CRISPR/Cas Genome Editing and Precision Plant Breeding in Agriculture

Harnessing haploid-inducer mediated genome editing for accelerated maize variety development

The integration of haploid induction and genome editing, termed HI-Edit/IMGE, is a promising tool for generating targeted mutations for crop breeding. However, the technical components and stacking suitable for the maize seed industry have yet to be fully characterised and tested. Here, we developed and assessed three HI-Edit/IMGE maize lines: EditWx, EditSh, and EditWx&Sh, using the haploid inducer CHOI3 and lines engineered using the CRISPR-Cas9 system targeting the Waxy1 (Wx1) and Shrunken2 (Sh2) genes. We meticulously characterised the HI-Edit/IMGE systems, focusing on copy numbers and the mutant alleles mtl and dmp, which facilitate haploid induction. Using B73 and six other parental lines of major commercial varieties as recipients, HI-Edit/IMGE demonstrated maternal haploid induction efficiencies ranging from 8.55% to 20.89% and targeted mutation rates between 0.38% and 1.46%. Comprehensive assessment verified the haploid identification, target gene editing accuracy, genome background integrity, and related agronomic traits. Notably, EditWx&Sh successfully combined distinct CRISPR-Cas9 systems to induce multiple desired mutations, highlighting the potential of HI-Edit/IMGE in accelerating the integration of edited traits into commercial maize varieties. Our findings underscore the importance of meticulous Cas9 copy number characterisation and highlight potential challenges related to somatic chimerism. We also validated the performance of single-cross haploids derived using the HI-Edit/IMGE process. Our results confirm the industrial applicability of generating targeted mutations through pollination and provide critical insights for further optimising this technology.

Enhanced pigment production from plants and microbes: a genome editing approach

Pigments are known for their vital roles in the growth and development of plants and microbes. In addition, they are also an imperative component of several industries, including textiles, foods, and pharmaceuticals, owing to their immense colours and therapeutic potential. Conventionally, pigments are obtained from plant resources, and the advent of in-vitro propagation techniques boosted the massive production. However, it could not meet the booming demand, leading to the incorporation of new genetic engineering tools. This review focuses on the role of various genetic engineering techniques in enhancing pigment production in plants and microorganisms. It also critically analyzes the efficacy and bottlenecks of these techniques in augmenting pigment biosynthesis. Furthermore, the use of microbes as pigment biofactories and the prospects in the field of genome editing to augment pigment synthesis are discussed. The limitations in the existing techniques underline the need for advanced genome editing strategies to broaden the mass production of pigments to meet the surging needs.

Viral delivery of an RNA-guided genome editor for transgene-free germline editing in Arabidopsis

Genome editing is transforming plant biology by enabling precise DNA modifications. However, delivery of editing systems into plants remains challenging, often requiring slow, genotype-specific methods such as tissue culture or transformation1. Plant viruses, which naturally infect and spread to most tissues, present a promising delivery system for editing reagents. However, many viruses have limited cargo capacities, restricting their ability to carry large CRISPR-Cas systems. Here we engineered tobacco rattle virus (TRV) to carry the compact RNA-guided TnpB enzyme ISYmu1 and its guide RNA. This innovation allowed transgene-free editing of Arabidopsis thaliana in a single step, with edits inherited in the subsequent generation. By overcoming traditional reagent delivery barriers, this approach offers a novel platform for genome editing, which can greatly accelerate plant biotechnology and basic research.

Demethylating drugs alter protoplast development, regeneration, and the genome stability of protoplast-derived regenerants of cabbage

BACKGROUND

Methylation is a major DNA modification contributing to the epigenetic regulation of nuclear gene expression and genome stability. DNA methyltransferases (DNMT) inhibitors are widely used in epigenetic and cancer research, but their biological effects and the mechanisms of their action are not well recognized in plants. This research focuses on comparing the effects of two DNMT inhibitors, namely 5-azacytidine (AZA) and zebularine (ZEB), on cellular processes, including organogenesis in vitro. Protoplasts are a unique single-cell system to analyze biological processes in plants; therefore in our study, both inhibitors were applied to protoplast culture medium or the medium used for the regeneration of protoplast-derived calluses.

RESULTS

AZA induced a dose-dependent reduction in protoplast viability, delayed cell wall reconstruction, and reduced mitotic activity, while ZEB in low concentration (2.5 µM) promoted mitoses and stimulated protoplast-derived callus development. The higher effectiveness of shoot regeneration was observed when drugs were applied directly to protoplasts compared to protoplast-derived callus treatments. Our findings reveal that both drugs affected the genome stability of the obtained regenerants by inducing polyploidization. Both drugs induced hypomethylation and modulated the distribution patterns of methylated DNA in the protoplast-derived callus.

CONCLUSION

AZA was more toxic to plant protoplasts compared to ZEB. Both inhibitors affect the ploidy status of protoplast-derived regenerants. A comparison of the data on global methylation levels with the regeneration efficiency suggests that organogenesis in cabbage is partially controlled by variations in DNA methylation levels.

A Truncated Endogenous U6 Promoter Enables High-Efficiency CRISPR Editing in Flax (Linum usitatissimum L.)

Functional U6 promoters are widely utilized in CRISPR gene editing systems for crops. The identification of endogenous U6 promoter activity and the establishment of CRISPR/Cas9 gene editing systems in various crops can enhance the efficiency and accuracy of gene editing in molecular breeding. In this study, four U6 snRNAs were identified in the genome of the oil flax (Linum usitatissimum L.) cultivar Longya 10, which exhibit high homology with the promoter regions of Arabidopsis thaliana U6 snRNA. We cloned and constructed fusion expression vectors with U6 promoter-driven dual-luciferase reporter genes. Transient transformation of flax and Nicotiana benthamiana was performed to measure the relative activity of dual luciferase. The U6-4 on chromosome 14 showed the highest transcriptional activity. Truncations of varying lengths from the 5' end of this promoter were tested, revealing that a 342 bp U6 promoter fragment possesses high transcriptional activity and an optimal length. Subsequently, we constructed a CRISPR/Cas9 gene editing vector with LuU6-5P/AtU6-P driving LusPDS sgRNA. Agrobacterium-mediated infection of flax hypocotyls yielded transgenic albino flax shoots. DNA from these shoots was used as a template to amplify LusPDS fragments, which were then sequenced. Sequencing analysis revealed that CRISPR/Cas9 vectors using Lu14U6-4-5P achieved higher editing frequencies at LusPDS compared to AtU6-P-driven systems.

