Large-scale genome editing in plants: approaches, applications, and future perspectives

Exploring the intricacies of antimicrobial resistance: Understanding mechanisms, overcoming challenges, and pioneering innovative solutions

Antimicrobial resistance (AMR) poses a growing global threat. This review examines AMR from diverse angles, tracing the story of antibiotic resistance from its origins to today's crisis. It explores the rise of AMR, from its historical roots to the urgent need to counter this escalating menace. The review explores antibiotic classes, mechanisms, resistance profiles, and genetics. It details bacterial resistance mechanisms with illustrative examples. Multidrug-resistant bacteria spotlight AMR's resilience. Modern AMR control offers hope through precision medicine, stewardship, combination therapy, surveillance, and international cooperation. Converging traditional and innovative treatments presents an exciting frontier as novel compounds seek to enhance antibiotic efficacy. This review calls for global unity and proactive engagement to address AMR collectively, emphasizing the quest for innovative solutions and responsible antibiotic use. It underscores the interconnectedness of science, responsibility, and action in combatting AMR. Humanity faces a choice between antibiotic efficacy and obsolescence. The call is clear: unite, innovate, and prevail against AMR.

Conditional knockdown of gene expression in plants via 3' UTR editing

The spatiotemporal knockdown of genes through genome editing heralds a new frontier in molecular breeding, yet it remains largely unexplored. Recognizing the intricate regulatory networks of endogenous microRNAs (miRNAs), we posited that integration of specific miRNA target sequences into the 3' untranslated region (UTR) of a gene could construct artificial miRNA-dependent regulatory circuits, facilitating precise spatiotemporal gene suppression. To test this hypothesis, we selected three endogenous miRNAs with unique expression profiles by analyzing rice miRNA expression profiles. Results from both transient assays and stably-edited rice plants confirmed that in-locus incorporation of miRNA targets into the 3' UTR of target genes can substantially reduce their expression in a spatiotemporal manner. Using GID1 as a target gene, we found that knockin of the miR156a target led to a remarkable 97% constitutive reduction; knockin of the tissue-specifically expressed miR396c target significantly reduced its expression in shoots alone; and knock-in of the long-day-induced miR528 target triggered a dramatic and temporal decrease of 95% specifically under such light exposure. These findings underscore the viability of miRNA-mediated, in-locus knockdown (MiRKD) as a convenient approach for crop breeding, leveraging miRNA expression traits and genome editing for conditional gene suppression.

Can the molecular and transgenic breeding of crops be an alternative and sustainable technology to meet food demand?

The gradual increase in the worldwide population represents various challenges, and one of the most alarming being the food demand. Historically technological advances led to the development of crops that meets the requirements and demands. Currently, molecular breeding unlocks the genetic potential of crops for their improvement, positioning it as a key technology for the development of new crops. The implementation of OMICs sciences, such spatial and single cell transcriptomics is providing a large and precise information, which can be exploited for crop improvement related to increasing yield, improving the nutritional value; designing new strategies for diseases resistance and management and for conserving biodiversity. Furthermore, the use of new technologies such CRISPR/CAS9 brought us the ability to modify the selected regions of the genome to select the superior's genotypes at a short time and the use of artificial intelligence aid in the analysis of big data generated by OMICS sciences. On the other hand, the application of molecular improvement technologies open up discussion on global regulatory measures, the socio-economic and socio-ethics, as the frameworks on its global regulation and its impact on the society create the public perception on its acceptance. In this review, the use and impact of OMICs sciences and genetic engineering in crops development, the regulatory measures, the socio-economic impact and as well as the mediatic information on genetically modified crops worldwide is discussed along with comprehensive insights on the potential of molecular plant breeding as an alternative and sustainable technology to meet global food demand.

