RNA-guided genome editing in plants using a CRISPR-Cas system

Cas9-Rep fusion tethers donor DNA in vivo and boosts the efficiency of HDR-mediated genome editing

Genome editing based on the homology-directed repair (HDR) pathway enables scar-free and precise genetic manipulations. However, the low frequency of HDR hinders its application in plant genome editing. In this study, we engineered the fusion of Cas9 and a viral replication protein (Rep) as a molecular bridge to tether donor DNA in vivo, which enhances the efficiency of targeted gene insertion via the HDR pathway. This Rep-bridged knock-in (RBKI) method combines the advantages of rolling cycle replication of viral replicons and in vivo enrichment of donor DNA at the target site for HDR. Chromatin immunoprecipitation indicated that the Cas9-Rep fusion protein bound up to 66-fold more donor DNA than Cas9 did. We exemplified the RBKI method by inserting small- to middle-sized tags (33-519 bp) into 3 rice genes. Compared to Cas9, Cas9-Rep fusion increased the KI frequencies by 4-7.6-fold, and up to 72.2% of stable rice transformants carried in-frame knock-in events in the T0 generation. Whole-genome sequencing of 6 plants segregated from heterozygous KI lines indicated that the knock-in events were faithfully inherited by the progenies with neither off-target editing nor random insertions of the donor DNA fragment. Further analysis suggested that the RBKI method reduced the number of byproducts from nonhomologous end joining; however, HDR-mediated knock-in tended to accompany microhomology-mediated end joining events. Together, these findings show that the in vivo tethering of donor DNAs with Cas9-Rep is an effective strategy to increase the frequency of HDR-mediated genome editing.

Osr40g3 imparts salt tolerance by regulating GF14e-mediated gibberellin metabolism to activate EG45 in rice

Under changing environmental conditions, salt stress is a serious threat to agriculture. The R40 family lectins are known to be associated with osmotic stress response, although their mechanism of action remains unclear. Here, we report that Osr40g3, upregulated by salt, improves salt tolerance but causes pollen sterility and poor seed development in rice when constitutively overexpressed. Osr40g3 knockout lines, on the other hand, display salt sensitivity with no other phenotypic aberration. Further studies revealed that the gene exhibits a precise tissue-specific expression pattern essential for seed development. Overexpressing the Osr40g3 with its native promoter alleviates pollen sterility and improves salt tolerance. In-depth molecular studies demonstrated that Osr40g3 positively regulates an expansin protein, OsEG45, while decreasing the stability of a 14-3-3 protein, OsGF14e. Correspondingly, OsEG45 overexpression, OsGF14e silencing lines, and the double mutants display salt tolerance, supporting the involvement of the Osr40g3-OsGF14e-OsEG45 module in salt tolerance. Moreover, constitutive overexpression of Osr40g3 or silencing of OsGF14e diminishes gibberellic acid (GA) accumulation that activates the OsEG45 gene. Together, our study highlights that the Osr40g3 confers salt tolerance by negatively regulating OsGF14e while positively regulating OsEG45 via a GA-dependent pathway.

Silencing of disease susceptibility genes: an effective disease resistance strategy against fungal pathogens

KEY MESSAGE

Silencing of target susceptibility (S) genes in plants exhibits a promising and durable strategy for enhanced resistance to fungal pathogens by causing disruption in the host mechanisms that the pathogens exploit, offering an alternative to the traditional resistance gene-based approaches. Devastating fungal diseases have significantly reduced crop productivity, posing a potential threat to global food security. Producing disease-resistant cultivars is the most effective strategy for protecting crops against these fungal pathogens. Typically, susceptibility (S) genes in host plants facilitate the penetration and proliferation of phytopathogens. Perturbation of these S genes can potentially impede the compatibility between the host and the fungal pathogens, thereby providing broad-spectrum and lasting resistance. Consequently, the identification and targeting of S-genes have gained increasing interest in enhancing disease resistance in plants. In this review, we describe three distinct categories of S genes that function during different stages of the infection process. We focus on various gene silencing technologies, including RNA interference (RNAi), virus-induced gene silencing (VIGS), and CRISPR-Cas9, to improve plant disease resistance against fungal pathogens. The numerous examples discussed here illustrate the potential of S-genes for use in plant disease-resistance breeding.

The pectin methylesterase OsPME14 modifies the cell wall to confer copper tolerance in Oryza sativa L

Pectin methylesterase (PME) dynamically regulates the biomechanical properties of the cell wall, which is involved in plant development and resistance to biotic and abiotic stress. However, its regulation mechanism of plant tolerance to heavy metal toxicity is limited. Here, we functionally characterized a member of the PME family, OsPME14 in rice, which is required for Cu tolerance. The expression of OsPME14 was induced by Cu. Compared to WT, lost function of OsPME14 decreased the PME activity and carboxyl group content, and weakened the retention capacity of the cell wall to Cu, thereby enhancing the Cu absorption by roots and Cu accumulation in the protoplasts. This promoted the Cu translocation from roots to shoots, resulting in the Cu hypersensitivity phenotype and more Cu concentration in grains. Notably, mutation of OsPME14 caused the expression change of the receptor kinase gene and the downstream MAPK cascade pathway. Besides, a PME inhibitor OsPMEI6 was identified to interact with OsPME14, and the spatiotemporal expression of OsPMEI6 was highly consistent with OsPME14, OsPMEI6 may regulate OsPME14-mediated Cu tolerance in rice. These results provide a novel insight into OsPME14-OsPMEI6 module-mediated mechanisms of heavy metal tolerance in rice.

OsMYB67 Knockout Promotes Rice Heading and Yield by Facilitating Copper Distribution in Panicles

Copper (Cu) is an essential micronutrient required for rice flowering and seed setting. Here, we identified that Cu-induced R2R3-MYB transcription factor, OsMYB67, acts as a negative regulator that controls rice heading and yield production by affecting Cu distribution in panicles. OsMYB67 was constitutively expressed, with the highest expression in the roots. OsMYB67 knockout did not affect plant growth, but significantly increased Cu concentrations in roots, shoots, and xylem sap at the seedling stage. At the reproductive stage, OsMYB67 mutants displayed an early heading phenotype, with significantly increased Cu distribution in panicles but decreased Cu distribution in leaves, whereas OsMYB67-overexpressing plants showed the opposite result. In addition, higher grain yield and Cu concentrations in seeds were observed in OsMYB67 mutants compared to the wild-type. The results of Y1H, transient co-expression, EMSA, in situ RT-PCR, and RT-qPCR showed that OsMYB67 directly binds to the promoter region of OsHMA9 and upregulates its expression. Significantly increased Cu concentrations were also observed in the roots, shoots, and seeds of oshma9 mutants, consistent with the results observed in OsMYB67 mutants. Interestingly, dramatically higher expression levels of OsATX1 and OsYSL16 were observed in the OsMYB67 mutants, which may contribute to the increased Cu distribution in the panicles.

