Engineering crops of the future: CRISPR approaches to develop climate-resilient and disease-resistant plants

The ability of Arabidopsis to recover from Basta and its application in isolating Cas9-free mutants

After successfully performing Agrobacterium-mediated CRISPR-Cas9-based gene editing in plants, isolation of the Cas9 T-DNA is essential for the stable inheritance of induced mutations. Here, we report a simple technique that allows the isolation of Cas9-free mutants, eliminating the need for outcrossing or other intricate methods. This method is based on the ability of Basta-sensitive Arabidopsis thaliana seedlings, which generally perish, to recover and grow once transplanted to Basta-free growth media. By growing gene-edited heterozygous populations of single-locus insertion Basta-resistant plants on Basta selection media, plants lacking the Cas9 T-DNA can be identified. These pale-looking plants lacking Cas9 are then rescued on media lacking the Basta to recover Cas9-free plants. The ability of seedlings to recover from Basta selection was also studied in camelina, canola, and wheat. All three crops showed different recovery rates, with wheat demonstrating the highest recovery once transplanted from Basta to normal growth media. In summary, our findings demonstrate that by harnessing the recovery capability of Basta-sensitive seedlings, we can effectively identify and rescue plants lacking the Cas9 T-DNA, enabling the isolation of Cas9-free mutants in Arabidopsis and potentially extending to other crops.

Application of CRISPR/Cas-based gene-editing for developing better banana

Banana (Musa spp.), including plantain, is one of the major staple food and cash crops grown in over 140 countries in the subtropics and tropics, with around 153 million tons annual global production, feeding about 400 million people. Despite its widespread cultivation and adaptability to diverse environments, banana production faces significant challenges from pathogens and pests that often coexist within agricultural landscapes. Recent advancements in CRISPR/Cas-based gene editing offer transformative solutions to enhance banana resilience and productivity. Researchers at IITA, Kenya, have successfully employed gene editing to confer resistance to diseases such as banana Xanthomonas wilt (BXW) by targeting susceptibility genes and banana streak virus (BSV) by disrupting viral sequences. Other breakthroughs include the development of semi-dwarf plants, and increased β-carotene content. Additionally, non-browning banana have been developed to reduce food waste, with regulatory approval in the Philippines. The future prospects of gene editing in banana looks promising with CRISPR-based gene activation (CRISPRa) and inhibition (CRISPRi) techniques offering potential for improved disease resistance. The Cas-CLOVER system provides a precise alternative to CRISPR/Cas9, demonstrating success in generating gene-edited banana mutants. Integration of precision genetics with traditional breeding, and adopting transgene-free editing strategies, will be pivotal in harnessing the full potential of gene-edited banana. The future of crop gene editing holds exciting prospects for producing banana that thrives across diverse agroecological zones and offers superior nutritional value, ultimately benefiting farmers and consumers. This article highlights the pivotal role of CRISPR/Cas technology in advancing banana resilience, yield and nutritional quality, with significant implications for global food security.

A simplified and improved protocol of rice transformation to cater wide range of rice cultivars

The latest CRISPR-Cas9-mediated genome editing technology is expected to bring about revolution in rice yield and quality improvement, and thus validation of rice transformation protocols using CRISPR-Cas9-gRNA constructs is the need of the hour. Moreover, regeneration of more number of transgenic rice plants is prerequisite for developing genome-edited rice lines, as recalcitrant rice varieties were shown to have lower editing efficiencies which necessities screening of large number of transgenic plants to find the suitable edits. In the present study, we have simplified the Agrobacterium-mediated rice transformation protocol for both Indica and Japonica rice cultivars using CRISPR/Cas9 empty vector construct, and the protocols have been suitably optimized for getting large numbers of the regenerated plantlets within the shortest possible time. The Japonica transgenic lines were obtained within 65 days and for the Indica cultivars, it took about 76-78 days. We also obtained about 90% regeneration efficiency for both Japonica and Indica cultivars. The transformation efficiency was about 97% in the case of Japonica and 69-83% in the case of Indica rice cultivars. Furthermore, we screened the OsWRKY24 gene editing efficiency by transforming rice cultivars with CRISPR/Cas9 construct harbouring sgRNA against OsWRKY24 gene and found about 90% editing efficiency in Japonica rice cultivars, while 30% of the transformed Indica cultivars were found to be edited. This implicated the presence of a robust repair mechanism in the Indica rice cultivars.

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.

Drought Stress Amelioration Attributes of Plant-Associated Microbiome on Agricultural Plants

The future global food security depends on the availability of water for agriculture. Yet, the ongoing rise in nonagricultural uses for water, such as urban and industrial uses, and growing environmental quality concerns have increased pressure of irrigation water demand and posed danger to food security. Nevertheless, its severity and duration are predicted to rise shortly. Drought pressure causes stunted growth, severe damage to photosynthesis activity, loss in crop yield, reduced seed germination, and reduced nutrient intake by plants. To overcome the effects of a devastating drought on plants, it is essential to think about the causes, mechanisms of action, and long-term agronomy management and genetics. As a result, there is an urgent need for long-term medication to deal with the harmful effects of drought pressure. The review focuses on the adverse impact of drought on the plant, physiological, and biochemical aspects, and management measures to control the severity of drought conditions. This article reviews the role of genome editing (GE) technologies such as CRISPR 9 (CRISPR-Cas9) related spaces and short palindromic relapse between proteins in reducing the effects of phytohormones, osmolytes, external compounds, proteins, microbes (plant growth-promoting microorganism [PGPM]), approach omics, and drought on plants that support plant growth. This research is to examine the potential of using the microbiome associated with plants for drought resistance and sustainable agriculture. Researchers also advocate using a mix of biotechnology, agronomic, and advanced GE technologies to create drought-tolerant plant varieties.

Breeding rice for yield improvement through CRISPR/Cas9 genome editing method: current technologies and examples

The impending climate change is threatening the rice productivity of the Asian subcontinent as instances of crop failures due to adverse abiotic and biotic stress factors are becoming common occurrences. CRISPR-Cas9 mediated genome editing offers a potential solution for improving rice yield as well as its stress adaptation. This technology allows modification of plant's genetic elements and is not dependent on foreign DNA/gene insertion for incorporating a particular trait. In this review, we have discussed various CRISPR-Cas9 mediated genome editing tools for gene knockout, gene knock-in, simultaneously disrupting multiple genes by multiplexing, base editing and prime editing the genes. The review here also presents how these genome editing technologies have been employed to improve rice productivity by directly targeting the yield related genes or by indirectly manipulating various abiotic and biotic stress responsive genes. Lately, many countries treat genome-edited crops as non-GMOs because of the absence of foreign DNA in the final product. Thus, genome edited rice plants with improved yield attributes and stress resilience are expected to be accepted by the public and solve food crisis of a major portion of the globe.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01423-y.