TTLOC: A Tn5 transposase-based approach to localize T-DNA integration sites

Thermal asymmetric interlaced-polymerase chain reaction-based and whole-genome sequencing-based T-DNA localization approaches have been developed for the recovery of T-DNA integration sites (TISs). Nevertheless, a low-cost and high-throughput technique for the detection of TISs, which would facilitate the identification of genetically engineered plants, is in high demand for rapid crop breeding and plant synthetic biology. Here, we present Tn5 transposase-based T-DNA integration site localization (TTLOC), a Tn5-based approach for TIS localization. TTLOC employs specialized adaptor-assembled Tn5 transposases for genomic DNA tagmentation. TTLOC library construction is straightforward, involving only six steps that requires two and a half hours to complete. The resulting pooled library is compatible with next-generation sequencing, which enables high-throughput determination. We demonstrate the ability of TTLOC to recover 95 non-redundant TISs from 65 transgenic Arabidopsis (Arabidopsis thaliana) lines, and 37 non-redundant TISs from the genomes of transgenic rice (Oryza sativa), soybean (Glycine max), tomato (Solanum lycopersicum), potato (Solanum tuberosum), and from the large hexaploid wheat (Triticum aestivum) genome. TTLOC is a cost-effective method, as 1 to 2 Gb of raw data for each multiplexing library are sufficient for efficient TIS calling, independent of the genome size. Our results establish TTLOC as a promising strategy for evaluation of genome engineered plants and for selecting genome safe harbors for trait stacking in crop breeding and plant synthetic biology.

Wheat2035: Integrating pan-omics and advanced biotechnology for future wheat design

Wheat (Triticum aestivum) production is vital for global food security, providing energy and protein to millions of people worldwide. Recent advancements in wheat research have led to significant increases in production, fueled by technological and scientific innovation. Here, we summarize the major advancements in wheat research, particularly the integration of biotechnologies and a deeper understanding of wheat biology. The shift from multi-omics to pan-omics approaches in wheat research has greatly enhanced our understanding of the complex genome, genomic variations, and regulatory networks to decode complex traits. We also outline key scientific questions, potential research directions, and technological strategies for improving wheat over the next decade. Since global wheat production is expected to increase by 60% in 2050, continued innovation and collaboration are crucial. Integrating biotechnologies and a deeper understanding of wheat biology will be essential for addressing future challenges in wheat production, ensuring sustainable practices and improved productivity.

Application and development of CRISPR technology in the secondary metabolic pathway of the active ingredients of phytopharmaceuticals

As an efficient gene editing tool, the CRISPR/Cas9 system has been widely employed to investigate and regulate the biosynthetic pathways of active ingredients in medicinal plants. CRISPR technology holds significant potential for enhancing both the yield and quality of active ingredients in medicinal plants. By precisely regulating the expression of key enzymes and transcription factors, CRISPR technology not only deepens our understanding of secondary metabolic pathways in medicinal plants but also opens new avenues for drug development and the modernization of traditional Chinese medicine. This article introduces the principles of CRISPR technology and its efficacy in gene editing, followed by a detailed discussion of its applications in the secondary metabolism of medicinal plants. This includes an examination of the composition of active ingredients and the implementation of CRISPR strategies within metabolic pathways, as well as the influence of Cas9 protein variants and advanced CRISPR systems in the field. In addition, this article examines the long-term impact of CRISPR technology on the progress of medicinal plant research and development. It also raises existing issues in research, including off-target effects, complexity of genome structure, low transformation efficiency, and insufficient understanding of metabolic pathways. At the same time, this article puts forward some insights in order to provide new ideas for the subsequent application of CRISPR in medicinal plants. In summary, CRISPR technology presents broad application prospects in the study of secondary metabolism in medicinal plants and is poised to facilitate further advancements in biomedicine and agricultural science. As technological advancements continue and challenges are progressively addressed, CRISPR technology is expected to play an increasingly vital role in the research of active ingredients in medicinal plants.