Directed mutagenesis in fruit crops

Fruit crops are rich source of important vitamins, minerals, and dietary fibres. They are essential for global agriculture with respect to nutritional security. Globally, there is a rapid decline in the genetic base of fruit crops warranting breeding strategies to overcome the challenge. Applied mutagenesis has emerged as a viable approach for the focused enhancement of fruit crops utilizing precise genetic alterations to increase a variety of desirable characteristics. However, traditional mutagenesis using physical and chemical mutagens are majorly random in nature. Directed mutagenesis with advancements in genetic engineering and molecular technology allows precise manipulation of genes, which facilitates the efficient and precise knockout of target genes and the targeted insertion or modification of specific DNA sequences within the genome via homologous recombination (HR)-mediated gene replacement. This review presents an in-depth exploration of several directed mutagenesis techniques including CRISPR-Cas9, TILLING, TALEN, MutMap, and MutMap + emphasizing their transformative applications in fruit crops. It also discusses about space mutagenesis. These advanced techniques empower researchers to precisely introduce specific mutations into the genome, skilfully altering gene expression and reshaping protein function with remarkable precision. This review highlights successful examples of directed mutagenesis in a variety of fruit crops such as apples, grapes, citrus, and strawberries and elucidates the impact of directed mutagenesis on traits such as fruit size, colour, flavour, shelf-life, and resistance to diseases and environmental stresses.

An efficient mRNA delivery system for genome editing in plants

Transgene-free genome editing is important for crop improvement as it reduces unanticipated genomic changes. While mRNA delivery systems offer a powerful method for achieving transgene-free genome editing, they remain inefficient and challenging in plants. Here we describe an efficient mRNA delivery system for plants with substantially improved editing efficiency. By optimizing the 5' untranslated regions (5'UTRs) and poly(A) tails of in vitro-transcribed (IVT) mRNAs and coating the mRNA with protamine during particle bombardment, we have developed an optimized mRNA delivery system termed v2_TMV/DEN2. This system enhanced the efficiencies of knock-out, A-to-G and C-to-T base editing by an average 4.7-, 3.4- and 2.5-fold at various endogenous sites compared with plasmid-based transient delivery system via particle bombardment in rice suspension cells and wheat immature embryos 48 h post-transformation. Furthermore, we obtained edited plants with efficiencies of 5.0-180.8% and 26.1-26.2% using v2_TMV/DEN2 in rice and wheat, respectively, compared with 0.0-43.2% and 4.7-10.4% using plasmids. Our study provides a convenient and efficient mRNA delivery system for transgene-free genome editing in plants.

Chloroplast alchemy: rewriting the chloroplast genome with high precision

In the past decade, precise genome editing has transitioned from theory to practical application. Yet, plastid genomes have largely remained impervious to these advances. A recent breakthrough by Mok et al. (2024) demonstrated successful plastid genome editing by developing transgene-free atrazine-resistant arabidopsis (Arabidopsis thaliana) plants.

Cis-regulatory dynamics in plant domestication

Cis-regulatory elements (CREs) are critical sequence determinants for spatiotemporal control of gene expression. Genetic variants within CREs have driven phenotypic transitions from wild to cultivated plants during domestication. This review summarizes our current understanding of genetic variants within CREs involved in plant domestication. We also propose avenues for studies to expand our understanding of both CRE biology and domestication processes, such as examining primary mechanisms that generate CRE genetic variants during plant domestication and investigating the roles of CREs in domestication syndrome. Additionally, we discuss existing challenges and highlight future opportunities for exploring CREs in plant domestication, emphasizing the potential of modifying CREs to contribute to crop improvement.

Transforming cancer treatment: integrating patient-derived organoids and CRISPR screening for precision medicine

The persistently high mortality rates associated with cancer underscore the imperative need for innovative, efficacious, and safer therapeutic agents, as well as a more nuanced understanding of tumor biology. Patient-derived organoids (PDOs) have emerged as innovative preclinical models with significant translational potential, capable of accurately recapitulating the structural, functional, and heterogeneous characteristics of primary tumors. When integrated with cutting-edge genomic tools such as CRISPR, PDOs provide a powerful platform for identifying cancer driver genes and novel therapeutic targets. This comprehensive review delves into recent advancements in CRISPR-mediated functional screens leveraging PDOs across diverse cancer types, highlighting their pivotal role in high-throughput functional genomics and tumor microenvironment (TME) modeling. Furthermore, this review highlights the synergistic potential of integrating PDOs with CRISPR screens in cancer immunotherapy, focusing on uncovering immune evasion mechanisms and improving the efficacy of immunotherapeutic approaches. Together, these cutting-edge technologies offer significant promise for advancing precision oncology.

Accelerating crop improvement via integration of transcriptome-based network biology and genome editing

MAIN CONCLUSION

Big data and network biology infer functional coupling between genes. In combination with machine learning, network biology can dramatically accelerate the pace of gene discovery using modern transcriptomics approaches and be validated via genome editing technology for improving crops to stresses. Unlike other living things, plants are sessile and frequently face various environmental challenges due to climate change. The cumulative effects of combined stresses can significantly influence both plant growth and yields. In navigating the complexities of climate change, ensuring the nourishment of our growing population hinges on implementing precise agricultural systems. Conventional breeding methods have been commonly employed; however, their efficacy has been impeded by limitations in terms of time, cost, and infrastructure. Cutting-edge tools focussing on big data are being championed to usher in a new era in stress biology, aiming to cultivate crops that exhibit enhanced resilience to multifactorial stresses. Transcriptomics, combined with network biology and machine learning, is proving to be a powerful approach for identifying potential genes to target for gene editing, specifically to enhance stress tolerance. The integration of transcriptomic data with genome editing can yield significant benefits, such as gaining insights into gene function by modifying or manipulating of specific genes in the target plant. This review provides valuable insights into the use of transcriptomics platforms and the application of biological network analysis and machine learning in the discovery of novel genes, thereby enhancing the understanding of plant responses to combined or sequential stress. The transcriptomics as a forefront omics platform and how it is employed through biological networks and machine learning that lead to novel gene discoveries for producing multi-stress-tolerant crops, limitations, and future directions have also been discussed.

The Application of DNA Viruses to Biotechnology

The delivery of biomolecules to target cells has been a longstanding challenge in biotechnology. DNA viruses naturally evolved the ability to deliver genetic material to cells and modulate cellular processes. As such, they inherently possess requisite characteristics that have led to their extensive study, engineering, and development as biotechnological tools. Here, we overview the application of DNA viruses to biotechnology, with specific implications in basic research, health, biomanufacturing, and agriculture. For each application, we review how an increasing understanding of virology and technological methods to genetically manipulate DNA viruses has enabled advances in these fields. Additionally, we highlight the remaining challenges to unlocking the full biotechnological potential of DNA viral technologies. Finally, we discuss the importance of balancing continued technological progress with ethical and biosafety considerations.

MEDIATOR15 destabilizes DELLA protein to promote gibberellin-mediated plant development

Mediator, a transcriptional coactivator, regulates plant growth and development by interacting with various transcriptional regulators. MEDIATOR15 (MED15) is a subunit in the Mediator complex potentially involved in developmental control. To uncover molecular functions of Arabidopsis MED15 in development, we searched for its interactors. MED15 was found to interact with DELLA proteins, which negatively regulate gibberellic acid (GA) signaling and positively regulate GA biosynthesis. Mutants and overexpressors of MED15 exhibited multiple GA-related growth phenotypes, which resembled the phenotypes of the DELLA overexpressor and mutant, respectively. Consistent with this observation, DELLA protein levels were inversely correlated with MED15 protein levels, suggesting that MED15 activates GA signaling through DELLA degradation. MED15 was required not only for DELLA-mediated induction of GA-biosynthesis gene expression but also for GA-mediated degradation of DELLA. Therefore, MED15 facilitates DELLA destruction not only by promoting GA biosynthesis but also by accelerating DELLA turnover. Furthermore, MED15-mediated GA signaling was required for timely developmental responses to dark and warm conditions. Our results provide insight into developmental control by Mediator via precise regulation of DELLA stability. These findings are potentially useful for the generation of new crop cultivars with ideal body architecture.