SYNCAS: Efficient CRISPR/Cas9 gene-editing in difficult to transform arthropods

The genome editing technique CRISPR/Cas9 has led to major advancements in many research fields and this state-of-the-art tool has proven its use in genetic studies for various arthropods. However, most transformation protocols rely on microinjection of CRISPR/Cas9 components into embryos, a method which is challenging for many species. Alternatively, injections can be performed on adult females, but transformation efficiencies can be very low as was shown for the two-spotted spider mite, Tetranychus urticae, a minute but important chelicerate pest on many crops. In this study, we explored different CRISPR/Cas9 formulations to optimize a maternal injection protocol for T. urticae. We observed a strong synergy between branched amphipathic peptide capsules and saponins, resulting in a significant increase of CRISPR/Cas9 knock-out efficiency, exceeding 20%. This CRISPR/Cas9 formulation, termed SYNCAS, was used to knock-out different T. urticae genes - phytoene desaturase, CYP384A1 and Antennapedia - but also allowed to develop a co-CRISPR strategy and facilitated the generation of T. urticae knock-in mutants. In addition, SYNCAS was successfully applied to knock-out white and white-like genes in the western flower thrips, Frankliniella occidentalis. The SYNCAS method allows routine genome editing in these species and can be a game changer for genetic research in other hard to transform arthropods.

CRISPR enables sustainable cereal production for a greener future

The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system has become the most important tool for targeted genome editing in many plant and animal species over the past decade. The CRISPR/Cas9 technology has also sparked a flood of applications and technical advancements in genome editing in the key cereal crops, including rice, wheat, maize, and barley. Here, we review advanced uses of CRISPR/Cas9 and derived systems in genome editing of cereal crops to enhance a variety of agronomically important features. We also highlight new technological advances for delivering preassembled Cas9-gRNA ribonucleoprotein (RNP)-editing systems, multiplex editing, gain-of-function strategies, the use of artificial intelligence (AI)-based tools, and combining CRISPR with novel speed breeding (SB) and vernalization strategies.

CRISPR/Cas system: A revolutionary tool for crop improvement

World's population is elevating at an alarming rate thus, the rising demands of producing crops with better adaptability to biotic and abiotic stresses, superior nutritional as well as morphological qualities, and generation of high-yielding varieties have led to encourage the development of new plant breeding technologies. The availability and easy accessibility of genome sequences for a number of crop plants as well as the development of various genome editing technologies such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) has opened up possibilities to develop new varieties of crop plants with superior desirable traits. However, these approaches has limitation of being more expensive as well as having complex steps and time-consuming. The CRISPR/Cas genome editing system has been intensively studied for allowing versatile target-specific modifications of crop genome that fruitfully aid in the generation of novel varieties. It is an advanced and promising technology with the potential to meet hunger needs and contribute to food production for the ever-growing human population. This review summarizes the usage of novel CRISPR/Cas genome editing tool for targeted crop improvement in stress resistance, yield, quality and nutritional traits in the desired crop plants.

Nanomaterials for intelligent CRISPR-Cas tools: improving environment sustainability

Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) is a desirable gene modification tool covering a wide area in various sectors of medicine, agriculture, and microbial biotechnology. The role of this incredible genetic engineering technology has been extensively investigated; however, it remains formidable with cargo choices, nonspecific delivery, and insertional mutagenesis. Various nanomaterials including lipid, polymeric, and inorganic are being used to deliver the CRISPR-Cas system. Progress in nanomaterials could potentially address these challenges by accelerating precision targeting, cost-effectiveness, and one-step delivery. In this review, we highlighted the advances in nanotechnology and nanomaterials as smart delivery systems for CRISPR-Cas so as to ameliorate applications for environmental remediation including biomedical research and healthcare, strategies for mitigating antimicrobial resistance, and to be used as nanofertilizers for enhancing crop growth, and reducing the environmental impact of traditional fertilizers. The timely co-evolution of nanotechnology and CRISPR technologies has contributed to smart novel nanostructure hybrids for improving the onerous tasks of environmental remediation and biological sustainability.

Harnessing genetic engineering to drive economic bioproduct production in algae

Our reliance on agriculture for sustenance, healthcare, and resources has been essential since the dawn of civilization. However, traditional agricultural practices are no longer adequate to meet the demands of a burgeoning population amidst climate-driven agricultural challenges. Microalgae emerge as a beacon of hope, offering a sustainable and renewable source of food, animal feed, and energy. Their rapid growth rates, adaptability to non-arable land and non-potable water, and diverse bioproduct range, encompassing biofuels and nutraceuticals, position them as a cornerstone of future resource management. Furthermore, microalgae's ability to capture carbon aligns with environmental conservation goals. While microalgae offers significant benefits, obstacles in cost-effective biomass production persist, which curtails broader application. This review examines microalgae compared to other host platforms, highlighting current innovative approaches aimed at overcoming existing barriers. These approaches include a range of techniques, from gene editing, synthetic promoters, and mutagenesis to selective breeding and metabolic engineering through transcription factors.

Fostering plant growth performance under drought stress using rhizospheric microbes, their gene editing, and biochar

Stress due to drought lowers crop yield and frequently leads to a rise in food scarcity. Plants' intricate metabolic systems enable them to tolerate drought stress, but they are unable to handle it well. Adding some external, environmentally friendly supplements can boost plant growth and productivity when it comes to drought-stressed plants. In order to prevent the detrimental effects of drought in agricultural regions, environmentally friendly practices must be upheld. Plant growth-promoting rhizobacteria (PGPR) can exhibit beneficial phytostimulation, mineralization, and biocontrol activities under drought stress. The significant impact of the PGPR previously reported has not been accepted as an effective treatment to lessen drought stress. Recent studies have successfully shown that manipulating microbes can be a better option to reduce the severity of drought in plants. In this review, we demonstrate how modifying agents such as biochar, PGPR consortia, PGPR, and mycorrhizal fungi can help overcome drought stress responses in crop plants. This article also discusses CRISPR/Cas9-modifiable genes, increase plant's effectiveness in drought conditions, and increase plant resistance to drought stress. With an eco-friendly approach in mind, there is a need for practical management techniques having potential prospects based on an integrated strategy mediated by CRISPR-Cas9 editing, PGPR, which may alleviate the effects of drought stress in crops and aid in achieving the United Nation Sustainable Development Goals (UN-SDGs-2030).

Cassava molecular genetics and genomics for enhanced resistance to diseases and pests

Cassava (Manihot esculenta) is one of the most important sources of dietary calories in the tropics, playing a central role in food and economic security for smallholder farmers. Cassava production is highly constrained by several pests and diseases, mostly cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). These diseases cause significant yield losses, affecting food security and the livelihoods of smallholder farmers. Developing resistant varieties is a good way of increasing cassava productivity. Although some levels of resistance have been developed for some of these diseases, there is observed breakdown in resistance for some diseases, such as CMD. A frequent re-evaluation of existing disease resistance traits is required to make sure they are still able to withstand the pressure associated with pest and pathogen evolution. Modern breeding approaches such as genomic-assisted selection in addition to biotechnology techniques like classical genetic engineering or genome editing can accelerate the development of pest- and disease-resistant cassava varieties. This article summarizes current developments and discusses the potential of using molecular genetics and genomics to produce cassava varieties resistant to diseases and pests.