Prospects for synthetic biology in 21st Century agriculture

Plant synthetic biology has emerged as a transformative field in agriculture, offering innovative solutions to enhance food security, provide resilience to climate change, and transition to sustainable farming practices. By integrating advanced genetic tools, computational modeling, and systems biology, researchers can precisely modify plant genomes to enhance traits such as yield, stress tolerance, and nutrient use efficiency. The ability to design plants with specific characteristics tailored to diverse environmental conditions and agricultural needs holds great potential to address global food security challenges. Here, we highlight recent advancements and applications of plant synthetic biology in agriculture, focusing on key areas such as photosynthetic efficiency, nitrogen fixation, drought tolerance, pathogen resistance, nutrient use efficiency, biofortification, climate resilience, microbiology engineering, synthetic plant genomes, and the integration of artificial intelligence (AI) with synthetic biology. These innovations aim to maximize resource use efficiency, reduce reliance on external inputs, and mitigate environmental impacts associated with conventional agricultural practices. Despite challenges related to regulatory approval and public acceptance, the integration of synthetic biology in agriculture holds immense promise for creating more resilient and sustainable agricultural systems, contributing to global food security and environmental sustainability. Rigorous multi-field testing of these approaches will undoubtedly be required to ensure reproducibility.

Identification, charectrization and genetic transformation of lignin and pectin polysaccharides through CRISPR/Cas9 in Nicotiana tobacum

CRISPR/Cas9 system has been successfully implemented in animals and plants is a second-generation genome editing tool. We are able to optimize a Cas9 system to edited Ntab06050 and Ntab0857410 genes in HD and K326 tobacco cultivars respectively. The gene Ntab06050 is related to lignin synthesis while the gene Ntab0857410 belongs to pectin synthesis by utilizing Agrobacterium-mediated leaf disc method. We have constructed total eight different constructs for the lignin related gene family CCoAMT, out of which three constructs have been selected from Ntab0184090, two constructs from Ntab0392460 while one construct from each Ntab0540120, Ntab0857410 and Ntab0135940 gene. To study the Cas9 system in pectin related genes, total five constructs have been utilized under Cas9 system and multiple target sites were selected by identifying PAM sequences. Out of which three constructs were targeted from NtabGAE1and NtabGAE6 homologous while two were targeted from NtabGAUT4 homologous. Where as, UDP-D-glucuronate 4-epimerase gene family is a Golgi localized, might have a role in the interconvertion of UDP-D-GlcA and UDP-D-GalA in pectin synthesis. We have succeeded in the mutation of pectin related NtabGAUT4 and lignin related NtabCCoAMT genes with 6.2% and 9.4% mutation frequency.

Revisiting growth-defence trade-offs and breeding strategies in crops

Plants have evolved a multi-layered immune system to fight off pathogens. However, immune activation is costly and is often associated with growth and development penalty. In crops, yield is the main breeding target and is usually affected by high disease resistance. Therefore, proper balance between growth and defence is critical for achieving efficient crop improvement. This review highlights recent advances in attempts designed to alleviate the trade-offs between growth and disease resistance in crops mediated by resistance (R) genes, susceptibility (S) genes and pleiotropic genes. We also provide an update on strategies for optimizing the growth-defence trade-offs to breed future crops with desirable disease resistance and high yield.

Plant genome information facilitates plant functional genomics

MAIN CONCLUSION

In this review, we give an overview of plant sequencing efforts and how this impacts plant functional genomics research. Plant genome sequence information greatly facilitates the studies of plant biology, functional genomics, evolution of genomes and genes, domestication processes, phylogenetic relationships, among many others. More than two decades of sequencing efforts have boosted the number of available sequenced plant genomes. The first plant genome, of Arabidopsis, was published in the year 2000 and currently, 4604 plant genomes from 1482 plant species have been published. Various large sequence initiatives are running, which are planning to produce tens of thousands of sequenced plant genomes in the near future. In this review, we give an overview on the status of sequenced plant genomes and on the use of genome information in different research areas.