Molecular breeding of tomato: Advances and challenges

The modern cultivated tomato (Solanum lycopersicum) was domesticated from Solanum pimpinellifolium native to the Andes Mountains of South America through a "two-step domestication" process. It was introduced to Europe in the 16th century and later widely cultivated worldwide. Since the late 19th century, breeders, guided by modern genetics, breeding science, and statistical theory, have improved tomatoes into an important fruit and vegetable crop that serves both fresh consumption and processing needs, satisfying diverse consumer demands. Over the past three decades, advancements in modern crop molecular breeding technologies, represented by molecular marker technology, genome sequencing, and genome editing, have significantly transformed tomato breeding paradigms. This article reviews the research progress in the field of tomato molecular breeding, encompassing genome sequencing of germplasm resources, the identification of functional genes for agronomic traits, and the development of key molecular breeding technologies. Based on these advancements, we also discuss the major challenges and perspectives in this field.

Molecular advances in research and applications of male sterility systems in tomato

Tomato, belonging to the nightshade family, is globally considered as a model system for classical and molecular genetics, genomics, and reproductive developmental studies. In the current scenario of climate change, hybrid development is among the crucial elements in the genetic improvement of crop plants. The phenomenon of male sterility is a viable approach for ensuring hybrid seed purity and reducing the cost of hybrid seed production. This review aims to shed light on the use of neoteric genomics and genome editing tools in understanding the genetics and molecular regulation of male sterility in tomato. Plant male gametophyte development is highly susceptible to environmental stress. Abnormalities at any stage of male reproductive development, such as premature or delayed tapetal cell degradation triggered by oxidative stress and programmed cell death (PCD) leads to male sterility in tomato. In tomato, more than 55 sporogenous, structural, and functional male sterile mutants, which are mainly under the control of recessive nuclear genes, have been reported. Recently, the role of open reading frames (ORFs) in governing cytoplasmic male sterility in tomato has also been documented. This review highlights the genetic and genomic progress in the investigation of underlying molecular pathways and practical application of potential male sterile mutants in tomato breeding. The applications and future prospects of genome engineering with CRISPR/Cas9 and mitoTALEN in the generation of novel male sterile systems to expedite tomato breeding is discussed.

Micronutrient Biofortification in Wheat: QTLs, Candidate Genes and Molecular Mechanism

Micronutrient deficiency (hidden hunger) is one of the serious health problems globally, often due to diets dominated by staple foods. Genetic biofortification of a staple like wheat has surfaced as a promising, cost-efficient, and sustainable strategy. Significant genetic diversity exists in wheat and its wild relatives, but the nutritional profile in commercial wheat varieties has inadvertently declined over time, striving for better yield and disease resistance. Substantial efforts have been made to biofortify wheat using conventional and molecular breeding. QTL and genome-wide association studies were conducted, and some of the identified QTLs/marker-trait association (MTAs) for grain micronutrients like Fe have been exploited by MAS. The genetic mechanisms of micronutrient uptake, transport, and storage have also been investigated. Although wheat biofortified varieties are now commercially cultivated in selected regions worldwide, further improvements are needed. This review provides an overview of wheat biofortification, covering breeding efforts, nutritional evaluation methods, nutrient assimilation and bioavailability, and microbial involvement in wheat grain enrichment. Emerging technologies such as non-destructive hyperspectral imaging (HSI)/red, green, and blue (RGB) phenotyping; multi-omics integration; CRISPR-Cas9 alongside genomic selection; and microbial genetics hold promise for advancing biofortification.

Enhancing tiny millets through genome editing: current status and future prospects

This study aims to address the critical need for genetic improvement of small millets, which are vital yet underutilized cereal crops cultivated in semi-arid regions of Africa and Asia. Given their high nutritional value and climate resilience, small millets hold significant potential for food security and sustainable agriculture in arid regions. However, traditional breeding methods have proven to be time-consuming and inefficient in enhancing desirable traits. This study highlights the transformative potential of genome editing technologies, particularly the CRISPR/Cas9 system, in accelerating the development of improved small millet varieties. The findings presented in this paper detail recent advancements in using CRISPR/Cas for enhancing resistance to biotic stresses, including bacterial, viral, and fungal pathogens. Additionally, we explore how genome editing can be applied to improve abiotic stress tolerance, addressing challenges such as drought, cold, heat, and herbicides in small millets. We discuss the existing challenges faced by breeders, including issues related to ploidy levels, off-target effects, and limitations in organelle genome modification. The review also suggests potential strategies for overcoming these bottlenecks, aiming to develop stress-resistant super cultivars. Overall, this paper provides an overview of the current state of genome editing research in small millets while identifying future opportunities to enhance key traits for nutrient enrichment and climate resilience, ultimately paving the way for advancements in these crucial crops.

Recent Advances of Carbon Dots: Synthesis, Plants Applications, Prospects, and Challenges

Nanomaterials and nanotechnology have garnered significant attention in the realm of agricultural production. Carbon dots (CDs), as a class of nanomaterials, play a crucial role in the field of plant growth due to their excellent properties. This review aims to summarize recent achievements on CDs, focusing on their methods of preparation and applications in plants systems. The effects of CDs on seed germination, growth, photosynthesis, nutritional quality, and stress resistance were studied. It has been demonstrated that CDs can promote seed germination and growth, as well as improve photosynthetic efficiency, ultimately leading to increase plants yield. The nutritional quality of the plants treated with CDs was significantly improved. Specifically, the levels of essential mineral elements, vitamins, amino acids, and other constituents that are beneficial to human health increased notably. Additionally, CDs show positive effects on augmenting plant resistance against environmental stresses, such as drought conditions, heavy metal toxicity, and high salinity. Finally, the prospects and challenges of the application of CDs in plant systems are also discussed, which provide a scientific basis for the future application of CDs in agricultural production.

Engineering a bacterial toxin deaminase from the DYW-family into a novel cytosine base editor for plants and mammalian cells

Base editors are precise editing tools that employ deaminases to modify target DNA bases. The DYW-family of cytosine deaminases is structurally and phylogenetically distinct and might be harnessed for genome editing tools. We report a novel CRISPR/Cas9-cytosine base editor using SsdA, a DYW-like deaminase and bacterial toxin. A G103S mutation in SsdA enhances C-to-T editing efficiency while reducing its toxicity. Truncations result in an extraordinarily small enzyme. The SsdA-base editor efficiently converts C-to-T in rice and barley protoplasts and induces mutations in rice plants and mammalian cells. The engineered SsdA is a highly efficient genome editing tool.