CRISPR/Cas9-gene editing approaches in plant breeding

CRISPR/Cas9 gene editing system is recently developed robust genome editing technology for accelerating plant breeding. Various modifications of this editing system have been established for adaptability in plant varieties as well as for its improved efficiency and portability. This review provides an in-depth look at the various strategies for synthesizing gRNAs for efficient delivery in plant cells, including chemical synthesis and in vitro transcription. It also covers traditional analytical tools and emerging developments in detection methods to analyze CRISPR/Cas9 mediated mutation in plant breeding. Additionally, the review outlines the various analytical tools which are used to detect and analyze CRISPR/Cas9 mediated mutations, such as next-generation sequencing, restriction enzyme analysis, and southern blotting. Finally, the review discusses emerging detection methods, including digital PCR and qPCR. Hence, CRISPR/Cas9 has great potential for transforming agriculture and opening avenues for new advancements in the system for gene editing in plants.

The applications of CRISPR/Cas-mediated microRNA and lncRNA editing in plant biology: shaping the future of plant non-coding RNA research

MAIN CONCLUSION

CRISPR/Cas technology has greatly facilitated plant non-coding RNA (ncRNA) biology research, establishing itself as a promising tool for ncRNA functional characterization and ncRNA-mediated plant improvement. Throughout the last decade, the promising genome editing tool clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated proteins (Cas; CRISPR/Cas) has allowed unprecedented advances in the field of plant functional genomics and crop improvement. Even though CRISPR/Cas-mediated genome editing system has been widely used to elucidate the biological significance of a number of plant protein-coding genes, this technology has been barely applied in the functional analysis of those non-coding RNAs (ncRNAs) that modulate gene expression, such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). Nevertheless, compelling findings indicate that CRISPR/Cas-based ncRNA editing has remarkable potential for deciphering the biological roles of ncRNAs in plants, as well as for plant breeding. For instance, it has been demonstrated that CRISPR/Cas tool could overcome the challenges associated with other approaches employed in functional genomic studies (e.g., incomplete knockdown and off-target activity). Thus, in this review article, we discuss the current status and progress of CRISPR/Cas-mediated ncRNA editing in plant science in order to provide novel prospects for further assessment and validation of the biological activities of plant ncRNAs and to enhance the development of ncRNA-centered protocols for crop improvement.

Revolutionizing Biological Science: The Synergy of Genomics in Health, Bioinformatics, Agriculture, and Artificial Intelligence

With climate emergency, COVID-19, and the rise of planetary health scholarship, the binary of human and ecosystem health has been deeply challenged. The interdependence of human and nonhuman animal health is increasingly acknowledged and paving the way for new frontiers in integrative biology. The convergence of genomics in health, bioinformatics, agriculture, and artificial intelligence (AI) has ushered in a new era of possibilities and applications. However, the sheer volume of genomic/multiomics big data generated also presents formidable sociotechnical challenges in extracting meaningful biological, planetary health and ecological insights. Over the past few years, AI-guided bioinformatics has emerged as a powerful tool for managing, analyzing, and interpreting complex biological datasets. The advances in AI, particularly in machine learning and deep learning, have been transforming the fields of genomics, planetary health, and agriculture. This article aims to unpack and explore the formidable range of possibilities and challenges that result from such transdisciplinary integration, and emphasizes its radically transformative potential for human and ecosystem health. The integration of these disciplines is also driving significant advancements in precision medicine and personalized health care. This presents an unprecedented opportunity to deepen our understanding of complex biological systems and advance the well-being of all life in planetary ecosystems. Notwithstanding in mind its sociotechnical, ethical, and critical policy challenges, the integration of genomics, multiomics, planetary health, and agriculture with AI-guided bioinformatics opens up vast opportunities for transnational collaborative efforts, data sharing, analysis, valorization, and interdisciplinary innovations in life sciences and integrative biology.

Nanotechnology and CRISPR/Cas9 system for sustainable agriculture

The clustered regularly interspaced short palindromic repeats (CRISPR-Cas9), a genome editing tool, has gained a tremendous position due to its therapeutic efficacy, ability to counteract abiotic/biotic stresses in plants, environmental remediation and sustainable agriculture with the aim of food security. This is mainly due to their potential of precised genome modification and numerous genetic engineering protocols with versatility as well as simplicity. This technique is quite useful for crop refinement and overcoming the agricultural losses and regaining the soil fertility hampered by hazardous chemicals. Since CRISPR/Cas9 has been widely accepted in genome editing in plants, however, their revolutionised nature and progress enable genetic engineers to face numerous challenges in plant biotechnology. Therefore, nanoparticles have addressed these challenges and improved cargo delivery and genomic editing processes. Henceforth, this barrier prevents CRISPR-based genetic engineering in plants in order to show efficacy in full potential and eliminate all the barriers. This advancement accelerates the genome editing process and its applications in plant biotechnology enable us to sustain and feed the massive population under varying environments. Genome editing tools using CRISPR/Cas9 and nanotechnology are advantageous that produce transgenic-free plants that overcome global food demands. Here, in this review, we have aimed towards the mechanisms/delivery systems linked with CRISPR/Cas9 system. We have elaborated on the applications of CRISPR/Cas9 and nanotechnology-based systems for sustainable agriculture. Moreover, the challenges and limitations associated with genome editing and delivery systems have also been discussed with a special emphasis on crop improvement.

CRISPR Variants for Gene Editing in Plants: Biosafety Risks and Future Directions

The CRISPR genome editing technology is a crucial tool for enabling revolutionary advancements in plant genetic improvement. This review shows the latest developments in CRISPR/Cas9 genome editing system variants, discussing their benefits and limitations for plant improvement. While this technology presents immense opportunities for plant breeding, it also raises serious biosafety concerns that require careful consideration, including potential off-target effects and the unintended transfer of modified genes to other organisms. This paper highlights strategies to mitigate biosafety risks and explores innovative plant gene editing detection methods. Our review investigates the international biosafety guidelines for gene-edited crops, analyzing their broad implications for agricultural and biotechnology research and advancement. We hope to provide illuminating and refined perspectives for industry practitioners and policymakers by evaluating CRISPR genome enhancement in plants.

Agrobacterium-mediated in planta transformation of cut coleoptile: a new, simplified, and tissue culture-independent method to deliver the CRISPR/Cas9 system in rice

BACKGROUND

Agrobacterium-mediated transformation and particle bombardment are the two common approaches for genome editing in plant species using CRISPR/Cas9 system. Both methods require careful manipulations of undifferentiated cells and tissue culture to regenerate the potentially edited plants. However, tissue culture techniques are laborious and time-consuming.

METHODS AND RESULTS

In this study, we have developed a simplified, tissue culture-independent protocol to deliver the CRISPR/Cas9 system through in planta transformation in Malaysian rice (Oryza sativa L. subsp. indica cv. MR 219). Sprouting seeds with cut coleoptile were used as the target for the infiltration by Agrobacterium tumefaciens and we achieved 9% transformation efficiency. In brief, the dehusked seeds were surface-sterilised and imbibed, and the coleoptile was cut to expose the apical meristem. Subsequently, the cut coleoptile was inoculated with A. tumefaciens strain EHA105 harbouring CRISPR/Cas9 expression vector. The co-cultivation was conducted for five to six days in a dark room (25 ± 2 °C) followed by rooting, acclimatisation, and growing phases. Two-month-old plant leaves were then subjected to a hygromycin selection, and hygromycin-resistant plants were identified as putative transformants. Further validation through the polymerase chain reaction verified the integration of the Cas9 gene in four putative T0 lines. During the fruiting stage, it was confirmed that the Cas9 gene was still present in three randomly selected tillers from two 4-month-old transformed plants.