An Oryza-specific histone H4 variant predisposes H4 lysine 5 acetylation to modulate salt stress responses

Paralogous variants of canonical histones guide accessibility to DNA and function as additional layers of genome regulation. Across eukaryotes, the mechanism of action and functional significance of several variants of core histones are well known except those of histone H4. Here we show that a variant of H4 (H4.V) expressing tissue-specifically among Oryza members mediated specific epigenetic changes contributing to salt tolerance. H4.V was incorporated into specific heterochromatic sites, where it blocked the deposition of active histone marks. Stress-dependent redistribution of H4.V enabled the incorporation of acetylated H4 lysine 5 (H4K5ac) in the gene bodies. The misexpression of H4.V led to defects in reproductive development and in mounting salt stress responses. H4.V formed homotypic nucleosomes and mediated these alterations by conferring distinct molecular properties to the nucleosomes, as seen with cryo electron microscopy structures and biochemical assays. These results reveal not only an H4 variant among plants but also a chromatin regulation that might have contributed to the adaptation of semi-aquatic Oryza members.

CRISPR/dCas12a-mediated activation of SlPAL2 enhances tomato resistance against bacterial canker disease

Crop protection is essential for maintaining and improving agricultural productivity. While pesticides are commonly used to control pests, they pose several challenges, including environmental harm and health risks. Alternative strategies to pesticides include breeding resistant crop varieties, biological control, and utilizing genome-editing tools like CRISPR/Cas. However, the application of epigenome editing, particularly CRISPR activation (CRISPRa), in plants remains underexplored. Phenylalanine ammonia-lyase (PAL), a key enzyme in the phenylpropanoid pathway, plays a pivotal role in plant defense by producing lignin and other secondary metabolites essential for pathogen resistance. In this study, we engineered tomato plants by fusing the SET-domain of the SlATX1 coding gene, a histone H3 lysine 4 tri-methyltransferase, to dCas12a, targeting the SlPAL2 promoter with the aim to increase PAL2 gene expression. CRISPRa-edited plants demonstrated increased deposition of the H3K4me3 epigenetic mark and significantly upregulated SlPAL2 expression. This enhanced lignin accumulation and conferred increased resistance to Clavibacter michiganensis subsp. michiganensis (Cmm) without significant reduction in plant height or fruit yield. Disease resistance was also associated with reduced pathogen load and lesion size, and higher lignin levels persisted even after SlPAL2 expression declined post-infection. These findings highlight the potential of CRISPRa for reprogramming plant defense responses through targeted histone modifications, offering a sustainable approach for crop improvement. Furthermore, CRISPRa could also be applied to enhance crop resilience in other contexts, such as addressing food security challenges by enhancing productivity.

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.

Advancements in genome editing tools for genetic studies and crop improvement

The rapid increase in global population poses a significant challenge to food security, compounded by the adverse effects of climate change, which limit crop productivity through both biotic and abiotic stressors. Despite decades of progress in plant breeding and genetic engineering, the development of new crop varieties with desirable agronomic traits remains a time-consuming process. Traditional breeding methods often fall short of addressing the urgent need for improved crop varieties. Genome editing technologies, which enable precise modifications at specific genomic loci, have emerged as powerful tools for enhancing crop traits. These technologies, including RNA interference, Meganucleases, ZFNs, TALENs, and CRISPR/Cas systems, allow for the targeted insertion, deletion, or alteration of DNA fragments, facilitating improvements in traits such as herbicide and insect resistance, nutritional quality, and stress tolerance. Among these, CRISPR/Cas9 stands out for its simplicity, efficiency, and ability to reduce off-target effects, making it a valuable tool in both agricultural biotechnology and plant functional genomics. This review examines the functional mechanisms and applications of various genome editing technologies for crop improvement, highlighting their advantages and limitations. It also explores the ethical considerations associated with genome editing in agriculture and discusses the potential of these technologies to contribute to sustainable food production in the face of growing global challenges.

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.

Mitochondrial AOX1a and an H2O2 feed-forward signalling loop regulate flooding tolerance in rice

Flooding is a widespread natural disaster that causes tremendous yield losses of global food production. Rice is the only cereal capable of growing in aquatic environments. Direct seeding by which seedlings grow underwater is an important cultivation method for reducing rice production cost. Hypoxic germination tolerance and root growth in waterlogged soil are key traits for rice adaptability to flooded environments. Alternative oxidase (AOX) is a non-ATP-producing terminal oxidase in the plant mitochondrial electron transport chain, but its role in hypoxia tolerance had been unclear. We have discovered that AOX1a is necessary and sufficient to promote germination/coleoptile elongation and root development in rice under flooding/hypoxia. Hypoxia enhances endogenous H2O2 accumulation, and H2O2 in turn activates an ensemble of regulatory genes including AOX1a to facilitate the conversion of deleterious reactive oxygen species to H2O2 in rice under hypoxia. We show that AOX1a and H2O2 act interdependently to coordinate three key downstream events, that is, glycolysis/fermentation for minimal ATP production, root aerenchyma development and lateral root emergence under hypoxia. Moreover, we reveal that ectopic AOX1a expression promotes vigorous root and plant growth, and increases grain yield under regular irrigation conditions. Our discoveries provide new insights into a unique sensor-second messenger pair in which AOX1a acts as the sensor perceiving low oxygen tension, while H2O2 accumulation serves as the second messenger triggering downstream root development in rice against hypoxia stress. This work also reveals AOX1a genetic manipulation and H2O2 pretreatment as potential targets for improving flooding tolerance in rice and other crops.

Geminivirus diseases of legumes in India: current status and approaches for management

India has a large potential for producing a variety of legumes which are proficiently valued for small grower to the highest producers. Plant viruses predominate among the many factors that affect the production of legumes. In tropical and subtropical locations, begomovirus has become a significant productivity barrier for legume production with significant losses. The detection and molecular characterization of various begomoviruses species have been done with regard to phylogenetic analyses, infectivity on host plants, DNA replication, transgenic resistance, promoter analysis, and development of virus-based gene-silencing vectors using several techniques. The molecular detection of begomoviruses involves a variety of techniques, including polymerase chain reaction (PCR), using degenerate primers, reverse transcription PCR (RT-PCR), real time quantitative PCR, rolling-circle amplification PCR (RCA-PCR assay), RCA, and microarray/DNA chip. Begomovirus infections can be prevented by various methods such as by controlling vector populations, use of culture practices, developing virus-free planting materials, developing resistant varieties, following quarantine regulations, and adapting modern methods, including pathogen-derived resistance (PDR), RNA interference (RNAi)-mediated resistance and genome editing approach. This review focuses on current status of geminiviruses infecting various legumes, pathogenesis, genetic flexibility, recombination of begomovirus responsible for the wide host range, modern methods of control, including PDR, RNAi-mediated resistance, small RNA (sRNA)- mediated resistance, Engineered Nucleases, Zinc Finger nucleases, Transcriptional Activator nucleases, CRISPR/Cas9 mediated genome editing and various strategies for management of begomoviruses. The present study entails the view and understanding of different approaches for the begomovirus management which state knowledge about limiting the crop losses.

