting GE for virus resistance, as well as the challenges that must be overcome to leverage this technology. Furthermore, regulatory policies impacting virus-resistant GM crops and some success cases of virus-resistant GM crops approved so far for cultivation are discussed.

A Strategy for the Production and Molecular Validation of Agrobacterium-Mediated Intragenic Octoploid Strawberry

Intragenesis is an all-native engineering technology for crop improvement. Using an intragenic strategy to bring genes from wild species to cultivated strawberry could expand the genetic variability. A robust regeneration protocol was developed for the strawberry cv. ‘Shanghai Angel’ by optimizing the dose of Thidiazuron and identifying the most suitable explants. The expression cassette was assembled with all DNA fragments from F. vesca, harboring a sugar transporter gene FvSTP8 driven by a fruit-specific FvKnox promoter. Transformed strawberry was developed through an Agrobacterium-mediated strategy without any selectable markers. Other than PCR selection, probe-based duplex droplet digital PCR (ddPCR) was performed to determine the T-DNA insert. Four independent transformed shoots were obtained with a maximum of 5.3% efficiency. Two lines were confirmed to be chimeras, while the other two were complete transformants with six and 11 copies of the intragene, respectively. The presence of a vector backbone beyond the T-DNA in these transformants indicated that intragenic strawberries were not obtained. The current work optimized the procedures for producing transformed strawberry without antibiotic selection, and accurately determined the insertion copies by ddPCR in the strawberry genome for the first time. These strategies might be promising for the engineering of ‘Shanghai Angel’ and other cultivars to improve agronomic traits.