CONCLUSION

This protocol provides a rapid method for editing the rice genome, bypassing the need for tissue culture. This article is the first to report the delivery of the CRISPR/Cas9 system for in planta transformation in rice.

CRISPR gene editing to improve crop resistance to parasitic plants

Parasitic plants pose a significant threat to global agriculture, causing substantial crop losses and hampering food security. In recent years, CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) gene-editing technology has emerged as a promising tool for developing resistance against various plant pathogens. Its application in combating parasitic plants, however, remains largely unexplored. This review aims to summarise current knowledge and research gaps in utilising CRISPR to develop resistance against parasitic plants. First, we outline recent improvements in CRISPR gene editing tools, and what has been used to combat various plant pathogens. To realise the immense potential of CRISPR, a greater understanding of the genetic basis underlying parasitic plant-host interactions is critical to identify suitable target genes for modification. Therefore, we discuss the intricate interactions between parasitic plants and their hosts, highlighting essential genes and molecular mechanisms involved in defence response and multilayer resistance. These include host resistance responses directly repressing parasitic plant germination or growth and indirectly influencing parasitic plant development via manipulating environmental factors. Finally, we evaluate CRISPR-mediated effectiveness and long-term implications for host resistance and crop improvement, including inducible resistance response and tissue-specific activity. In conclusion, this review highlights the challenges and opportunities CRISPR technology provides to combat parasitic plants and provides insights for future research directions to safeguard global agricultural productivity.

Biofortification revisited: Addressing the role of beneficial soil microbes for enhancing trace elements concentration in staple crops

Trace element deficiency is a pervasive issue contributing to malnutrition on a global scale. The primary cause of this hidden hunger is related to low dietary intake of essential trace elements, which is highly prevalent in numerous regions across the world. To address deficiency diseases in humans, fortification of staple crops with vital trace elements has emerged as a viable solution. Current methods for fortifying crops encompass chemical amendments, genetic breeding, and transgenic approaches, yet these approaches possess certain limitations, constraining their agricultural application. In contrast, fortifying staple crops through the utilization of soil-beneficial microbes has emerged as a promising and economically feasible approach to enhance trace element content in crops. A specific subset of these beneficial soil microbes, referred to as plant growth-promoting microbes, have demonstrated their ability to influence the interactions between plants, soil, and minerals. These microbes facilitate the transport of essential soil minerals, such as zinc, iron, and selenium, into plants, offering the potential for the development of tailored bioinoculants that can enhance the nutritional quality of cereals, pulses, and vegetable crops. Nevertheless, further research efforts are necessary to comprehensively understand the molecular mechanisms underlying the uptake, transport, and augmentation of trace element concentrations in staple crops. By delving deeper into these mechanisms, customized bioinoculants of soil-beneficial microbes can be developed to serve as highly effective strategies in combating trace element deficiency and promoting global nutritional well-being.

Genome Editing and Improvement of Abiotic Stress Tolerance in Crop Plants

Genome editing aims to revolutionise plant breeding and could assist in safeguarding the global food supply. The inclusion of a 12-40 bp recognition site makes mega nucleases the first tools utilized for genome editing and first generation gene-editing tools. Zinc finger nucleases (ZFNs) are the second gene-editing technique, and because they create double-stranded breaks, they are more dependable and effective. ZFNs were the original designed nuclease-based approach of genome editing. The Cys2-His2 zinc finger domain's discovery made this technique possible. Clustered regularly interspaced short palindromic repeats (CRISPR) are utilized to improve genetics, boost biomass production, increase nutrient usage efficiency, and develop disease resistance. Plant genomes can be effectively modified using genome-editing technologies to enhance characteristics without introducing foreign DNA into the genome. Next-generation plant breeding will soon be defined by these exact breeding methods. There is abroad promise that genome-edited crops will be essential in the years to come for improving the sustainability and climate-change resilience of food systems. This method also has great potential for enhancing crops' resistance to various abiotic stressors. In this review paper, we summarize the most recent findings about the mechanism of abiotic stress response in crop plants and the use of the CRISPR/Cas mediated gene-editing systems to improve tolerance to stresses including drought, salinity, cold, heat, and heavy metals.

Genome engineering of disease susceptibility genes for enhancing resistance in plants

Introgression of disease resistance genes (R-genes) to fight against an array of phytopathogens takes several years using conventional breeding approaches. Pathogens develop mechanism(s) to escape plants immune system by evolving new strains/races, thus making them susceptible to disease. Conversely, disruption of host susceptibility factors (or S-genes) provides opportunities for resistance breeding in crops. S-genes are often exploited by phytopathogens to promote their growth and infection. Therefore, identification and targeting of disease susceptibility genes (S-genes) are gaining more attention for the acquisition of resistance in plants. Genome engineering of S-genes results in targeted, transgene-free gene modification through CRISPR-Cas-mediated technology and has been reported in several agriculturally important crops. In this review, we discuss the defense mechanism in plants against phytopathogens, tug of war between R-genes and S-genes, in silico techniques for identification of host-target (S-) genes and pathogen effector molecule(s), CRISPR-Cas-mediated S-gene engineering, its applications, challenges, and future prospects.

Major viral diseases in grain legumes: designing disease resistant legumes from plant breeding and OMICS integration

Grain legumes play a crucial role in human nutrition and as a staple crop for low-income farmers in developing and underdeveloped nations, contributing to overall food security and agroecosystem services. Viral diseases are major biotic stresses that severely challenge global grain legume production. In this review, we discuss how exploring naturally resistant grain legume genotypes within germplasm, landraces, and crop wild relatives could be used as promising, economically viable, and eco-environmentally friendly solution to reduce yield losses. Studies based on Mendelian and classical genetics have enhanced our understanding of key genetic determinants that govern resistance to various viral diseases in grain legumes. Recent advances in molecular marker technology and genomic resources have enabled us to identify genomic regions controlling viral disease resistance in various grain legumes using techniques such as QTL mapping, genome-wide association studies, whole-genome resequencing, pangenome and 'omics' approaches. These comprehensive genomic resources have expedited the adoption of genomics-assisted breeding for developing virus-resistant grain legumes. Concurrently, progress in functional genomics, especially transcriptomics, has helped unravel underlying candidate gene(s) and their roles in viral disease resistance in legumes. This review also examines the progress in genetic engineering-based strategies, including RNA interference, and the potential of synthetic biology techniques, such as synthetic promoters and synthetic transcription factors, for creating viral-resistant grain legumes. It also elaborates on the prospects and limitations of cutting-edge breeding technologies and emerging biotechnological tools (e.g., genomic selection, rapid generation advances, and CRISPR/Cas9-based genome editing tool) in developing virus-disease-resistant grain legumes to ensure global food security.