Nature Inspired Delivery Vehicles for CRISPR-Based Genome Editing

The advent of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based genome editing technologies has opened up groundbreaking possibilities for treating a wide spectrum of genetic disorders and diseases. However, the success of these technologies relies heavily on the development of efficient and safe delivery systems. Among the most promising approaches are natural and synthetic nanocarrier-mediated delivery systems, including viral vectors, extracellular vesicles (EVs), engineered cellular membrane particles, liposomes, and various nanoparticles. These carriers enhance the efficacy of the CRISPR system by providing a unique combination of efficiency, specificity, and reduced immunogenicity. Synthetic carriers such as liposomes and nanoparticles facilitate CRISPR delivery with high reproducibility and customizable functions. Viral vectors, renowned for their high transduction efficiency and broad tropism, serve as powerful vehicles for delivering CRISPR components to various cell types. EVs, as natural carriers of RNA and proteins, offer a stealth mechanism to evade immune detection, allowing for the targeted delivery of genome editors with minimal off-target effects. Engineered cellular membrane particles further improve delivery by simulating the cellular environment, enhancing uptake, and minimizing immune response. This review explores the innovative integration of CRISPR genome editors with various nanocarrier systems, focusing on recent advancements, applications, and future directions in therapeutic genome editing.

Advancing vegetable genetics with gene editing: a pathway to food security and nutritional resilience in climate-shifted environments

As global populations grow and climate change increasingly disrupts agricultural systems, ensuring food security and nutritional resilience has become a critical challenge. In addition to grains and legumes, vegetables are very important for both human and animals because they contain vitamins, minerals, and fibre. Enhancing the ability of vegetables to withstand climate change threats is essential; however, traditional breeding methods face challenges due to the complexity of the genomic clonal multiplication process. In the postgenomic era, gene editing (GE) has emerged as a powerful tool for improving vegetables. GE can help to increase traits such as abiotic stress tolerance, herbicide tolerance, and disease resistance; improve agricultural productivity; and improve nutritional content and shelf-life by fine-tuning key genes. GE technologies such as Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (CRISPR-Cas9) have revolutionized vegetable breeding by enabling specific gene modifications in the genome. This review highlights recent advances in CRISPR-mediated editing across various vegetable species, highlighting successful modifications that increase their resilience to climatic stressors. Additionally, it explores the potential of GE to address malnutrition by increasing the nutrient content of vegetable crops, thereby contributing to public health and food system sustainability. Additionally, it addresses the implementation of GE-guided breeding strategies in agriculture, considering regulatory, ethical, and public acceptance issues. Enhancing vegetable genetics via GE may provide a reliable and nutritious food supply for an expanding global population under more unpredictable environmental circumstances.

Unlocking crops' genetic potential: Advances in genome and epigenome editing of regulatory regions

Genome editing tools could precisely and efficiently target plant genomes leading to the development of improved crops. Besides editing the coding regions, researchers can employ editing technologies to target specific gene regulatory elements or modify epigenetic marks associated with distal regulatory regions, thereby regulating gene expression in crops. This review outlines several prominent genome editing technologies, including CRISPR-Cas9, TALENs, and ZFNs and recent advancements. The applications for genome and epigenome editing especially of regulatory regions in crop plants is also discussed, including efforts to enhance abiotic stress tolerance, yield, disease resistance and plant phenotype. Additionally, the review addresses the potential of epigenetic modifications, such as DNA methylation and histone modifications, to alter gene expression for crop improvement. Finally, the limitations and future scope of utilizing various genome editing tools to manipulate regulatory elements for gene regulation to unlock the full potential of these tools in plant breeding has been discussed.

DNA-free base editing in lettuce via in vitro transcribed base editors

A newly developed RNA-based adenine and cytosine base editing system achieves targeted and efficient A-to-G and C-to-T conversions in lettuce. This DNA-free base editing method has potential uses in crop breeding and biotechnology.

Synthetic biology for the food industry: advances and challenges

As global environmental pollution increases, climate change worsens, and population growth continues, the challenges of securing a safe, nutritious, and sustainable food supply have become enormous. This has led to new requirements for future food supply methods and functions. The use of synthetic biology technology to create cell factories suitable for food industry production and renewable raw material conversion into: important food components, functional food additives, and nutritional chemicals, represents an important method of solving the problems faced by the food industry. Here, we review the recent progress and applications of synthetic biology in the food industry, including alternatives to: traditional (artificial pigments, meat, starch, and milk), functional (sweeteners, sugar substitutes, nutrients, flavoring agents), and green (green fiber, degradable packing materials, green packaging materials and food traceability) foods. Furthermore, we discuss the future prospects of synthetic biology-based applications in the food industry. Thus, this review may serve as a reference for research on synthetic biology in the: food safety, food nutrition, public health, and health-related fields.

Efficient promoter editing of the SBEIIb gene enables fine-tuning of the resistant starch content in rice

Rice, a staple in diets, undergoes digestion post-consumption, often triggering a swift surge in blood sugar among diabetics, intensifying their health burden. Notably, resistant starch (RS) emerges as a potent ally in fostering satiety and mitigating metabolic syndrome in diabetes. The SBEIIb gene, a key orchestrator of starch branching enzymes, plays a pivotal role in starch synthesis, and its genetic alteration can dramatically boost RS content in rice. Cultivating RS-rich functional germplasms is of great significance for improving human nutrition and health. In this study, the application of CRISPR/Cas9 technology was investigated for precise multi-target editing within the SBEIIb promoter, aiming to generate valuable germplasm resources enriched with RS. The results revealed extensive mutations in the SBEIIb promoter region, resulting in a varied reduction in SBEIIb expression levels. Remarkably, the grains from the homozygous T1 mutant lines displayed a substantial elevation in RS content, ranging from 3 to 12 times greater than that of the wild-type, accompanied by notable alterations in the starch granule morphology of these grains. This study presents an effective breeding strategy for the precise enhancement of RS content and establishes a foundation for further insights into the molecular mechanisms governing cis-element regulation of RS synthesis.

Genetic Improvement of rice Grain size Using the CRISPR/Cas9 System

Rice grain size influences both grain yield and quality, making it a significant target for rice genetic improvement. In recent years, numerous genes related to grain size with differential effects have been cloned. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) gene editing system is a convenient tool for modifying genes. The use of the CRISPR/Cas9 tool for the genetic improvement of grain size-related genes is worth exploring. This paper summarizes the known grain size-related genes and the use of CRISPR/Cas9 for grain size modification and discusses the potential applications of CRISPR/Cas9 for improving rice grain size.

Application of machine learning and genomics for orphan crop improvement

Orphan crops are important sources of nutrition in developing regions and many are tolerant to biotic and abiotic stressors; however, modern crop improvement technologies have not been widely applied to orphan crops due to the lack of resources available. There are orphan crop representatives across major crop types and the conservation of genes between these related species can be used in crop improvement. Machine learning (ML) has emerged as a promising tool for crop improvement. Transferring knowledge from major crops to orphan crops and using machine learning to improve accuracy and efficiency can be used to improve orphan crops.