Designing future peanut: the power of genomics-assisted breeding

KEY MESSAGE

Integrating GAB methods with high-throughput phenotyping, genome editing, and speed breeding hold great potential in designing future smart peanut cultivars to meet market and food supply demands. Cultivated peanut (Arachis hypogaea L.), a legume crop greatly valued for its nourishing food, cooking oil, and fodder, is extensively grown worldwide. Despite decades of classical breeding efforts, the actual on-farm yield of peanut remains below its potential productivity due to the complicated interplay of genotype, environment, and management factors, as well as their intricate interactions. Integrating modern genomics tools into crop breeding is necessary to fast-track breeding efficiency and rapid progress. When combined with speed breeding methods, this integration can substantially accelerate the breeding process, leading to faster access of improved varieties to farmers. Availability of high-quality reference genomes for wild diploid progenitors and cultivated peanuts has accelerated the process of gene/quantitative locus discovery, developing markers and genotyping assays as well as a few molecular breeding products with improved resistance and oil quality. The use of new breeding tools, e.g., genomic selection, haplotype-based breeding, speed breeding, high-throughput phenotyping, and genome editing, is probable to boost genetic gains in peanut. Moreover, renewed attention to efficient selection and exploitation of targeted genetic resources is also needed to design high-quality and high-yielding peanut cultivars with main adaptation attributes. In this context, the combination of genomics-assisted breeding (GAB), genome editing, and speed breeding hold great potential in designing future improved peanut cultivars to meet market and food supply demands.

Plant Functional Genomics Based on High-Throughput CRISPR Library Knockout Screening: A Perspective

Plant biology studies in the post-genome era have been focused on annotating genome sequences' functions. The established plant mutant collections have greatly accelerated functional genomics research in the past few decades. However, most plant genome sequences' roles and the underlying regulatory networks remain substantially unknown. Clustered, regularly interspaced short palindromic repeat (CRISPR)-associated systems are robust, versatile tools for manipulating plant genomes with various targeted DNA perturbations, providing an excellent opportunity for high-throughput interrogation of DNA elements' roles. This study compares methods frequently used for plant functional genomics and then discusses different DNA multi-targeted strategies to overcome gene redundancy using the CRISPR-Cas9 system. Next, this work summarizes recent reports using CRISPR libraries for high-throughput gene knockout and function discoveries in plants. Finally, this work envisions the future perspective of optimizing and leveraging CRISPR library screening in plant genomes' other uncharacterized DNA sequences.

Plant responses to climate change, how global warming may impact on food security: a critical review

Global agricultural production must double by 2050 to meet the demands of an increasing world human population but this challenge is further exacerbated by climate change. Environmental stress, heat, and drought are key drivers in food security and strongly impacts on crop productivity. Moreover, global warming is threatening the survival of many species including those which we rely on for food production, forcing migration of cultivation areas with further impoverishing of the environment and of the genetic variability of crop species with fall out effects on food security. This review considers the relationship of climatic changes and their bearing on sustainability of natural and agricultural ecosystems, as well as the role of omics-technologies, genomics, proteomics, metabolomics, phenomics and ionomics. The use of resource saving technologies such as precision agriculture and new fertilization technologies are discussed with a focus on their use in breeding plants with higher tolerance and adaptability and as mitigation tools for global warming and climate changes. Nevertheless, plants are exposed to multiple stresses. This study lays the basis for the proposition of a novel research paradigm which is referred to a holistic approach and that went beyond the exclusive concept of crop yield, but that included sustainability, socio-economic impacts of production, commercialization, and agroecosystem management.

Nanoenabled Enhancement of Plant Tolerance to Heat and Drought Stress on Molecular Response

Global warming has posed significant pressure on agricultural productivity. The resulting abiotic stresses from high temperatures and drought have become serious threats to plants and subsequent global food security. Applying nanomaterials in agriculture can balance the plant's oxidant level and can also regulate phytohormone levels and thus maintain normal plant growth under heat and drought stresses. Nanomaterials can activate and regulate specific stress-related genes, which in turn increase the activity of heat shock protein and aquaporin to enable plants' resistance against abiotic stresses. This review aims to provide a current understanding of nanotechnology-enhanced plant tolerance to heat and drought stress. Molecular mechanisms are explored to see how nanomaterials can alleviate abiotic stresses on plants. In comparison with organic molecules, nanomaterials offer the advantages of targeted transportation and slow release. These advantages help the nanomaterials in mitigating drought and heat stress in plants.