Recent Trends and Advancements in CRISPR-Based Tools for Enhancing Resistance against Plant Pathogens

Targeted genome editing technologies are becoming the most important and widely used genetic tools in studies of phytopathology. The "clustered regularly interspaced short palindromic repeats (CRISPR)" and its accompanying proteins (Cas) have been first identified as a natural system associated with the adaptive immunity of prokaryotes that have been successfully used in various genome-editing techniques because of its flexibility, simplicity, and high efficiency in recent years. In this review, we have provided a general idea about different CRISPR/Cas systems and their uses in phytopathology. This review focuses on the benefits of knock-down technologies for targeting important genes involved in the susceptibility and gaining resistance against viral, bacterial, and fungal pathogens by targeting the negative regulators of defense pathways of hosts in crop plants via different CRISPR/Cas systems. Moreover, the possible strategies to employ CRISPR/Cas system for improving pathogen resistance in plants and studying plant-pathogen interactions have been discussed.

Strategies for Engineering Virus Resistance in Potato

Potato (Solanum tuberosum L.) is an important vegetable crop that plays a pivotal role in the world, especially given its potential to feed the world population and to act as the major staple food in many developing countries. Every year, significant crop loss is caused by viral diseases due to a lack of effective agrochemical treatments, since only transmission by insect vectors can be combated with the use of insecticides, and this has been an important factor hindering potato production. With the rapid development of molecular biology and plant genetic engineering technology, transgenic approaches and non-transgenic techniques (RNA interference and CRISPR-cas9) have been effectively employed to improve potato protection against devastating viruses. Moreover, the availability of viral sequences, potato genome sequences, and host immune mechanisms has remarkably facilitated potato genetic engineering. In this study, we summarize the progress of antiviral strategies applied in potato through engineering either virus-derived or plant-derived genes. These recent molecular insights into engineering approaches provide the necessary framework to develop viral resistance in potato in order to provide durable and broad-spectrum protection against important viral diseases of solanaceous crops.

Soil microbiome feedback to climate change and options for mitigation

Microbes are a critical component of soil ecosystems, performing crucial functions in biogeochemical cycling, carbon sequestration, and plant health. However, it remains uncertain how their community structure, functioning, and resultant nutrient cycling, including net GHG fluxes, would respond to climate change at different scales. Here, we review global and regional climate change effects on soil microbial community structure and functioning, as well as the climate-microbe feedback and plant-microbe interactions. We also synthesize recent studies on climate change impacts on terrestrial nutrient cycles and GHG fluxes across different climate-sensitive ecosystems. It is generally assumed that climate change factors (e.g., elevated CO₂ and temperature) will have varying impacts on the microbial community structure (e.g., fungi-to-bacteria ratio) and their contribution toward nutrient turnover, with potential interactions that may either enhance or mitigate each other's effects. Such climate change responses, however, are difficult to generalize, even within an ecosystem, since they are subjected to not only a strong regional influence of current ambient environmental and edaphic conditions, historical exposure to fluctuations, and time horizon but also to methodological choices (e.g., network construction). Finally, the potential of chemical intrusions and emerging tools, such as genetically engineered plants and microbes, as mitigation strategies against global change impacts, particularly for agroecosystems, is presented. In a rapidly evolving field, this review identifies the knowledge gaps complicating assessments and predictions of microbial climate responses and hindering the development of effective mitigation strategies.

Agricultural biotechnology for sustainable food security

Of late, global food security has been under threat by the coronavirus disease 2019 (COVID-19) pandemic and the recent military conflict in Eastern Europe. This article presents the objectives of the Sustainable Development Goals and the European Green Deal related to achieving food security and sustainable development in European Union (EU) agriculture, taking the aforementioned threats into account. In addition, it discusses the future of plant agricultural biotechnology and artificial intelligence (AI) systems, considering their potential for reaching the goal of food security. Paradoxically, the present challenging situation may allow politicians and stakeholders of the EU to realize opportunities and use the potential of the biotechnology sector.

Biotechnological interventions for improving the seed longevity in cereal crops: progress and prospects

Seed longevity is a measure of the viability of seeds during long-term storage and is crucial for germplasm conservation and crop improvement programs. Also, longevity is an important trait for ensuring food and nutritional security. Thus, a better understanding of various factors regulating seed longevity is requisite to improve this trait and to minimize the genetic drift during the regeneration of germplasm. In particular, seed deterioration of cereal crops during storage adversely affects agricultural productivity and food security. The irreversible process of seed deterioration involves a complex interplay between different genes and regulatory pathways leading to: loss of DNA integrity, membrane damage, inactivation of storage enzymes and mitochondrial dysfunction. Identifying the genetic determinants of seed longevity and manipulating them using biotechnological tools hold the key to ensuring prolonged seed storage. Genetics and genomics approaches had identified several genomic regions regulating the longevity trait in major cereals such as: rice, wheat, maize and barley. However, very few studies are available in other Poaceae members, including millets. Deploying omics tools, including genomics, proteomics, metabolomics, and phenomics, and integrating the datasets will pinpoint the precise molecular determinants affecting the survivability of seeds. Given this, the present review enumerates the genetic factors regulating longevity and demonstrates the importance of integrated omics strategies to dissect the molecular machinery underlying seed deterioration. Further, the review provides a roadmap for deploying biotechnological approaches to manipulate the genes and genomic regions to develop improved cultivars with prolonged storage potential.

Gene Editing for Plant Resistance to Abiotic Factors: A Systematic Review

Agricultural crops are exposed to various abiotic stresses, such as salinity, water deficits, temperature extremes, floods, radiation, and metal toxicity. To overcome these challenges, breeding programs seek to improve methods and techniques. Gene editing by Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR/Cas-is a versatile tool for editing in all layers of the central dogma with focus on the development of cultivars of plants resistant or tolerant to multiple biotic or abiotic stresses. This systematic review (SR) brings new contributions to the study of the use of CRISPR/Cas in gene editing for tolerance to abiotic stress in plants. Articles deposited in different electronic databases, using a search string and predefined inclusion and exclusion criteria, were evaluated. This SR demonstrates that the CRISPR/Cas system has been applied to several plant species to promote tolerance to the main abiotic stresses. Among the most studied crops are rice and Arabidopsis thaliana, an important staple food for the population, and a model plant in genetics/biotechnology, respectively, and more recently tomato, whose number of studies has increased since 2021. Most studies were conducted in Asia, specifically in China. The Cas9 enzyme is used in most articles, and only Cas12a is used as an additional gene editing tool in plants. Ribonucleoproteins (RNPs) have emerged as a DNA-free strategy for genome editing without exogenous DNA. This SR also identifies several genes edited by CRISPR/Cas, and it also shows that plant responses to stress factors are mediated by many complex-signaling pathways. In addition, the quality of the articles included in this SR was validated by a risk of bias analysis. The information gathered in this SR helps to understand the current state of CRISPR/Cas in the editing of genes and noncoding sequences, which plays a key role in the regulation of various biological processes and the tolerance to multiple abiotic stresses, with potential for use in plant genetic improvement programs.