Transformation of Plant Breeding Using Data Analytics and Information Technology: Innovations, Applications, and Prospective Directions

Our study focused on plant breeding, from traditional methods to the present most advanced genetic and data-driven concepts. Conventional breeding techniques, such as mass selection and cross-breeding, have been instrumental in crop improvement, although they possess inherent limitations in precision and efficiency. Advanced molecular methods allow breeders to improve crops quicker by more accurately targeting specific traits. Data analytics and information technology (IT) are crucial in modern plant breeding, providing tools for data management, analysis, and interpretation of large volumes of data from genomic, phenotypic, and environmental sources. Meanwhile, emerging technologies in machine learning, high-throughput phenotyping, and the Internet of Things (IoT) provide real-time insights into the performance and responses of plants to environmental variables, enabling precision breeding. These tools will allow breeders to select complex traits related to yield, disease resistance, and abiotic stress tolerance more precisely and effectively. Moreover, this data-driven approach will enable breeders to use resources judiciously and make crops resilient, thus contributing to sustainable agriculture. Data analytics integrated into IT will enhance traditional breeding and other key applications in sustainable agriculture, such as crop yield improvement, biofortification, and climate change adaptation. This review aims to highlight the role of interdisciplinary collaboration among breeders, data scientists, and agronomists in absorbing these technologies. Further, this review discusses the future trends that will make plant breeding even more effective with this new wave of artificial intelligence (AI), blockchain, and collaborative platforms, bringing new data transparency, collaboration, and predictability levels. Data and IT-based breeding will greatly contribute to future global food security and sustainable food production. Thus, creating high-performing, resource-efficient crops will be the foundation of a future agricultural vision that balances environmental care. More technological integration in plant breeding is needed for resilient and sustainable food systems to handle the growing population and changing climate challenges.

Diversity, characterization, and biotechnological potential of plant growth-promoting bacteria from Bryophyllum pinnatum (Lam.) (Crassulaceae) roots and rhizosphere soil

Cultivable microbial communities associated with plants inhabiting extreme environments have great potential in biotechnological applications. However, there is a lack of knowledge about these microorganisms from Bryophyllum pinnatum (which survives in severely barren soil) and their ability to promote plant growth. The present study focused on the isolation, identification, biochemical characterization, and potential applications of root endophytic bacteria and rhizosphere bacteria. A total of 73 bacterial isolates were obtained, with 50 derived from rhizospheric soil and 23 from root tissue. The identified strains were categorized into 16 genera, with Bacillus, Priestia, Pseudarthrobacter, Neobacillus, Mesobacillus, and Arthrobacter being the most species-rich genera. Heat stress experiments indicated that almost half (50.7%) of the selected isolates were tolerant to heat stress. Furthermore, most strains present diverse capabilities for biotechnological applications, including the potential for indole-3-acetic acid (IAA) production, organic phosphorus solubilization, inorganic phosphorus solubilization, and nitrogen fixation. Some isolates (21.92%) exhibited broad-spectrum antagonistic activity against various phytopathogenic fungi, including Fusarium spp. Agar plate assays revealed that the Cellulomonas hominis strain LS43 and Bacillus inaquosorum strain LS77 significantly increased the total fresh weight of Arabidopsis (P < 0.05), yet these strains did not significantly affect the primary root length or the number of leaves. Notably, a subset of the strains tested did not significantly increase the growth of Arabidopsis and, in fact, had inhibitory effects on certain growth parameters. This is the first investigation highlighting the potential of root endophytic bacteria and rhizosphere bacteria in association with B. pinnatum in barren soils. Thus, these isolated strains positively influence plant nutrient uptake, stress resilience, and biocontrol to reduce chemical inputs in conventional agricultural practices, highlighting the importance of their development as biofertilizers for improving the quality of barren soil.

Critical considerations and computational tools in plant genome editing

Recent advances in genome editing tools and CRISPR-Cas technologies have enabled plant genome engineering reach new heights. The current regulatory exemptions for certain categories of genome edited products, such as those derived from SDN-1 and SDN-2, which are free of any transgene, have significantly accelerated genome editing research in a number of agricultural crop plants in different countries. Although CRISPR-Cas technology is becoming increasingly popular, it is still important to carefully consider a number of factors before planning and carrying conducting CRISPR-Cas studies. To attempt genome editing in a plant, a high-quality genome sequence and a repeatable tissue culture protocol for in vitro regeneration are essential. One of the most important steps in plant genome editing is the designing of a CRISPR construct, which involves selecting the appropriate Cas protein, sgRNA sequence, and appropriate regulatory sequence to trigger expression. Computational tools and algorithms play a crucial role in construct design and gRNA selection to minimize off-target effects and also to optimize their delivery techniques. Researchers may need to select appropriate software tools capable of analyzing post-editing detection of mutation events and other DNA sequence abnormalities to identify off-target effects. To fully fulfill the potential of plant genome editing, continued advances in computational biology are essential to meet the challenges it faces today.

Enhancing virus-mediated genome editing for cultivated tomato through low temperature

KEY MESSAGE

Viral vector-mediated gene editing is enhanced for cultivated tomato under low temperature conditions, enabling higher mutation rates, heritable, and virus-free gene editing for efficient breeding. The CRISPR/Cas system, a versatile gene-editing tool, has revolutionized plant breeding by enabling precise genetic modifications. The development of robust and efficient genome-editing tools for crops is crucial for their application in plant breeding. In this study, we highly improved virus-induced genome-editing (VIGE) system for cultivated tomato. Vectors of tobacco rattle virus (TRV) and potato virus X (PVX) were used to deliver sgRNA targeting phytoene desaturase (SlPDS), along with mobile RNA sequences of tFT or tRNAIleu, into Cas9-overexpressing cultivated tomato (S. lycopersicum cv. Moneymaker). Our results demonstrate that low temperature significantly enhanced viral vector-mediated gene editing efficiency in both cotyledons and systemic upper leaves. However, no mutant progeny was obtained from TRV- and PVX301-infected MM-Cas9 plants. To address this challenge, we employed tissue culture techniques and found that low-temperature incubations at the initiation stage of tissue culture lead to enhanced editing efficiency in both vectors, resulting in a higher mutation rate (> 70%) of SlPDS in regenerated plants. Heritable gene-edited and virus-free progenies were successfully identified. This study presents a straightforward approach to enhance VIGE efficiency and the expeditious production of gene-edited lines in tomato breeding.

Gene Targeting via CRISPR/Cas9-Mediated DNA Double-Strand Break Induction in Rice

Gene targeting (GT) is a precise genome editing tool to achieve desired modification of a target gene, e.g., introduction of point mutations, knock-in of a reporter gene, or swapping of a functional domain, through homologous recombination. However, due to its low frequency, it has proved difficult to establish a universal GT system. The availability of the CRISPR/Cas9 system for genome editing in plants has opened up possibilities to apply GT successfully to some plant species. Here, we provide protocols for CRISPR/Cas9-mediated DNA double-strand break (DSB)-induced GT in rice.