Limonene enhances rice plant resistance to a piercing-sucking herbivore and rice pathogens

Terpene synthases (TPSs) are key enzymes in terpenoids synthesis of plants and play crucial roles in regulating plant defence against pests and diseases. Here, we report the functional characterization of OsTPS19 and OsTPS20, which were upregulated by the attack of brown planthopper (BPH). BPH female adults performed concentration-dependent behavioural responses to (S)-limonene showing preference behaviour at low concentrations and avoidance behaviour at high concentrations. Overexpression lines of OsTPS19 and OsTPS20, which emitted higher amounts of the monoterpene (S)-limonene, decreased the hatching rate of BPH eggs, reduced the lesion length of sheath blight caused by Rhizoctonia solani and bacterial blight caused by Xanthomonas oryzae. While knockout lines of OsTPS19 and OsTPS20, which emitted lower amounts of (S)-limonene, were more susceptible to these pathogens. Overexpression of OsTPS19 and OsTPS20 in rice plants had adverse effects on the incidence of BPH, rice blast, and sheath blight in the field and had no significant impacts on rice yield traits. OsTPS19 and OsTPS20 were found to be involved in fine-tuning the emission of (S)-limonene in rice plants and play an important role in defence against both BPH and rice pathogens.

CRISPR-Cas9-mediated homology-directed repair for precise gene editing

CRISPR-Cas9-mediated homology-directed repair (HDR) is a versatile platform for creating precise site-specific DNA insertions, deletions, and substitutions. These precise edits are made possible through the use of exogenous donor templates that carry the desired sequence. CRISPR-Cas9-mediated HDR can be widely used to study protein functions, disease modeling, and gene therapy. However, HDR is limited by its low efficiency, especially in postmitotic cells. Here, we review CRISPR-Cas9-mediated HDR, with a focus on methodologies for boosting HDR efficiency, and applications of precise editing via HDR. First, we describe two common mechanisms of DNA repair, non-homologous end joining (NHEJ), and HDR, and discuss their impact on CRISPR-Cas9-mediated precise genome editing. Second, we discuss approaches for improving HDR efficiency through inhibition of the NHEJ pathway, activation of the HDR pathway, modification of donor templates, and delivery of Cas9/sgRNA reagents. Third, we summarize the applications of HDR for protein labeling in functional studies, disease modeling, and ex vivo and in vivo gene therapies. Finally, we discuss alternative precise editing platforms and their limitations, and describe potential avenues to improving CRISPR-Cas9-mediated HDR efficiency and fidelity in future research.

Differential editing efficiencies in cereal crops: a comparative analysis of tRNA and ribozyme multiplexed guide delivery

Cereal transformation and gene editing can be a complex and costly undertaking. It is therefore important to validate and understand the performance of the components to achieve high rates of transformation and gene editing. Here, we have made a direct comparison of different CRISPR/Cas9 guide systems to target the genome in three cereal species. We show that the guide sequences driven by the same pol II promoter in rice, wheat and barley show large differences in editing efficiency. The differences seen were based on the way the guides were presented and factors outside of the guide sequence itself. While both the tRNA system and ribozyme system performed well in rice, their effectiveness varied in wheat and barley. Specifically, the tRNA system outperformed the ribozyme system, achieving higher rates of editing in stable transformed plants. Overall, high levels of editing are observed in all three species when strong expression of the SpCas9 is coupled with the CmYLCV promoter to drive a tRNA array of guide RNAs. Stable inheritance is also achievable in all three species when plants are sampled shortly after the tissue culture concludes. Overall, inheritance rates were above 85% in all three species, particularly when mutations are detected early after plants emerge from tissue culture.

Adaptation of bacterial natural single guide RNA (tracr-L) for efficient plant genome editing

KEY MESSAGE

A long tracrRNA (tracr-L), which naturally act as single guide RNA, and its truncated version, Δtracr-L, from S. pyogenes, efficiently induce Cas9-mediated double-strand breaks (DSBs) in plant genomic loci, as demonstrated by in vitro cleavage assay and protoplast transfection. CRISPR-Cas system provides a form of immune memory in prokaryotes and archaea, protecting them against viruses and foreign genetic elements. In Streptococcus pyogenes, this system includes the pre-crRNA along with another non-coding RNA, tracrRNA, which aids in CRISPR-based immunity. In S. pyogenes, two distinct tracrRNAs are produced: a long form (tracr-L) and a short form (tracr-S). The tracr-S regulates crRNA biogenesis and Cas9 cleavage, while tracr-L suppresses CRISPR-Cas expression by targeting the Cas9 promoter to prevent autoimmunity. Deleting 79 nucleotides from tracr-L results in Δtracr-L, which retains similar functionality in gene repression. This study investigates, for the first time, the effectiveness of tracr-L, and Δtracr-L in genome editing within plant systems. In vitro cleavage assays using purified Cas9 and synthesized sgRNAs targeting the Cas9 gene, OsPDS, and the OsSWEET11 promoter revealed that across all target sites, tracr-S demonstrated the highest cleavage efficiency compared to tracr-L and Δtracr-L. For in vivo genome editing, we transfected rice protoplasts with tracr-L, Δtracr-L, and tracr-S, targeting three rice genes: OsPDS, OsSPL14, and the promoter of OsSWEET14. Amplicon deep sequencing revealed various types of indels at the target regions across all three tracrRNA versions, indicating comparable levels of efficiency. This study establishes the utility of both the long-form tracrRNA (tracr-L) and its truncated variant (Δtracr-L) in eukaryote genome editing. These two new forms of tracrRNA provide proof of concept and expand the CRISPR-Cas toolkit for plant genome editing applications, and for eukaryotes more broadly.

OsIAA23 Promotes Heading by Directly Downregulating Ghd7 in rice

Ghd7 is a central regulator to multiple growth and development processes in rice. While it is not clear how Ghd7 is regulated by upstream factors. To identify its upstream regulator, the truncated Ghd7 promoter fragments were used to screen cis elements binding to rice total nuclear proteins. Electrophoretic mobility shift assays screened one truncated fragment f3 binding to the proteins. Subsequently, the fragment f3 was employed to screen a yeast one-hybrid library, and a transcription factor OsIAA23 was screened as a direct upstream regulator of Ghd7. Dual-luciferase transient assay demonstrated the transcriptional repression effect of OsIAA23 on the activity of Ghd7, and the location of the cis elements binding to OsIAA23 in the region 1264 to 1255 bp upstream of ATG. Genetic analysis between the wild type Ghd7-OsIAA23 and single/double mutants further verified that OsIAA23 downregulated Ghd7 expression and led to a delayed heading under long day conditions. Moreover, natural variations in fragment f3 were associated with heading and geographic distribution in rice. This study sheds light on the direct regulatory mechanism of OsIAA23 on Ghd7, which enriches the understanding of the Ghd7 involved flowering regulatory network in rice.

PhieDBEs: a DBD-containing, PAM-flexible, high-efficiency dual base editor toolbox with wide targeting scope for use in plants

Dual base editors (DBEs) enable simultaneous A-to-G and C-to-T conversions, expanding mutation types. However, low editing efficiency and narrow targeting range limit the widespread use of DBEs in plants. The single-strand DNA binding domain of RAD51 DBD can be fused to base editors to improve their editing efficiency. However, it remains unclear how the DBD affects dual base editing performance in plants. In this study, we generated a series of novel plant DBE-SpGn tools consisting of nine constructs using the high-activity cytidine deaminase evoFERNY, adenosine deaminase TadA8e and DBD in various fusion modes with the PAM-flexible Streptococcus pyogenes Cas9 (SpCas9) nickase variant SpGn (with NG-PAM). By analysing their editing performance on 48 targets in rice, we found that DBE-SpGn constructs containing a single DBD and deaminases located at the N-terminus of SpGn exhibited the highest editing efficiencies. Meanwhile, constructs with deaminases located at the C-terminus and/or multiple DBDs failed to function normally and exhibited inhibited editing activity. We identified three particularly high-efficiency dual base editors (C-A-SpGn, C-A-D-SpGn and A-C-D-SpGn), named PhieDBEs (Plant high-efficiency dual base editors), capable of producing efficient dual base conversions within a narrow editing window (M5 ~ M9, M = A/C). The editing efficiency of C-A-D-SpGn was as high as 95.2% at certain target sites, with frequencies of simultaneous C-to-T and A-to-G conversions as high as 81.0%. In summary, PhieDBEs (especially C-A-D-SpGn) can produce diverse mutants and may prove useful in a wide variety of applications, including plant functional genomics, precise mutagenesis, directed evolution and crop genetic improvement, among others.