Multi-locus genome-wide association studies reveal genomic regions and putative candidate genes associated with leaf spot diseases in African groundnut (Arachis hypogaea L.) germplasm

Early leaf spot (ELS) and late leaf spot (LLS) diseases are the two most destructive groundnut diseases in Ghana resulting in ≤ 70% yield losses which is controlled largely by chemical method. To develop leaf spot resistant varieties, the present study was undertaken to identify single nucleotide polymorphism (SNP) markers and putative candidate genes underlying both ELS and LLS. In this study, six multi-locus models of genome-wide association study were conducted with the best linear unbiased predictor obtained from 294 African groundnut germplasm screened for ELS and LLS as well as image-based indices of leaf spot diseases severity in 2020 and 2021 and 8,772 high-quality SNPs from a 48 K SNP array Axiom platform. Ninety-seven SNPs associated with ELS, LLS and five image-based indices across the chromosomes in the 2 two sub-genomes. From these, twenty-nine unique SNPs were detected by at least two models for one or more traits across 16 chromosomes with explained phenotypic variation ranging from 0.01 - 62.76%, with exception of chromosome (Chr) 08 (Chr08), Chr10, Chr11, and Chr19. Seventeen potential candidate genes were predicted at ± 300 kbp of the stable/prominent SNP positions (12 and 5, down- and upstream, respectively). The results from this study provide a basis for understanding the genetic architecture of ELS and LLS diseases in African groundnut germplasm, and the associated SNPs and predicted candidate genes would be valuable for breeding leaf spot diseases resistant varieties upon further validation.

Biotechnology and biodiversity for the sustainable development of our society

Biotechnology has the potential to play a significant role in the sustainable development of our society. This technology involves using living organisms or their products to develop or modify products or processes for specific use. It is a broad term that encompasses a range of technologies, including genetic engineering, tissue culture, and fermentation. While it has many potential benefits, it must be compatible with biodiversity. Biodiversity refers to the variety of life on Earth, including the different plants, animals, and microorganisms that make up our ecosystems. It is essential for the health and functioning of these ecosystems and the sustainable development of our society1, 2.

A Landscape of CRISPR/Cas Technique for Emerging Viral Disease Diagnostics and Therapeutics: Progress and Prospects

Viral diseases have emerged as a serious threat to humanity and as a leading cause of morbidity worldwide. Many viral diagnostic methods and antiviral therapies have been developed over time, but we are still a long way from treating certain infections caused by viruses. Acquired immunodeficiency syndrome (AIDS) is one of the challenges where current medical science advancements fall short. As a result, new diagnostic and treatment options are desperately needed. The CRISPR/Cas9 system has recently been proposed as a potential therapeutic approach for viral disease treatment. CRISPR/Cas9 is a specialised, effective, and adaptive gene-editing technique that can be used to modify, delete, or correct specific DNA sequences. It has evolved into an advanced, configurable nuclease-based single or multiple gene-editing tool with a wide range of applications. It is widely preferred simply because its operational procedures are simple, inexpensive, and extremely efficient. Exploration of infectious virus genomes is required for a comprehensive study of infectious viruses. Herein, we have discussed the historical timeline-based advancement of CRISPR, CRISPR/Cas9 as a gene-editing technology, the structure of CRISPR, and CRISPR as a diagnostic tool for studying emerging viral infections. Additionally, utilizing CRISPR/Cas9 technology to fight viral infections in plants, CRISPR-based diagnostics of viruses, pros, and cons, and bioethical issues of CRISPR/Cas9-based genomic modification are discussed.

Advancing Grain Legumes Domestication and Evolution Studies with Genomics

Grain legumes were domesticated in parallel with cereals in several regions of the world and formed the economic basis of early farming cultures. Since then, legumes have played a vital role in human and animal diets and in fostering agrobiodiversity. Increasing grain legume cultivation will be crucial to safeguard nutritional security and the resilience of agricultural ecosystems across the globe. A better understanding of the molecular underpinnings of domestication and crop evolution of grain legumes may be translated into practical approaches in modern breeding programs to stabilize yield, which is threatened by evolving pathogens and changing climates. During recent decades, domestication research in all crops has greatly benefited from the fast progress in genomic technologies. Yet still, many questions surrounding the domestication and diversification of legumes remain unanswered. In this review, we assess the potential of genomic approaches in grain legume research. We describe the centers of origin and the crucial domestication traits of grain legumes. In addition, we survey the effect of domestication on both above-ground and below-ground traits that have economic importance. Finally, we discuss open questions in grain legume domestication and diversification and outline how to bridge the gap between the preservation of historic crop diversity and their utilization in modern plant breeding.

Mitigating the Mistletoe Menace: Biotechnological and Smart Management Approaches

Mistletoes have been considered a keystone resource for biodiversity, as well as a remarkable source of medicinal attributes that attract pharmacologists. Due to their hemiparasitic nature, mistletoes leach water and nutrients, including primary and secondary metabolites, through the vascular systems of their plant hosts, primarily trees. As a result of intense mistletoe infection, the hosts suffer various growth and physiological detriments, which often lead to tree mortality. Because of their easy dispersal and widespread tropism, mistletoes have become serious pests for commercial fruit and timber plantations. A variety of physical and chemical treatment methods, along with silvicultural practices, have shaped conventional mistletoe management. Others, however, have either failed to circumvent the growing range and tropism of these parasitic plants or present significant environmental and public health risks. A biocontrol approach that could sidestep these issues has never achieved full proof of concept in real-field applications. Our review discusses the downsides of conventional mistletoe control techniques and explores the possibilities of biotechnological approaches using biocontrol agents and transgenic technologies. It is possible that smart management options will pave the way for technologically advanced solutions to mitigate mistletoes that are yet to be exploited.

Raffinose family oligosaccharides (RFOs): role in seed vigor and longevity

Seed vigor and longevity are important agronomic attributes, as they are essentially associated with crop yield and thus the global economy. Seed longevity is a measure of seed viability and the most essential property in gene bank management since it affects regeneration of seed recycling. Reduced seed life or storability is a serious issue in seed storage since germplasm conservation and agricultural enhancement initiatives rely on it. The irreversible and ongoing process of seed deterioration comprises a complex gene regulatory network and altered metabolism that results in membrane damage, DNA integrity loss, mitochondrial dysregulation, protein damage, and disrupted antioxidative machinery. Carbohydrates and/or sugars, primarily raffinose family oligosaccharides (RFOs), have emerged as feasible components for boosting or increasing seed vigor and longevity in recent years. RFOs are known to perform diverse functions in plants, including abiotic and biotic stress tolerance, besides being involved in regulating seed germination, desiccation tolerance, vigor, and longevity. We emphasized and analyzed the potential impact of RFOs on seed vigor and longevity in this review. Here, we comprehensively reviewed the molecular mechanisms involved in seed longevity, RFO metabolism, and how RFO content is critical and linked with seed vigor and longevity. Further molecular basis, biotechnological approaches, and CRISPR/Cas applications have been discussed briefly for the improvement of seed attributes and ultimately crop production. Likewise, we suggest advancements, challenges, and future possibilities in this area.