CRISPR-mediated acceleration of wheat improvement: advances and perspectives

Common wheat (Triticum aestivum) is one of the most widely cultivated and consumed crops globally. In the face of limited arable land and climate changes, it is a great challenge to maintain current and increase future wheat production. Enhancing agronomic traits in wheat by introducing mutations across all three homoeologous copies of each gene has proven to be a difficult task due to its large genome with high repetition. However, clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease (Cas) genome editing technologies offer a powerful means of precisely manipulating the genomes of crop species, thereby opening up new possibilities for biotechnology and breeding. In this review, we first focus on the development and optimization of the current CRISPR-based genome editing tools in wheat, emphasizing recent breakthroughs in precise and multiplex genome editing. We then describe the general procedure of wheat genome editing and highlight different methods to deliver the genome editing reagents into wheat cells. Furthermore, we summarize the recent applications and advancements of CRISPR/Cas technologies for wheat improvement. Lastly, we discuss the remaining challenges specific to wheat genome editing and its future prospects.

CRISPR/Cas9 Editing Sites Identification and Multi-Elements Association Analysis in Camellia sinensis

CRISPR/Cas9 is an efficient genome-editing tool, and the identification of editing sites and potential influences in the Camellia sinensis genome have not been investigated. In this study, bioinformatics methods were used to characterise the Camellia sinensis genome including editing sites, simple sequence repeats (SSRs), G-quadruplexes (GQ), gene density, and their relationships. A total of 248,134,838 potential editing sites were identified in the genome, and five PAM types, AGG, TGG, CGG, GGG, and NGG, were observed, of which 66,665,912 were found to be specific, and they were present in all structural elements of the genes. The characteristic region of high GC content, GQ density, and PAM density in contrast to low gene density and SSR density was identified in the chromosomes in the joint analysis, and it was associated with secondary metabolites and amino acid biosynthesis pathways. CRISPR/Cas9, as a technology to drive crop improvement, with the identified editing sites and effector elements, provides valuable tools for functional studies and molecular breeding in Camellia sinensis.

Negative regulators of grain yield and mineral contents in rice: potential targets for CRISPR-Cas9-mediated genome editing

Rice is a major global staple food crop, and improving its grain yield and nutritional quality has been a major thrust research area since last decades. Yield and nutritional quality are complex traits which are controlled by multiple signaling pathways. Sincere efforts during past decades of research have identified several key genetic and molecular regulators that governed these complex traits. The advent of clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-mediated gene knockout approaches has accelerated the development of improved varieties; however, finding out target gene with negative regulatory function in particular trait without giving any pleiotropic effect remains a challenge. Here, we have reviewed past and recent literature and identified important negative regulators of grain yield and mineral contents which could be potential targets for CRISPR-Cas9-mediated gene knockout. Additionally, we have also compiled a list of microRNAs (miRNAs), which target positive regulators of grain yield, plant stress tolerance, and grain mineral contents. Knocking out these miRNAs could help to increase expression of such positive regulators and thus improve the plant trait. The knowledge presented in this review would help to further accelerate the CRISPR-Cas9-mediated trait improvement in rice.

Redesigning crop varieties to win the race between climate change and food security

Climate change poses daunting challenges to agricultural production and food security. Rising temperatures, shifting weather patterns, and more frequent extreme events have already demonstrated their effects on local, regional, and global agricultural systems. Crop varieties that withstand climate-related stresses and are suitable for cultivation in innovative cropping systems will be crucial to maximize risk avoidance, productivity, and profitability under climate-changed environments. We surveyed 588 expert stakeholders to predict current and novel traits that may be essential for future pearl millet, sorghum, maize, groundnut, cowpea, and common bean varieties, particularly in sub-Saharan Africa. We then review the current progress and prospects for breeding three prioritized future-essential traits for each of these crops. Experts predict that most current breeding priorities will remain important, but that rates of genetic gain must increase to keep pace with climate challenges and consumer demands. Importantly, the predicted future-essential traits include innovative breeding targets that must also be prioritized; for example, (1) optimized rhizosphere microbiome, with benefits for P, N, and water use efficiency, (2) optimized performance across or in specific cropping systems, (3) lower nighttime respiration, (4) improved stover quality, and (5) increased early vigor. We further discuss cutting-edge tools and approaches to discover, validate, and incorporate novel genetic diversity from exotic germplasm into breeding populations with unprecedented precision, accuracy, and speed. We conclude that the greatest challenge to developing crop varieties to win the race between climate change and food security might be our innovativeness in defining and boldness to breed for the traits of tomorrow.