Revolutionizing cotton cultivation: A comprehensive review of genome editing technologies and their impact on breeding and production

Cotton (Gossypium hirsutum L.), a vital global cash crop, significantly impacts both the agricultural and industrial sectors, providing essential fiber for textiles and valuable byproducts such as cottonseed oil and animal feed. The cultivation of cotton supports millions of livelihoods worldwide, particularly in developing regions, making it a cornerstone of rural economies. Despite its importance, cotton production faces numerous challenges, including biotic stresses from pests and diseases, and abiotic stresses like drought, salinity, and extreme temperatures. These challenges necessitate innovative solutions to ensure sustainable production. Genome editing technologies, particularly CRISPR/Cas9, have revolutionized cotton breeding by enabling precise genetic modifications. These advancements hold promise for developing cotton varieties with enhanced resistance to pests, diseases, and environmental stresses. Early genome editing tools like ZFNs and TALENs paved the way for more precise modifications but were limited by complexity and cost. The introduction of CRISPR/Cas-based technology with its simplicity and efficiency, has dramatically transformed the field, making it the preferred tool for genome editing in crops. Improved version of the technology like CRISPR/Cas12a, CRISPR/Cas13, base and prime editing, developed from CRISPR/Cas systems, provide additional tools with distinct mechanisms, further expanding their potential applications in crop improvement. This comprehensive review explores the impact of genome editing on cotton breeding and production. It discusses the technical challenges, including off-target effects and delivery methods for genome editing components, and highlights ongoing research efforts to overcome these hurdles. The review underscores the potential of genome editing technologies to revolutionize cotton cultivation, enhancing yield, quality, and resilience, ultimately contributing to a sustainable future for the cotton industry.

Enhancing CRISPR-Cas-based gene targeting in tomato using a dominant-negative ku80

The CRISPR-Cas-based gene targeting (GT) method has enabled precise modifications of genomic DNA ranging from single base to several kilobase scales through homologous recombination (HR). In plant somatic cells, canonical non-homologous end-joining (cNHEJ) is the predominant mechanism for repairing double-stranded breaks (DSBs), thus limiting the HR-mediated GT. In this study, we implemented an approach to shift the repair pathway preference toward HR by using a dominant-negative ku80 mutant protein (KUDN) to disrupt the initiation of cNHEJ. The employment of KUDN conferred a 1.71- to 3.55-fold improvement in GT efficiency at the callus stage. When we screened transformants, there was a more remarkable increase in GT efficiency, ranging from 1.62- to 9.84-fold, at two specific tomato loci, SlHKT1;2 and SlEPSPS1. With practical levels of efficiency, this enhanced KUDN-based GT tool successfully facilitated a 9-bp addition at an additional locus, SlCAB13. These findings provide another promising method for more efficient and precise plant breeding.

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.

Genetic Diversity and Differentiation of Silkworm (Bombyx mori) Local Germplasm Resources in China and Uzbekistan

Silkworm (Bombyx mori) is an economically significant insect that produces silk and makes important contributions to the development of silk-producing countries. The genetic diversity and unique adaptive traits of silkworm germplasm resources form the foundation for breeding efforts. In various geographical regions, silkworm have developed distinct traits through long-term adaptive selection. In this study, we focused on identifying and evaluating representative silkworm germplasm resources from both China and Uzbekistan. We discovered notable differences in the morphology and production traits of local silkworm strains, likely influenced by differing geographical environments. It is also possible that China has a long history of silkworm rearing and after a long time of breeding selection, the diversity of silkworm morphology is less than that of Uzbekistan, but the production characteristics are more suitable for silk utilization. Phylogenetic analysis based on genomic comparisons revealed that Uzbekistan's local silkworm strains are positioned between China's local and improved strains. This suggests that Uzbekistan silkworms primarily originated from China. The further analysis of genetic diversity and strain differentiation highlights the unique differences of each country's silkworms, especially in terms of genetic diversity on chromosome 1 (sex chromosome). By identifying and evaluating these germplasm resources and linking them to unique advantageous traits, it provides a scientific basis for improving cocoon silk quality and optimizing sericulture productivity.

Construction and Validation of CRISPR/Cas Vectors for Editing the PDS Gene in Banana (Musa spp.)

Bananas and plantains are important staple food crops affected by biotic and abiotic stresses. The gene editing technique via Clustered Regularly Interspaced Short Palindromic Repeats associated with the Cas protein (CRISPR/Cas) has been used as an important tool for development of cultivars with high tolerance to stresses. This study sought to develop a protocol for the construction of vectors for gene knockout. Here we use the phytoene desaturase (PDS) gene as a case study in Prata-Anã banana by the nonhomologous end junction (NHEJ) method. PDS is a key gene in the carotenoid production pathway in plants and its knockout leads to easily visualized phenotypes such as dwarfism and albinism in plants. Agrobacterium-mediated transformation delivered CRISPR/Cas9 constructs containing gRNAs were inserted into embryogenic cell suspension cultures. This is the first study to provide an effective method/protocol for constructing gene knockout vectors, demonstrating gene editing potential in a Brazilian banana variety. The constitutive (CaMV 35S) and root-specific vectors were successfully assembled and confirmed in transformed Agrobacterium by DNA extraction and PCR. The specificity of transformation protocols makes it possible to use the CRISPR-Cas9 technique to develop Prata-Anã banana plants with enhanced tolerance/resistance to major biotic and abiotic factors.

CRISPR-AsCas12f1 couples out-of-protospacer DNA unwinding with exonuclease activity in the sequential target cleavage

Type V-F CRISPR-Cas12f is a group of hypercompact RNA-guided nucleases that present a versatile in vivo delivery platform for gene therapy. Upon target recognition, Acidibacillus sulfuroxidans Cas12f (AsCas12f1) distinctively engenders three DNA break sites, two of which are located outside the protospacer. Combining ensemble and single-molecule approaches, we elucidate the molecular details underlying AsCas12f1-mediated DNA cleavages. We find that following the protospacer DNA unwinding and non-target strand (NTS) DNA nicking, AsCas12f1 surprisingly carries out bidirectional exonucleolytic cleavage from the nick. Subsequently, DNA unwinding is extended to the out-of-protospacer region, and AsCas12f1 gradually digests the unwound DNA beyond the protospacer. Eventually, the single endonucleolytic target-strand DNA cleavage at 3 nt downstream of the protospacer readily dissociates the ternary AsCas12f1-sgRNA-DNA complex from the protospacer adjacent motif-distal end, leaving a staggered double-strand DNA break. The coupling between the unwinding and cleavage of both protospacer and out-of-protospacer DNA is promoted by Mg2+. Kinetic analysis on the engineered AsCas12f1-v5.1 variant identifies the only accelerated step of the protospacer NTS DNA trimming within the sequential DNA cleavage. Our findings provide a dynamic view of AsCas12f1 catalyzing DNA unwinding-coupled nucleolytic cleavage and help with practical improvements of Cas12f-based genome editing tools.