Advances in Crop Breeding Through Precision Genome Editing

The global climate change and unfavourable abiotic and biotic factors are limiting agricultural productivity and therefore intensifying the challenges for crop scientists to meet the rising demand for global food supply. The introduction of applied genetics to agriculture through plant breeding facilitated the development of hybrid varieties with improved crop productivity. However, the development of new varieties with the existing gene pools poses a challenge for crop breeders. Genetic engineering holds the potential to broaden genetic diversity by the introduction of new genes into crops. But the random insertion of foreign DNA into the plant's nuclear genome often leads to transgene silencing. Recent advances in the field of plant breeding include the development of a new breeding technique called genome editing. Genome editing technologies have emerged as powerful tools to precisely modify the crop genomes at specific sites in the genome, which has been the longstanding goal of plant breeders. The precise modification of the target genome, the absence of foreign DNA in the genome-edited plants, and the faster and cheaper method of genome modification are the remarkable features of the genome-editing technology that have resulted in its widespread application in crop breeding in less than a decade. This review focuses on the advances in crop breeding through precision genome editing. This review includes: an overview of the different breeding approaches for crop improvement; genome editing tools and their mechanism of action and application of the most widely used genome editing technology, CRISPR/Cas9, for crop improvement especially for agronomic traits such as disease resistance, abiotic stress tolerance, herbicide tolerance, yield and quality improvement, reduction of anti-nutrients, and improved shelf life; and an update on the regulatory approval of the genome-edited crops. This review also throws a light on development of high-yielding climate-resilient crops through precision genome editing.

Pangenomics and Crop Genome Adaptation in a Changing Climate

During crop domestication and breeding, wild plant species have been shaped into modern high-yield crops and adapted to the main agro-ecological regions. However, climate change will impact crop productivity in these regions, and agriculture needs to adapt to support future food production. On a global scale, crop wild relatives grow in more diverse environments than crop species, and so may host genes that could support the adaptation of crops to new and variable environments. Through identification of individuals with increased climate resilience we may gain a greater understanding of the genomic basis for this resilience and transfer this to crops. Pangenome analysis can help to identify the genes underlying stress responses in individuals harbouring untapped genomic diversity in crop wild relatives. The information gained from the analysis of these pangenomes can then be applied towards breeding climate resilience into existing crops or to re-domesticating crops, combining environmental adaptation traits with crop productivity.

The Past, Present, and Future of Host Plant Resistance in Cotton: An Australian Perspective

Cotton is a key global fiber crop. However, yield potential is limited by the presence of endemic and introduced pests and diseases. The introduction of host plant resistance (HPR), defined as the purposeful use of resistant crop cultivars to reduce the impact of pests and diseases, has been a key breeding target for the Commonwealth Scientific and Industrial Research Organisation (CSIRO) cotton breeding program. The program has seen success in releasing cultivars resistant to Bacterial blight, Verticillium wilt, Fusarium wilt, and Cotton bunchy top. However, emerging biotic threats such as Black root rot and secondary pests, are becoming more frequent in Australian cotton production systems. The uptake of tools and breeding methods, such as genomic selection, high throughput phenomics, gene editing, and landscape genomics, paired with the continued utilization of sources of resistance from Gossypium germplasm, will be critical for the future of cotton breeding. This review celebrates the success of HPR breeding activities in the CSIRO cotton breeding program and maps a pathway for the future in developing resistant cultivars.

Gene-Editing Technologies and Applications in Legumes: Progress, Evolution, and Future Prospects

Legumes are rich in protein and phytochemicals and have provided a healthy diet for human beings for thousands of years. In recognition of the important role they play in human nutrition and agricultural production, the researchers have made great efforts to gain new genetic traits in legumes such as yield, stress tolerance, and nutritional quality. In recent years, the significant increase in genomic resources for legume plants has prepared the groundwork for applying cutting-edge breeding technologies, such as transgenic technologies, genome editing, and genomic selection for crop improvement. In addition to the different genome editing technologies including the CRISPR/Cas9-based genome editing system, this review article discusses the recent advances in plant-specific gene-editing methods, as well as problems and potential benefits associated with the improvement of legume crops with important agronomic properties. The genome editing technologies have been effectively used in different legume plants including model legumes like alfalfa and lotus, as well as crops like soybean, cowpea, and chickpea. We also discussed gene-editing methods used in legumes and the improvements of agronomic traits in model and recalcitrant legumes. Despite the immense opportunities genome editing can offer to the breeding of legumes, governmental regulatory restrictions present a major concern. In this context, the comparison of the regulatory framework of genome editing strategies in the European Union and the United States of America was also discussed. Gene-editing technologies have opened up new possibilities for the improvement of significant agronomic traits in legume breeding.

Exploitation of Plant Growth Promoting Bacteria for Sustainable Agriculture: Hierarchical Approach to Link Laboratory and Field Experiments

To feed a world population, which will reach 9.7 billion in 2050, agricultural production will have to increase by 35-56%. Therefore, more food is urgently needed. Yield improvements for any given crop would require adequate fertilizer, water, and plant protection from pests and disease, but their further abuse will be economically disadvantageous and will have a negative impact on the environment. Using even more agricultural inputs is simply not possible, and the availability of arable land will be increasingly reduced due to climate changes. To improve agricultural production without further consumption of natural resources, farmers have a powerful ally: the beneficial microorganisms inhabiting the rhizosphere. However, to fully exploit the benefits of these microorganisms and therefore to widely market microbial-based products, there are still gaps that need to be filled, and here we will describe some critical issues that should be better addressed.

CRISPR/Cas9 and Nanotechnology Pertinence in Agricultural Crop Refinement

The CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9) method is a versatile technique that can be applied in crop refinement. Currently, the main reasons for declining agricultural yield are global warming, low rainfall, biotic and abiotic stresses, in addition to soil fertility issues caused by the use of harmful chemicals as fertilizers/additives. The declining yields can lead to inadequate supply of nutritional food as per global demand. Grains and horticultural crops including fruits, vegetables, and ornamental plants are crucial in sustaining human life. Genomic editing using CRISPR/Cas9 and nanotechnology has numerous advantages in crop development. Improving crop production using transgenic-free CRISPR/Cas9 technology and produced fertilizers, pesticides, and boosters for plants by adopting nanotechnology-based protocols can essentially overcome the universal food scarcity. This review briefly gives an overview on the potential applications of CRISPR/Cas9 and nanotechnology-based methods in developing the cultivation of major agricultural crops. In addition, the limitations and major challenges of genome editing in grains, vegetables, and fruits have been discussed in detail by emphasizing its applications in crop refinement strategy.