WRKY transcription factors in plant defense

Environmental stressors caused by climate change are fundamental barriers to agricultural sustainability. Enhancing the stress resilience of crops is a key strategy in achieving global food security. Plants perceive adverse environmental conditions and initiate signaling pathways to activate precise responses that contribute to their survival. WRKY transcription factors (TFs) are essential players in several signaling cascades and regulatory networks that have crucial implications for defense responses in plants. This review summarizes advances in research concerning how WRKY TFs mediate various signaling cascades and metabolic adjustments as well as how epigenetic modifications involved in environmental stress responses in plants can modulate WRKYs and/or their downstream genes. Emerging research shows that clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas)-mediated genome editing of WRKYs could be used to improve crop resilience.

Mutagenesis in the Age of Next-Generation-Sequencing and Genome Editing

Mutagenesis is a proven, classical technique for inducing a broad spectrum of DNA variations and has led to the creation of thousands of improved varieties in many crop species [...].

FLASH Genome Editing Pipeline: An Efficient and High-Throughput Method to Construct Arrayed CRISPR Library for Plant Functional Genomics

CRISPR/Cas9 genome editing is a revolutionary technology for plant functional genomics and crop breeding. In this system, the Cas9 nuclease is directed by a guide RNA (gRNA) to cut the DNA target and introduce mutation through error-prone DNA break repair. Owing to its simplicity, CRISPR/Cas9-mediated targeted gene knockout is widely used for high-throughput genetic screening in animal cell cultures and bacteria. However, high-throughput genetic screening using CRISPR/Cas9 is still challenging in plants. We recently established a new approach, named the FLASH genome editing pipeline, to construct an arrayed CRISPR library in plants. In this pipeline, a set of 12 PCR fragments with different lengths (referred to as FLASH tags) are used to index the Cas9/gRNA vectors. Subsequently, a mixture of 12 Agrobacterium strains, in which each strain contained a FLASH-tag indexed vector, was transformed into rice plants. As a result, a unique link between the target gene/gRNA and FLASH tag is generated, which allows reading gRNA information in bacterial strains and gene-edited plants using regular PCR and gel electrophoresis. This protocol includes step-by-step instructions for gRNA design, high throughput assembly of FLASH-tag indexed Cas9/gRNA plasmids, Agrobacterium-mediated transformation of 12 indexed plasmids, and fast assignment of target gene information in primary transformants. The arrayed CRISPR library described here is suitable for small- to large-scale genetic screening and allows fast and comprehensive gene function discovery in plants. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Assembly of FLASH-tag-indexed Cas9/gRNA plasmids Basic Protocol 2: Preparation of the Cas9/gRNA plasmid library Basic Protocol 3: Library preparation of Agrobacterium strains and mixing FLASH-tag indexed strains Basic Protocol 4: Grouped transformation and assignments of gRNA information of gene-edited plants.

Strategies and Methods for Improving the Efficiency of CRISPR/Cas9 Gene Editing in Plant Molecular Breeding

Following recent developments and refinement, CRISPR-Cas9 gene-editing technology has become increasingly mature and is being widely used for crop improvement. The application of CRISPR/Cas9 enables the generation of transgene-free genome-edited plants in a short period and has the advantages of simplicity, high efficiency, high specificity, and low production costs, which greatly facilitate the study of gene functions. In plant molecular breeding, the gene-editing efficiency of the CRISPR-Cas9 system has proven to be a key step in influencing the effectiveness of molecular breeding, with improvements in gene-editing efficiency recently becoming a focus of reported scientific research. This review details strategies and methods for improving the efficiency of CRISPR/Cas9 gene editing in plant molecular breeding, including Cas9 variant enzyme engineering, the effect of multiple promoter driven Cas9, and gRNA efficient optimization and expression strategies. It also briefly introduces the optimization strategies of the CRISPR/Cas12a system and the application of BE and PE precision editing. These strategies are beneficial for the further development and optimization of gene editing systems in the field of plant molecular breeding.