The OsSRO1c-OsDREB2B complex undergoes protein phase transition to enhance cold tolerance in rice

Cold stress is one of the major abiotic stress factors affecting rice growth and development, leading to significant yield loss in the context of global climate change. Exploring natural variants that confer cold resistance and the underlying molecular mechanism responsible for this is the major strategy to breed cold-tolerant rice varieties. Here, we show that natural variations of a SIMILAR to RCD ONE (SRO) gene, OsSRO1c, confer cold tolerance in rice at both seedling and booting stages. Our in vivo and in vitro experiments demonstrated that OsSRO1c possesses intrinsic liquid-liquid phase-separation ability and recruits OsDREB2B, an AP2/ERF transcription factor that functions as a positive regulator of cold stress, into its biomolecular condensates in the nucleus, resulting in elevated transcriptional activity of OsDREB2B. We found that the OsSRO1c-OsDREB2B complex directly responds to low temperature through dynamic phase transitions and regulates key cold-response genes, including COLD1. Furthermore, we showed that introgression of an elite haplotype of OsSRO1c into a cold-susceptible indica rice could significantly increase its cold resistance. Collectively, our work reveals a novel cold-tolerance regulatory module in rice and provides promising genetic targets for molecular breeding of cold-tolerant rice varieties.

Use of CRISPR Technology in Gene Editing for Tolerance to Biotic Factors in Plants: A Systematic Review

The objective of this systematic review (SR) was to select studies on the use of gene editing by CRISPR technology related to plant resistance to biotic stresses. We sought to evaluate articles deposited in six electronic databases, using pre-defined inclusion and exclusion criteria. This SR demonstrates that countries such as China and the United States of America stand out in studies with CRISPR/Cas. Among the most studied crops are rice, tomatoes and the model plant Arabidopsis thaliana. The most cited biotic agents include the genera, Xanthomonas, Manaporthe, Pseudomonas and Phytophthora. This SR also identifies several CRISPR/Cas-edited genes and demonstrates that plant responses to stressors are mediated by many complex signaling pathways. The Cas9 enzyme is used in most articles and Cas12 and 13 are used as additional editing tools. Furthermore, the quality of the articles included in this SR was validated by a risk of bias analysis. The information collected in this SR helps to understand the state of the art of CRISPR/Cas aimed at improving resistance to diseases and pests to understand the mechanisms involved in most host-pathogen relationships. This SR shows that the CRISPR/Cas system provides a straightforward method for rapid gene targeting, providing useful information for plant breeding programs.

Editing of the MeSWEET10a promoter yields bacterial blight resistance in cassava cultivar SC8

Cassava starch is a widely used raw material for industrial production and food source for people. However, cassava bacterial blight (CBB) caused by Xanthomonas axonopodis pv. manihotis (Xam) results in severe yield losses and is the most destructive bacterial disease in all worldwide cassava-growing regions. Xam11 is a highly pathogenic subspecies from China that infects the Chinese local cassava South China No. 8 (SC8) cultivar with marked symptoms. This study showed that the transcription activator-like effector TALE20Xam11 of Xam11 strain regulates the expression of disease-susceptibility gene MeSWEET10a by binding to the EBETALE20 region of the MeSWEET10a promoter in cassava cultivar SC8. CRISPR/Cas9-generated mutations of the EBETALE20 region resulted in a significant reduction in MeSWEET10a expression after infection by Xam11, correlating with reduced disease symptoms, smaller lesion sizes and decreased bacterial proliferation compared with the wild type. Importantly, the edited plants maintained normal growth, development and yield characteristics under greenhouse conditions. The results lay a research foundation for breeding resistant cassava cultivar SC8 to bacterial blight.

Variation in phytotoxicity of rice seedlings caused by differential accumulation of azoxystrobin and pyraclostrobin in leaves

The effectiveness of pyraclostrobin (Pyr) and azoxystrobin (Azo) with highly targeting the rice blast is noteworthy, but they have varied toxic levels towards non-target aquatic organisms. Nevertheless, the toxic selectivity and mechanism of non-target plants, specifically rice, remain uncertain. In this study, we investigated the potential phytotoxic effects of Pyr and Azo on rice seedlings, including plant morphology, plant growth, physiological and biochemical changes. The findings revealed that both Pyr and Azo caused toxic effects on rice, resulting in symptoms of chlorosis and inhibited growth. The toxicity of Azo was found to be more severe when applied at the recommended field dose. Disruption of oxidative stress could significantly impact the demonstrated levels of REC, leading to a decrease in photosynthetic pigments and potentially culminating in cell death. Furthermore, the toxic effect of Azo had a greater impact on rice leaves compared to Pyr at treatments of 400, 800, 1600, and 4000 mg/L. However, the in vitro cytotoxicity of Azo on rice leaves was lower than that of Pyr. Therefore, it can be inferred that the mechanism of phytotoxicity of Azo is directly linked to the increased accumulation of the compound on the leaf tips and edges. Additionally, the positive effects observed on plant morphology and growth parameters suggest that the mixed application of plant growth regulators (sodium nitrophenolate aqueous solution of 14 mg/L and diethyl aminoethyl hexanoat of 50 mg/L) can be a promising approach to mitigate the rice phytotoxicity of Azo at 400 and 800 mg/L.

The transcription factor OsSPL9 endows rice with copper deficiency resilience

Copper (Cu) is a crucial micronutrient essential for the growth and development of plants. Rice exhibits remarkable resistance to Cu deficiency, but the underlying molecular mechanisms are not well understood. In this study, we reveal that the plant's ability to withstand Cu deficiency is orchestrated by a transcription factor known as OsSPL9. We have demonstrated that OsSPL9 functions as a central regulator of Cu homeostasis. Disrupting OsSPL9 through knockout significantly reduced the plant's tolerance to Cu deficiency. As a result, the spl9 mutants exhibited reduced Cu accumulation in their shoots when compared with wild-type plants. This reduction was linked to a disruption in the transport of Cu from older leaves to younger ones. Furthermore, we show that OsSPL9 directly bound to GTAC motifs in the promoters of key genes involved in Cu uptake and transport, as well as Cu-miRNAs, and enhanced their transcription under Cu-deficient conditions. Overall, our findings shed light on the molecular basis of rice resilience to Cu deficiency stress and place the transcription factor OsSPL9 as a master regulator of this response.