Nonhomologous end joining as key to CRISPR/Cas-mediated plant chromosome engineering

Although clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas)-mediated gene editing has revolutionized biology and plant breeding, large-scale, heritable restructuring of plant chromosomes is still in its infancy. Duplications and inversions within a chromosome, and also translocations between chromosomes, can now be achieved. Subsequently, genetic linkages can be broken or can be newly created. Also, the order of genes on a chromosome can be changed. While natural chromosomal recombination occurs by homologous recombination during meiosis, CRISPR/Cas-mediated chromosomal rearrangements can be obtained best by harnessing nonhomologous end joining (NHEJ) pathways in somatic cells. NHEJ can be subdivided into the classical (cNHEJ) and alternative NHEJ (aNHEJ) pathways, which partially operate antagonistically. The cNHEJ pathway not only protects broken DNA ends from degradation but also suppresses the joining of previously unlinked broken ends. Hence, in the absence of cNHEJ, more inversions or translocations can be obtained which can be ascribed to the unrestricted use of the aNHEJ pathway for double-strand break (DSB) repair. In contrast to inversions or translocations, short tandem duplications can be produced by paired single-strand breaks via a Cas9 nickase. Interestingly, the cNHEJ pathway is essential for these kinds of duplications, whereas aNHEJ is required for patch insertions that can also be formed during DSB repair. As chromosome engineering has not only been accomplished in the model plant Arabidopsis (Arabidopsis thaliana) but also in the crop maize (Zea mays), we expect that this technology will soon transform the breeding process.

The Exploitation of Orphan Legumes for Food, Income, and Nutrition Security in Sub-Saharan Africa

Poverty, food, and nutrition insecurity in sub-Saharan Africa (SSA) have become major concerns in recent times. The effects of climate change, drought, and unpredictable rainfall patterns threaten food production and sustainable agriculture. More so, insurgency, youth restiveness, and politico-economic instability amidst a burgeoning population requiring a sufficient and healthy diet remain front-burner issues in the region. Overdependence on only a few major staple crops is increasingly promoting the near extinction of many crops, especially orphan legumes, which possess immense potentials as protein and nutritional security crops. The major staple crops are declining in yield partly to their inability to adapt to the continuously changing climatic conditions. Remarkably, the orphan legumes are climate-smart crops with enormous agronomic features which foster sustainable livelihood. Research efforts on these crops have not attained a reasonable comparative status with most commercial crops. Though many research organizations and scientists have made efforts to promote the improvement and utilization of these orphan legumes, there is still more to be done. These legumes' vast genetic resources and economic utility are grossly under-exploited, but their values and promising impacts are immeasurable. Given the United Nations sustainable development goals (SDGs) of zero hunger, improved nutrition, health, and sustainable agriculture, the need to introduce these crops into food systems in SSA and other poverty-prone regions of the world is now more compelling than ever. This review unveils inherent values in orphan legumes needing focus for exploitation viz-a-viz cultivation, commercialization, and social acceptance. More so, this article discusses some of the nutraceutical potentials of the orphan legumes, their global adaptability, and modern plant breeding strategies that could be deployed to develop superior phenotypes to enrich the landraces. Advanced omics technologies, speed breeding, as well as the application of genome editing techniques, could significantly enhance the genetic improvement of these useful but underutilized legumes. Efforts made in this regard and the challenges of these approaches were also discussed.

The CRISPR-Cas toolbox and gene editing technologies

The emergence of CRISPR-Cas systems has accelerated the development of gene editing technologies, which are widely used in the life sciences. To improve the performance of these systems, workers have engineered and developed a variety of CRISPR-Cas tools with a broader range of targets, higher efficiency and specificity, and greater precision. Moreover, CRISPR-Cas-related technologies have also been expanded beyond making cuts in DNA by introducing functional elements that permit precise gene modification, control gene expression, make epigenetic changes, and so on. In this review, we introduce and summarize the characteristics and applications of different types of CRISPR-Cas tools. We discuss certain limitations of current approaches and future prospects for optimizing CRISPR-Cas systems.

Genome-editing in millets: current knowledge and future perspectives

Millets are small seeded cereal crops predominantly cultivated and consumed by resource-poor farmers in the semi-arid tropics of Asia and Africa. Millets possess rich nutrients and a climate resilience property when compared to the other cereals such as rice and wheat. Millet improvement using modern genetic and genomic tools is falling behind other cereal crops due to their cultivation being restricted to less developed countries. Genome editing tools have been successfully applied to major cereal crops and, as a result, many key traits have been introduced into rice, wheat and maize. However, genome editing tools have not yet been used for most millets although they possess rich nutrients. The foxtail millet is the only millet utilised up to now for genome editing works. Limited genomic resources and lack of efficient transformation systems may slow down genome editing in millets. As millets possess many important traits of agricultural importance, high resolution studies with genome editing tools will help to understand the specific mechanism and transfer such traits to major cereals in the future. This review covers the current status of genome editing studies in millets and discusses the future prospects of genome editing in millets to understand key traits of nutrient fortification and develop climate resilient crops in the future.

Integrating CRISPR-Cas and Next Generation Sequencing in Plant Virology

Plant pathology has been revolutionized by the emergence and intervention of next-generation sequencing technologies (NGS) which provide a fast, cost-effective, and reliable diagnostic for any class of pathogens. NGS has made tremendous advancements in the area of research and diagnostics of plant infecting viromes and has bridged plant virology with other advanced research fields like genome editing technologies. NGS in a broader perspective holds the potential for plant health improvement by diagnosing and mitigating the new or unusual symptoms caused by novel/unidentified viruses. CRISPR-based genome editing technologies can enable rapid engineering of efficient viral/viroid resistance by directly targeting specific nucleotide sites of plant viruses and viroids. Critical genes such as eIf (iso) 4E or eIF4E have been targeted via the CRISPR platform to produce plants resistant to single-stranded RNA (ssRNA) viruses. CRISPR/Cas-based multi-target DNA or RNA tests can be used for rapid and accurate diagnostic assays for plant viruses and viroids. Integrating NGS with CRISPR-based genome editing technologies may lead to a paradigm shift in combating deadly disease-causing plant viruses/viroids at the genomic level. Furthermore, the newly discovered CRISPR/Cas13 system has unprecedented potential in plant viroid diagnostics and interference. In this review, we have highlighted the application and importance of sequencing technologies on covering the viral genomes for precise modulations. This review also provides a snapshot vision of emerging developments in NGS technologies for the characterization of plant viruses and their potential utilities, advantages, and limitations in plant viral diagnostics. Furthermore, some of the notable advances like novel virus-inducible CRISPR/Cas9 system that confers virus resistance with no off-target effects have been discussed.

Genomic Variation and Diversification in Begomovirus Genome in Implication to Host and Vector Adaptation

Begomoviruses (family Geminiviridae, genus Begomovirus) are DNA viruses transmitted in a circulative, persistent manner by the whitefly Bemisia tabaci (Gennadius). As revealed by their wide host range (more than 420 plant species), worldwide distribution, and effective vector transmission, begomoviruses are highly adaptive. Still, the genetic factors that facilitate their adaptation to a diverse array of hosts and vectors remain poorly understood. Mutations in the virus genome may confer a selective advantage for essential functions, such as transmission, replication, evading host responses, and movement within the host. Therefore, genetic variation is vital to virus evolution and, in response to selection pressure, is demonstrated as the emergence of new strains and species adapted to diverse hosts or with unique pathogenicity. The combination of variation and selection forms a genetic imprint on the genome. This review focuses on factors that contribute to the evolution of Begomovirus and their global spread, for which an unforeseen diversity and dispersal has been recognized and continues to expand.