Genetic and physiological characteristics of CsNPR3 edited citrus and their impact on HLB tolerance

Huanglongbing (HLB) disease, caused by Candidatus Liberibacter asiaticus (CaLas), severely impacts citrus production, and currently, there is no cure. Developing HLB-resistant or tolerant cultivars is crucial, with modifying defense-related genes being a promising approach to managing HLB. NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) is a positive regulator of systemic acquired resistance (SAR), which enhances resistance to pathogens, whereas NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 3 (NPR3) is a negative regulator of SAR. To unambiguously address the role of CsNPR3 in HLB, we introduced mutations into the CsNPR3 gene in sweet orange (Citrus sinensis L. Osbeck) through genome editing and assessed their effects on morphology, physiology, and resistance/tolerance to HLB. Several genome-edited 'Hamlin' sweet orange trees harboring frameshift-inducing insertions or deletions were identified. After confirming the genome editing using Sanger sequencing, selected lines were grafted onto C-146 trifoliate hybrid rootstocks for clonal propagation. The progenies were then infected with CaLas using a no-choice Asian Citrus Psyllid (ACP) feeding assay. Evaluation of the genetic and physiological characteristics of CsNPR3-edited citrus trees under greenhouse conditions revealed that the edited trees exhibited greater vigor than the wild-type trees, despite the lack of significant differences in CaLas titers. Although further field evaluation is needed, our findings indicate that CsNPR3 contributes to HLB-caused tree deterioration and demonstrate that editing CsNPR3 can enhance tolerance to HLB.

Applications and Prospects of CRISPR/Cas9 Technology in the Breeding of Major Tropical Crops

China is a major producer of tropical crops globally, boasting rich varieties and diverse functions. Tropical crops account for two-thirds of the plant species in this country. Many crops and their products, such as oil palm, rubber, banana, sugarcane, cassava, and papaya are well known to people. Most of these products are irreplaceable and possess special functions. They not only supply important raw materials for people's daily life and for industrial and agricultural production but also contribute to the economic growth in the tropical and subtropical regions of China. However, the modern molecular breeding of these crops is severely hampered by their biological characteristics and genetic complexity. Issues such as polyploidy, heterozygosity, vegetative propagation, long juvenile periods, and large plant sizes result in time consuming, low efficiency, and slow progress in conventional breeding of the major tropical crops. The development of genome-editing technologies has brought a new way in tropical crops breeding. As an emerging gene-editing technology, the CRISPR-Cas9 system has been widely used in plants, adopted for its higher targeting efficiency, versatility, and ease of usage. This approach has been applied in oil palm, rubber, banana, sugarcane, cassava, and papaya. This review summarized the delivery patterns, mutation detection, and application of the CRISPR-Cas9 system in tropical crop breeding, discussed the existing problems, and addressed prospects for future applications in this field, providing references to relevant studies.

A DNA-free and genotype-independent CRISPR/Cas9 system in soybean

Here, we report a smart genome editing system for soybean (Glycine max) using the in planta bombardment-ribonucleoprotein (iPB-RNP) method without introducing foreign DNA or requiring traditional tissue culture processes such as embryogenesis and organogenesis. Shoot apical meristem (SAM) of embryonic axes was used as the target tissue for genome editing because the SAM in soybean mature seeds has stem cells and specific cell layers that develop germ cells during the reproductive growth stage. In the iPB-RNP method, the RNP complex of the CRISPR/Cas9 system was directly delivered into SAM stem cells via particle bombardment, and genome-edited plants were generated from these SAMs. Soybean allergenic gene Gly m Bd 30K was targeted in this study. Many E0 (the first generation of genome-edited) plants in this experiment harbored mutant alleles at the targeted locus. Editing frequency of inducing mutations transmissible to the E1 generation was approximately 0.4% to 4.6% of all E0 plants utilized in various soybean varieties. Furthermore, simultaneous mutagenesis by iPB-RNP method was also successfully performed at other loci. Our results offer a practical approach for both plant regeneration and DNA-free genome editing achieved by delivering RNP into the SAM of dicotyledonous plants.

Facts, uncertainties, and opportunities in wheat molecular improvement

The year 2020 was a landmark year for wheat. The wheat HB4 event harboring a drought-resistant gene from sunflowers, received regulatory approval and was grown commercially in Argentina, with approval for food and feed in other countries. This, indeed, is many years after the adoption of genetic modifications in other crops. The lack of consumer acceptance and resulting trade barriers halted the commercialization of the earliest events and had a chilling effect on, especially, private Research & Development (R&D) investments. As regulations for modern breeding technologies such as genome-edited cultivars are being discussed and/or adopted across the globe, we would like to propose a framework to ensure that wheat is not left behind a second time as the potential benefits far outweigh the perceived risks. In this paper, after a review of the technical challenges wheat faces with the generation of trans- and cis-genic wheat varieties, we discuss some of the factors that could help demystify the risk/reward equation and thereby the consumer's reluctance or acceptance of these techniques for future wheat improvement. The advent of next-generation sequencing is shedding light on natural gene transfer between species and the number of perturbations other accepted techniques like mutagenesis create. The transition from classic breeding techniques and embracing transgenic, cisgenic, and genome editing approaches feels inevitable for wheat improvement if we are to develop climate-resilient wheat varieties to feed a growing world population.

Diversity of Gibberellin 2-oxidase genes in the barley genome offers opportunities for genetic improvement

INTRODUCTION

Gibberellin (GA) is a vital phytohormone in regulating plant growth and development. During the "Green Revolution", modification of GA-related genes created semi-dwarfing phenotype in cereal crops but adversely affected grain weight. Gibberellin 2-oxidases (GA2oxs) in barley act as key catabolic enzymes in deactivating GA, but their functions are still less known.

OBJECTIVES

This study investigates the physiological function of two HvGA2ox genes in barley and identifies novel semi-dwarf alleles with minimum impacts on other agronomic traits.

METHODS

Virus-induced gene silencing and CRISPR/Cas9 technology were used to manipulate gene expression of HvGA2ox9 and HvGA2ox8a in barley and RNA-seq was conducted to compare the transcriptome between wild type and mutants. Also, field trials in multiple environments were performed to detect the functional haplotypes.

RESULTS

There were ten GA2oxs that distinctly expressed in shoot, tiller, inflorescence, grain, embryo and root. Knockdown of HvGA2ox9 did not affect plant height, while ga2ox8a mutants generated by CRISPR/Cas9 increased plant height and significantly altered seed width and weight due to the increased bioactive GA4 level. RNA-seq analysis revealed that genes involved in starch and sucrose metabolism were significantly decreased in the inflorescence of ga2ox8a mutants. Furthermore, haplotype analysis revealed one naturally occurring HvGA2ox8a haplotype was associated with decreased plant height, early flowering and wider and heavier seed.

CONCLUSION

Our results demonstrate the potential of manipulating GA2ox genes to fine tune GA signalling and biofunctions in desired plant tissues and open a promising avenue for minimising the trade-off effects of Green Revolution semi-dwarfing genes on grain size and weight. The knowledge will promote the development of next generation barley cultivars with better adaptation to a changing climate.