Upstream regulator of genomic imprinting in rice endosperm is a small RNA-associated chromatin remodeler

Genomic imprinting is observed in endosperm, a placenta-like seed tissue, where transposable elements (TEs) and repeat-derived small RNAs (sRNAs) mediate epigenetic changes in plants. In imprinting, uniparental gene expression arises due to parent-specific epigenetic marks on one allele but not on the other. The importance of sRNAs and their regulation in endosperm development or in imprinting is poorly understood in crops. Here we show that a previously uncharacterized CLASSY (CLSY)-family chromatin remodeler named OsCLSY3 is essential for rice endosperm development and imprinting, acting as an upstream player in the sRNA pathway. Comparative transcriptome and genetic analysis indicated its endosperm-preferred expression and its likely paternal imprinted nature. These important features are modulated by RNA-directed DNA methylation (RdDM) of tandemly arranged TEs in its promoter. Upon perturbation of OsCLSY3 in transgenic lines, we observe defects in endosperm development and a loss of around 70% of all sRNAs. Interestingly, well-conserved endosperm-specific sRNAs (siren) that are vital for reproductive fitness in angiosperms are also dependent on OsCLSY3. We observed that many imprinted genes and seed development-associated genes are under the control of OsCLSY3. These results support an essential role of OsCLSY3 in rice endosperm development and imprinting, and propose similar regulatory strategies involving CLSY3 homologs among other cereals.

The germin-like protein OsGLP8-7 is involved in lignin synthesis for acclimation to copper toxicity in rice

Although copper (Cu) is an essential microelement for plant growth and development, excess Cu results in a dramatic reduction in crop yield and quality. In the present study, we report that rice germin-like protein 8-7 (OsGLP8-7) plays a crucial role against Cu toxicity. The results showed that the transcriptional expression of the OsGLP8-7 gene was remarkably upregulated in the root and leaf by Cu treatment. The depletion of OsGLP8-7 significantly decreased the elongation of the primary root and plant height of rice under excess Cu. This hypersensitivity of osglp8-7 mutants towards excess Cu may be attributed to the weaker Cu retention in the cell wall compared with wild-type rice (Dongjin, DJ). Consistently, Cu-induced phenylpropanoid biosynthesis was compromised in osglp8-7 mutants based on RNA-Seq and qRT-PCR analysis. Furthermore, osglp8-7 mutants displayed a reduction of lignin deposition in the cell wall, and subsequently altered cell morphology. Osglp8-7 mutant lines also had higher Cu-induced O2•- and H2O2 levels than those of DJ under Cu stress. The results suggest that OsGLP8-7 participates in lignin synthesis for the acclimation to excess Cu. These findings provide a better understanding of a novel mechanism of germin-like proteins in the alleviation of heavy metal toxicity in rice.

Genome editing for improvement of biotic and abiotic stress tolerance in cereals

Global agricultural production must quadruple by 2050 to fulfil the needs of a growing global population, but climate change exacerbates the difficulty. Cereals are a very important source of food for the world population. Improved cultivars are needed, with better resistance to abiotic stresses like drought, salt, and increasing temperatures, and resilience to biotic stressors like bacterial and fungal infections, and pest infestation. A popular, versatile, and helpful method for functional genomics and crop improvement is genome editing. Rapidly developing genome editing techniques including clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) are very important. This review focuses on how CRISPR/Cas9 genome editing might enhance cereals' agronomic qualities in the face of climate change, providing important insights for future applications. Genome editing efforts should focus on improving characteristics that confer tolerance to conditions exacerbated by climate change (e.g. drought, salt, rising temperatures). Improved water usage efficiency, salt tolerance, and heat stress resilience are all desirable characteristics. Cultivars that are more resilient to insect infestations and a wide range of biotic stressors, such as bacterial and fungal diseases, should be created. Genome editing can precisely target genes linked to disease resistance pathways to strengthen cereals' natural defensive systems.

Single-cell transcriptome atlases of soybean root and mature nodule reveal new regulatory programs that control the nodulation process

The soybean root system is complex. In addition to being composed of various cell types, the soybean root system includes the primary root, the lateral roots, and the nodule, an organ in which mutualistic symbiosis with N-fixing rhizobia occurs. A mature soybean root nodule is characterized by a central infection zone where atmospheric nitrogen is fixed and assimilated by the symbiont, resulting from the close cooperation between the plant cell and the bacteria. To date, the transcriptome of individual cells isolated from developing soybean nodules has been established, but the transcriptomic signatures of cells from the mature soybean nodule have not yet been characterized. Using single-nucleus RNA-seq and Molecular Cartography technologies, we precisely characterized the transcriptomic signature of soybean root and mature nodule cell types and revealed the co-existence of different sub-populations of B. diazoefficiens-infected cells in the mature soybean nodule, including those actively involved in nitrogen fixation and those engaged in senescence. Mining of the single-cell-resolution nodule transcriptome atlas and the associated gene co-expression network confirmed the role of known nodulation-related genes and identified new genes that control the nodulation process. For instance, we functionally characterized the role of GmFWL3, a plasma membrane microdomain-associated protein that controls rhizobial infection. Our study reveals the unique cellular complexity of the mature soybean nodule and helps redefine the concept of cell types when considering the infection zone of the soybean nodule.

The potential of genome editing to create novel alleles of resistance genes in rice

Rice, a staple food for a significant portion of the global population, faces persistent threats from various pathogens and pests, necessitating the development of resilient crop varieties. Deployment of resistance genes in rice is the best practice to manage diseases and reduce environmental damage by reducing the application of agro-chemicals. Genome editing technologies, such as CRISPR-Cas, have revolutionized the field of molecular biology, offering precise and efficient tools for targeted modifications within the rice genome. This study delves into the application of these tools to engineer novel alleles of resistance genes in rice, aiming to enhance the plant's innate ability to combat evolving threats. By harnessing the power of genome editing, researchers can introduce tailored genetic modifications that bolster the plant's defense mechanisms without compromising its essential characteristics. In this study, we synthesize recent advancements in genome editing methodologies applicable to rice and discuss the ethical considerations and regulatory frameworks surrounding the creation of genetically modified crops. Additionally, it explores potential challenges and future prospects for deploying edited rice varieties in agricultural landscapes. In summary, this study highlights the promise of genome editing in reshaping the genetic landscape of rice to confront emerging challenges, contributing to global food security and sustainable agriculture practices.

Integrating machine learning and genome editing for crop improvement

Genome editing is a promising technique that has been broadly utilized for basic gene function studies and trait improvements. Simultaneously, the exponential growth of computational power and big data now promote the application of machine learning for biological research. In this regard, machine learning shows great potential in the refinement of genome editing systems and crop improvement. Here, we review the advances of machine learning to genome editing optimization, with emphasis placed on editing efficiency and specificity enhancement. Additionally, we demonstrate how machine learning bridges genome editing and crop breeding, by accurate key site detection and guide RNA design. Finally, we discuss the current challenges and prospects of these two techniques in crop improvement. By integrating advanced genome editing techniques with machine learning, progress in crop breeding will be further accelerated in the future.

Optimized protoplast isolation and transfection with a breakpoint: accelerating Cas9/sgRNA cleavage efficiency validation in monocot and dicot

The CRISPR-Cas genome editing tools are revolutionizing agriculture and basic biology with their simplicity and precision ability to modify target genomic loci. Software-predicted guide RNAs (gRNAs) often fail to induce efficient cleavage at target loci. Many target loci are inaccessible due to complex chromatin structure. Currently, there is no suitable tool available to predict the architecture of genomic target sites and their accessibility. Hence, significant time and resources are spent on performing editing experiments with inefficient guides. Although in vitro-cleavage assay could provide a rough assessment of gRNA efficiency, it largely excludes the interference of native genomic context. Transient in-vivo testing gives a proper assessment of the cleavage ability of editing reagents in a native genomic context. Here, we developed a modified protocol that offers highly efficient protoplast isolation from rice, Arabidopsis, and chickpea, using a sucrose gradient, transfection using PEG (polyethylene glycol), and validation of single guide RNAs (sgRNAs) cleavage efficiency of CRISPR-Cas9. We have optimized various parameters for PEG-mediated protoplast transfection and achieved high transfection efficiency using our protocol in both monocots and dicots. We introduced plasmid vectors containing Cas9 and sgRNAs targeting genes in rice, Arabidopsis, and chickpea protoplasts. Using dual sgRNAs, our CRISPR-deletion strategy offers straightforward detection of genome editing success by simple agarose gel electrophoresis. Sanger sequencing of PCR products confirmed the editing efficiency of specific sgRNAs. Notably, we demonstrated that isolated protoplasts can be stored for up to 24/48 h with little loss of viability, allowing a pause between isolation and transfection. This high-efficiency protocol for protoplast isolation and transfection enables rapid (less than 7 days) validation of sgRNA cleavage efficiency before proceeding with stable transformation. The isolation and transfection method can also be utilized for rapid validation of editing strategies, evaluating diverse editing reagents, regenerating plants from transfected protoplasts, gene expression studies, protein localization and functional analysis, and other applications.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-024-00139-7.

Towards DNA-free CRISPR/Cas9 genome editing for sustainable oil palm improvement

The CRISPR/Cas9 genome editing system has been in the spotlight compared to programmable nucleases such as ZFNs and TALENs due to its simplicity, versatility, and high efficiency. CRISPR/Cas9 has revolutionized plant genetic engineering and is broadly used to edit various plants' genomes, including those transformation-recalcitrant species such as oil palm. This review will comprehensively present the CRISPR-Cas9 system's brief history and underlying mechanisms. We then highlighted the establishment of the CRISPR/Cas9 system in plants with an emphasis on the strategies of highly efficient guide RNA design, the establishment of various CRISPR/Cas9 vector systems, approaches of multiplex editing, methods of transformation for stable and transient techniques, available methods for detecting and analyzing mutations, which have been applied and could be adopted for CRISPR/Cas9 genome editing in oil palm. In addition, we also provide insight into the strategy of DNA-free genome editing and its potential application in oil palm.

C-terminal frameshift mutations generate viable knockout mutants with developmental defects for three essential protein kinases

Loss-of-function mutants are fundamental resources for gene function studies. However, it is difficult to generate viable and heritable knockout mutants for essential genes. Here, we show that targeted editing of the C-terminal sequence of the embryo lethal gene MITOGEN-ACTIVATED PROTEIN KINASES 1 (OsMPK1) results in weak mutants. This C-terminal-edited osmpk1 mutants displayed severe developmental defects and altered disease resistance but generated tens of viable seeds that inherited the mutations. Using the same C-terminal editing approach, we also obtained viable mutants for a wall-associated protein kinase (Os07g0493200) and a leucine-rich repeat receptor-like protein kinase (Os01g0239700), while the null mutations of these genes were lethal. These data suggest that protein kinase activity could be reduced by introducing frameshift mutations adjacent to the C-terminus, which could generate valuable resources for gene function studies and tune protein kinase activity for signaling pathway engineering.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-024-00165-5.

OsGLP8-7 interacts with OsPRX111 to detoxify excess copper in rice

Lignin is a phenolic biopolymer generated from phenylpropanoid pathway in the secondary cell wall and is required for defense of plants against various stress. Although the fact of stress-induced lignin deposition has been clearly demonstrated, it remains largely elusive how the formation of lignin is promoted under Cu stress. The present study showed that OsGLP8-7, an extracellular glycoprotein of rice (Oryza sativa L.), plays an important function against Cu stress. The loss function of OsGLP8-7 results in Cu sensitivity whereas overexpression of OsGLP8-7 scavenges Cu-induced superoxide anion (O2•-). OsGLP8-7 interacts with apoplastic peroxidase111 (OsPRX111) and elevates OsPRX111 stability when exposed to excess Cu. In OsGLP8-7 overexpressing (OE) lines, the retention of Cu within cell wall limiting Cu uptake into cytoplasm is attributed to the enhanced lignification required for Cu tolerance. Exogenous application of a lignin inhibitor can impair the Cu tolerance of transgenic Arabidopsis lines overexpressing OsGLP8-7. In addition, co-expression of OsGLP8-7 and OsPRX111 genes in tobacco leaves leads to an improved lignin deposition compared to leaves expressing each gene individually or the empty vector. Taken together, our findings provided the convincing evidences that the interaction between OsGLP8-7 and OsPRX111 facilitates effectively lignin polymerization, thereby contributing to Cu tolerance in rice.

A newly evolved rice-specific gene JAUP1 regulates jasmonate biosynthesis and signalling to promote root development and multi-stress tolerance

Root architecture and function are critical for plants to secure water and nutrient supply from the soil, but environmental stresses alter root development. The phytohormone jasmonic acid (JA) regulates plant growth and responses to wounding and other stresses, but its role in root development for adaptation to environmental challenges had not been well investigated. We discovered a novel JA Upregulated Protein 1 gene (JAUP1) that has recently evolved in rice and is specific to modern rice accessions. JAUP1 regulates a self-perpetuating feed-forward loop to activate the expression of genes involved in JA biosynthesis and signalling that confers tolerance to abiotic stresses and regulates auxin-dependent root development. Ectopic expression of JAUP1 alleviates abscisic acid- and salt-mediated suppression of lateral root (LR) growth. JAUP1 is primarily expressed in the root cap and epidermal cells (EPCs) that protect the meristematic stem cells and emerging LRs. Wound-activated JA/JAUP1 signalling promotes crosstalk between the root cap of LR and parental root EPCs, as well as induces cell wall remodelling in EPCs overlaying the emerging LR, thereby facilitating LR emergence even under ABA-suppressive conditions. Elevated expression of JAUP1 in transgenic rice or natural rice accessions enhances abiotic stress tolerance and reduces grain yield loss under a limited water supply. We reveal a hitherto unappreciated role for wound-induced JA in LR development under abiotic stress and suggest that JAUP1 can be used in biotechnology and as a molecular marker for breeding rice adapted to extreme environmental challenges and for the conservation of water resources.

The transcription factor OsbZIP48 governs rice responses to zinc deficiency

Zinc (Zn) deficiency is the most prevalent micronutrient disorder in rice and leads to delayed development and decreased yield. Nevertheless, despite its primary importance, how rice responds to Zn deficiency remains poorly understood. This study presents genetic evidence supporting the crucial role of OsbZIP48 in regulating rice's response to Zn deficiency, consistent with earlier findings in the model plant Arabidopsis. Genetic inactivation of OsbZIP48 in rice seedlings resulted in heightened sensitivity to Zn deficiency and reduced Zn translocation from roots to shoots. Consistently, OsbZIP48 was constitutively expressed in roots, slightly induced by Zn deficiency in shoots and localized into nuclei induced by Zn deficiency. Comparative transcriptome analysis of the wild-type plants and osbzip48 mutant grown under Zn deficiency enabled the identification of OsbZIP48 target genes, including key Zn transporter genes (OsZIP4 and OsZIP8). We demonstrated that OsbZIP48 controlled the expressions of these genes by directly binding to their promoters, specifically to the Zn deficiency response element motif. This study establishes OsbZIP48 as a critical transcription factor in rice's response to Zn deficiency, offering valuable insights for developing Zn-biofortified rice varieties to combat global Zn limitation.