Advancements in Plant Gene Editing Technology: From Construct Design to Enhanced Transformation Efficiency

Plant gene editing technology has significantly advanced in recent years, thereby transforming both biotechnological research and agricultural practices. This review provides a comprehensive summary of recent advancements in this rapidly evolving field, showcasing significant discoveries from improved transformation efficiency to advanced construct design. The primary focus is on the maturation of the Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas)9 system, which has emerged as a powerful tool for precise gene editing in plants. Through a detailed exploration, we elucidate the intricacies of integrating genetic modifications into plant genomes, shedding light on transport mechanisms, transformation techniques, and optimization strategies specific to CRISPR constructs. Furthermore, we explore the initiatives aimed at extending the frontiers of gene editing to nonmodel plant species, showcasing the growing scope of this technology. Overall, this comprehensive review highlights the significant impact of recent advancements in plant gene editing, illuminating its transformative potential in driving agricultural innovation and biotechnological progress.

Application of uniconazole in improving the high-throughput genetic transformation efficiency in maize

Agrobacterium-mediated genetic transformation is the most effective and widely used delivery system for candidate genes and genome editors in maize, which is an important crop with the largest planting area and the highest yield. Here, we used gibberellin synthesis inhibitor, uniconazole, to enhance the stem strength of regenerated plantlets resulting in a significantly increase from 11.6 % to 18.2 % in the percentage of regenerated plantlets, and the transformation frequency was also improved from 9.4 % to 15.6 % in the test experiments. The physiological condition of immature embryo is greatly affected by ear source, season and insect pests, while it can cause significant fluctuations in the transformation frequency. Our optimization works at the differentiation subculture stage, avoiding the impact on the physiological condition of immature embryo. So, it can be applicated to high-throughput genetic transformation in different seasons and different ear sources throughout the year. The productive experiment results indicated that the annual average transformation frequency significantly improved from 2.76 % to 7.14 % (approximately 2.6 folds improvement), and the tissue culture cycle was shortened from 115 days to 106 days by using optimized system. Our optimized genetic transformation system opens avenues for maize improvement based on transgenic and genome editing technology.

Application of genome editing in plant reproductive biology: recent advances and challenges

KEY MESSAGE

This comprehensive review underscores the application of genome editing in plant reproductive biology, including recent advances and challenges associated with it. Genome editing (GE) is a powerful technology that has the potential to accelerate crop improvement by enabling efficient, precise, and rapid engineering of plant genomes. Over the last decade, this technology has rapidly evolved from the use of meganucleases (homing endonucleases), zinc-finger nucleases, transcription activator-like effector nucleases to the use of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (CRISPR/Cas), which has emerged as a popular GE tool in recent times and has been extensively used in several organisms, including plants. GE has been successfully employed in several crops to improve plant reproductive traits. Improving crop reproductive traits is essential for crop yields and securing the world's food supplies. In this review, we discuss the application of GE in various aspects of plant reproductive biology, including its potential application in haploid induction, apomixis, parthenocarpy, development of male sterile lines, and the regulation of self-incompatibility. We also discuss current challenges and future prospects of this technology for crop improvement, focusing on plant reproduction.

Rational nanoparticle design for efficient biomolecule delivery in plant genetic engineering

The pressing issue of food security amid climate change necessitates innovative agricultural practices, including advanced plant genetic engineering techniques. Efficient delivery of biomolecules such as DNA, RNA, and proteins into plant cells is essential for targeted crop improvements, yet traditional methods face significant barriers. This review discusses the multifaceted challenges of biomolecule delivery into plant cells, emphasizing the limitations of conventional methods. We explore the promise of nanoparticle-mediated delivery systems as a versatile alternative. By highlighting the diverse design parameters used to tune the physical and chemical properties of nanoparticles, we analyze how these factors influence delivery efficacy. Furthermore, we summarize recent advancements in nanoparticle-mediated delivery, showcasing successful examples of DNA, RNA, and protein transport into plant cells. By understanding and optimizing these design parameters, we can enhance the potential of nanoparticle technologies in plant genetic engineering, paving the way for more resilient and productive agriculture.

Genetic Insights and Molecular Breeding Approaches for Downy Mildew Resistance in Cucumber (Cucumis sativus L.): Current Progress and Future Prospects

Cucurbit downy mildew, caused by Pseudoperonospora cubensis, is a devastating disease in cucumbers that leads to significant yield losses in many cucurbit-growing regions worldwide. Developing resistant cucumber varieties is a sustainable approach to managing this disease, especially given the limitations of chemical control and the evolving nature of pathogens. This article reviews the genetic basis of downy mildew resistance in cucumbers, emphasizing key resistance (R) genes and quantitative trait loci (QTLs) that have been mapped. Recent advances in molecular breeding tools, including marker-assisted selection (MAS), genomic selection (GS), and CRISPR/Cas9 genome editing, have accelerated the development of resistant cultivars. This review also explores the role of transcriptomics, genomics, and other 'omics' technologies in unraveling the molecular mechanisms behind resistance and offers insights into the future of breeding strategies aimed at long-term disease management. Management strategies for cucurbit downy mildew are discussed, along with the potential impacts of climate change on the occurrence and severity of downy mildew, highlighting how changing environmental conditions may influence disease dynamics. Integrating these advanced genetic approaches with traditional breeding promises to accelerate the development of downy mildew-resistant cucumber varieties, contributing to the sustainability and resilience of cucumber production.

CRISPR/Cas: An Emerging Toolbox for Engineering Virus Resistance in Plants

Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas have been recognized as powerful genome-editing tools in diverse eukaryotic species, including plants, and thus hold great promise for engineering virus resistance in plants. Nevertheless, further attention is required regarding various issues associated with applying new powerful technologies in the field. This mini-review focuses on the recent advances in using CRISPR/Cas9 and CRISPR/Cas13 systems to combat DNA and RNA viruses in plants. We explored the utility of CRISPR/Cas for targeting the viral genome and editing host susceptibility genes in plants. We also provide insights into the limitations and challenges of using CRISPR/Cas for plant virus interference and propose individual combinatorial solutions. In conclusion, CRISPR/Cas technology has the potential to offer innovative and highly efficient approaches for controlling viruses in important crops in the near future.

Interplays of Cuticle Biosynthesis and Stomatal Development: From Epidermal Adaptation to Crop Improvement

Crop production is limited by environmental stresses such as a water deficit, salinity, and extreme temperature. Lipophilic cuticle and stomatal pore govern plant transpirational water loss and photosynthetic gas exchange and contribute to plant adaptation to stressful environments. Intricate interplays between cuticle biosynthesis and stomatal development are supported by increasing evidence from phenotypic observations. Several mutants, initially identified as being deficient in cuticle development, have exhibited altered phenotypes in terms of stomatal ridges, numbers, patterns, and shapes. Similarly, mutants with abnormal stomatal patterning have shown defective cuticle formation. Recently, signaling components and transcription factors orchestrating cuticle biosynthesis and stomatal formation have been characterized in both model and crop plants. In this review, we summarize the genetic interplay between cuticle biosynthesis and stomata formation. Current strategies and future perspectives on exploiting the intertwined cuticle biosynthesis and stomatal development for crop stress resistance improvement are discussed.