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.

CRISPR/Cas9: an advanced platform for root and tuber crops improvement

Root and tuber crops (RTCs), which include cassava, potato, sweet potato, and yams, principally function as staple crops for a considerable fraction of the world population, in addition to their diverse applications in nutrition, industry, and bioenergy sectors. Even then, RTCs are an underutilized group considering their potential as industrial raw material. Complexities in conventional RTC improvement programs curb the extensive exploitation of the potentials of this group of crop species for food, energy production, value addition, and sustainable development. Now, with the advent of whole-genome sequencing, sufficient sequence data are available for cassava, sweet potato, and potato. These genomic resources provide enormous scope for the improvement of tuber crops, to make them better suited for agronomic and industrial applications. There has been remarkable progress in RTC improvement through the deployment of new strategies like gene editing over the last decade. This review brings out the major areas where CRISPR/Cas technology has improved tuber crops. Strategies for genetic transformation of RTCs with CRISPR/Cas9 constructs and regeneration of edited lines and the bottlenecks encountered in their establishment are also discussed. Certain attributes of tuber crops requiring focus in future research along with putative editing targets are also indicated. Altogether, this review provides a comprehensive account of developments achieved, future lines of research, bottlenecks, and major experimental concerns regarding the establishment of CRISPR/Cas9-based gene editing in RTCs.

Comprehensive review of CRISPR-based gene editing: mechanisms, challenges, and applications in cancer therapy

The CRISPR system is a revolutionary genome editing tool that has the potential to revolutionize the field of cancer research and therapy. The ability to precisely target and edit specific genetic mutations that drive the growth and spread of tumors has opened up new possibilities for the development of more effective and personalized cancer treatments. In this review, we will discuss the different CRISPR-based strategies that have been proposed for cancer therapy, including inactivating genes that drive tumor growth, enhancing the immune response to cancer cells, repairing genetic mutations that cause cancer, and delivering cancer-killing molecules directly to tumor cells. We will also summarize the current state of preclinical studies and clinical trials of CRISPR-based cancer therapy, highlighting the most promising results and the challenges that still need to be overcome. Safety and delivery are also important challenges for CRISPR-based cancer therapy to become a viable clinical option. We will discuss the challenges and limitations that need to be overcome, such as off-target effects, safety, and delivery to the tumor site. Finally, we will provide an overview of the current challenges and opportunities in the field of CRISPR-based cancer therapy and discuss future directions for research and development. The CRISPR system has the potential to change the landscape of cancer research, and this review aims to provide an overview of the current state of the field and the challenges that need to be overcome to realize this potential.

Chitosan nanoplatforms in agriculture for multi-potential applications - Adsorption/removal, sustained release, sensing of pollutants & delivering their alternatives - A comprehensive review

An increase in the global population has led to an increment in the food consumption, which has demanded high food production. To meet the production demands, different techniques and technologies are adopted in agriculture the past 70 years, where utilization of the industry-manufactured/synthetic pesticides (SPTCs - e.g., herbicides, insecticides, fungicides, bactericides, nematicides, acaricides, avicides, and so on) is one of them. However, it has been later revealed that the usage of SPTCs has negatively impacted the environment - especially water and soil, and also agricultural products - mainly foods. Though preventive measures are taken by government agencies, still the utilization rate of SPTCs is high, and consequently, their maximum residual limit (MRL) levels in food are above tolerance, which further results in serious health concerns in humans. So, there is an immediate need for decreasing the utilization of the SPTCs by delivering them effectively at reduced levels in agriculture but with the required efficacy. Apart from that, it is mandatory to detect/sense and also to remove them to lessen the environmental pollution, while developing effective alternative techniques/technologies. Among many suitable materials that are developed/idenified, chitosan, a bio-polymer has gained great attention and is comprehensively implemented in all the above-mentioned applications - sensing, delivery and removal, due to their excellent and required properties. Though many works are available, in this work, a special attention is given to chitosan and its derivatives (i.e., chitosan nanoparticles (CNPs))based removal, controlled release and sensing of the SPTCs - specifically herbicides and insecticides. Moreover, the chitosan/CNPs-based protective effects on the in vivo models during/after their exposure to the SPTCs, and the current technologies like clustered regularly interspaced short palindromic repeats (CRISPR) as alternatives for SPTCs are also reviewed.

A Comprehensive Protocol for Assembly of Multiple gRNAs into a Direct Vector for Genome Editing in Tomato

The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas 9 (CRISPR-associated protein 9) is a robust DNA-encoded, RNA-mediated sequence-specific nuclease system widely used for genome editing of various plants. Although there are many reports on the assembly of gRNAs and plant transformation, there is no single resource for the complete gene editing methodology in tomato. This chapter provides a comprehensive protocol for designing gRNAs, their assembly into the vector, plant transformation, and final mutant analysis in tomato.

CRISPR/Cas9-mediated genome editing techniques and new breeding strategies in cereals - current status, improvements, and perspectives

Cereal crops, including triticeae species (barley, wheat, rye), as well as edible cereals (wheat, corn, rice, oat, rye, sorghum), are significant suppliers for human consumption, livestock feed, and breweries. Over the past half-century, modern varieties of cereal crops with increased yields have contributed to global food security. However, presently cultivated elite crop varieties were developed mainly for optimal environmental conditions. Thus, it has become evident that taking into account the ongoing climate changes, currently a priority should be given to developing new stress-tolerant cereal cultivars. It is necessary to enhance the accuracy of methods and time required to generate new cereal cultivars with the desired features to adapt to climate change and keep up with the world population expansion. The CRISPR/Cas9 system has been developed as a powerful and versatile genome editing tool to achieve desirable traits, such as developing high-yielding, stress-tolerant, and disease-resistant transgene-free lines in major cereals. Despite recent advances, the CRISPR/Cas9 application in cereals faces several challenges, including a significant amount of time required to develop transgene-free lines, laboriousness, and a limited number of genotypes that may be used for the transformation and in vitro regeneration. Additionally, developing elite lines through genome editing has been restricted in many countries, especially Europe and New Zealand, due to a lack of flexibility in GMO regulations. This review provides a comprehensive update to researchers interested in improving cereals using gene-editing technologies, such as CRISPR/Cas9. We will review some critical and recent studies on crop improvements and their contributing factors to superior cereals through gene-editing technologies.

Dissecting the promotional effect of zinc on cadmium translocation from roots to shoots in rice

It is often expected that Zn decreases Cd accumulation in plants due to competition for the same transporters. Here, we found that increasing Zn supply markedly increased the root-to-shoot translocation of Cd in rice. RNA sequencing showed that high Zn up-regulated expression of genes involved in glutathione biosynthesis and metabolism and the Zn/Cd transporter gene OsHMA2, but down-regulated expression of genes related to Zn uptake. Knockout of the iron or Zn transporter genes OsIRT1, OsIRT2, or OsZIP9 did not affect the Zn promotional effect on Cd translocation. Knockout of the manganese/Cd transporter gene OsNRAMP5 greatly reduced Cd uptake but did not affect the Zn promotional effect. Variation in the tonoplast transporter gene OsHMA3 affected Cd translocation but did not change the Zn promotional effect. Knockout of the Zn/Cd transporter gene OsHMA2 not only decreased Cd and Zn translocation, but also abolished the Zn promotional effect. Increased expression of OsHMA2 under high Zn conditions supports the hypothesis that this transporter participates in the promotional effect of Zn on Cd translocation. The results also show that OsIRT1, OsIRT2, and OsZIP9 made only small contributions to Cd uptake under low Zn conditions but not under high Zn conditions, whereas the dominant role of OsNRAMP5 in Cd uptake diminished under low Zn conditions.

The rice annexin gene OsAnn5 is involved in cold stress tolerance at the seedling stage

Annexins exist widely in plants as multigene families and play critical roles in stress responses and a range of cellular processes. This study provides a comprehensive account of the cloning and functional characterization of the rice annexin gene OsAnn5. The findings reveal that a cold stress treatment at the seedling stage of rice induced OsAnn5 expression. GUS staining assay indicated that the expression of OsAnn5 was non tissue-specific and was detected in almost all rice tissues. Subcellular localization indicated that OsAnn5-GFP (green fluorescent protein) signals were found in the endoplasmic reticulum apparatus. Compared with wild type rice, knocking out OsAnn5 using the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR associated proteins) mediated genome editing resulted in sensitivity to cold treatments. These results indicate that OsAnn5 is involved in cold stress tolerance at the seedling stage.

Guidelines for Performing CRISPR/Cas9 Genome Editing for Gene Validation and Trait Improvement in Crops

With the rapid advances in plant genome editing techniques over the past 10 years, more efficient and powerful crop genome editing applications are now possible. Candidate genes for key traits can be validated using CRISPR/Cas9-based knockouts and through the up- and down-regulation of gene expression. Likewise, new trait improvement approaches can take advantage of targeted editing to improve stress tolerance, disease resistance, and nutritional traits. However, several key steps in the process can prove tricky for researchers who might be new to plant genome editing. Here, we present step-by-step guidelines and best practices for a crop genome editing pipeline that should help to improve the rate of success. Important factors in the process include proper target sequence analysis and single guide RNA (sgRNA) design, sequencing of the target site in the genotypes of interest, performing an in vitro CRISPR/Cas9 ribonucleoprotein (RNP) assay to validate the designed sgRNAs, preparing the transformation constructs, considering a protoplast editing step as further validation, and, finally, stable plant transformation and mutation detection by Sanger and/or next-generation sequencing. With these detailed guidelines, a new user should be able to quickly set up a genome editing pipeline in their crop of interest and start making progress with the different CRISPR/Cas-based editing variants for gene validation and trait improvement purposes.

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

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

Green revolution to genome revolution: driving better resilient crops against environmental instability

Crop improvement programmes began with traditional breeding practices since the inception of agriculture. Farmers and plant breeders continue to use these strategies for crop improvement due to their broad application in modifying crop genetic compositions. Nonetheless, conventional breeding has significant downsides in regard to effort and time. Crop productivity seems to be hitting a plateau as a consequence of environmental issues and the scarcity of agricultural land. Therefore, continuous pursuit of advancement in crop improvement is essential. Recent technical innovations have resulted in a revolutionary shift in the pattern of breeding methods, leaning further towards molecular approaches. Among the promising approaches, marker-assisted selection, QTL mapping, omics-assisted breeding, genome-wide association studies and genome editing have lately gained prominence. Several governments have progressively relaxed their restrictions relating to genome editing. The present review highlights the evolutionary and revolutionary approaches that have been utilized for crop improvement in a bid to produce climate-resilient crops observing the consequence of climate change. Additionally, it will contribute to the comprehension of plant breeding succession so far. Investing in advanced sequencing technologies and bioinformatics will deepen our understanding of genetic variations and their functional implications, contributing to breakthroughs in crop improvement and biodiversity conservation.

A Digital PCR Method Based on Highly Specific Taq for Detecting Gene Editing and Mutations

Digital PCR (dPCR) has great potential for assessing gene editing or gene mutation due to its ability to independently inspect each DNA template in parallel. However, current dPCR methods use a fluorescence-labeled probe to detect gene variation events, and their ability to distinguish variated sequences from the wild-type sequence is limited by the probe's tolerance to mismatch. To address this, we have developed a novel dPCR method that uses a primer instead of a probe to sense gene variation. The enhanced Taq DNA polymerase in the PCR system has a high mismatch sensitivity, which enables our dPCR method to distinguish gene mutations from wild-type sequences. Compared to current dPCR methods, our method shows superior precision in assessing gene editing efficiency and single-base DNA mutation. This presents a promising opportunity to advance gene editing research and rare gene mutation detection.

Breakthrough in CRISPR/Cas system: Current and future directions and challenges

Targeted genome editing (GE) technology has brought a significant revolution in fictional genomic research and given hope to plant scientists to develop desirable varieties. This technology involves inducing site-specific DNA perturbations that can be repaired through DNA repair pathways. GE products currently include CRISPR-associated nuclease DNA breaks, prime editors generated DNA flaps, single nucleotide-modifications, transposases, and recombinases. The discovery of double-strand breaks, site-specific nucleases (SSNs), and repair mechanisms paved the way for targeted GE, and the first-generation GE tools, ZFNs and TALENs, were successfully utilized in plant GE. However, CRISPR-Cas has now become the preferred tool for GE due to its speed, reliability, and cost-effectiveness. Plant functional genomics has benefited significantly from the widespread use of CRISPR technology for advancements and developments. This review highlights the progress made in CRISPR technology, including multiplex editing, base editing (BE), and prime editing (PE), as well as the challenges and potential delivery mechanisms.

Recent Developments in CRISPR/Cas9 Genome-Editing Technology Related to Plant Disease Resistance and Abiotic Stress Tolerance

The revolutionary CRISPR/Cas9 genome-editing technology has emerged as a powerful tool for plant improvement, offering unprecedented precision and efficiency in making targeted gene modifications. This powerful and practical approach to genome editing offers tremendous opportunities for crop improvement, surpassing the capabilities of conventional breeding techniques. This article provides an overview of recent advancements and challenges associated with the application of CRISPR/Cas9 in plant improvement. The potential of CRISPR/Cas9 in terms of developing crops with enhanced resistance to biotic and abiotic stresses is highlighted, with examples of genes edited to confer disease resistance, drought tolerance, salt tolerance, and cold tolerance. Here, we also discuss the importance of off-target effects and the efforts made to mitigate them, including the use of shorter single-guide RNAs and dual Cas9 nickases. Furthermore, alternative delivery methods, such as protein- and RNA-based approaches, are explored, and they could potentially avoid the integration of foreign DNA into the plant genome, thus alleviating concerns related to genetically modified organisms (GMOs). We emphasize the significance of CRISPR/Cas9 in accelerating crop breeding processes, reducing editing time and costs, and enabling the introduction of desired traits at the nucleotide level. As the field of genome editing continues to evolve, it is anticipated that CRISPR/Cas9 will remain a prominent tool for crop improvement, disease resistance, and adaptation to challenging environmental conditions.