Directed evolution rice genes with randomly multiplexed sgRNAs assembly of base editors

Enhanced Genome Editing Activity with Novel Chimeric ScCas9 Variants in Rice

The Streptococcus canis Cas9 protein (ScCas9) recognizes the NNG protospacer adjacent motif (PAM), offering a wider range of targets than that offered by the commonly used S. pyogenes Cas9 protein (SpCas9). However, both ScCas9 and its evolved Sc++ variant still exhibit low genome editing efficiency in plants, particularly at the less preferred NTG and NCG PAM targets. In this study, a chimeric SpcRN++ variant is engineered by grafting the recognition (REC) domain of SpCas9 into the Sc++ variant, incorporating the R221K/N394K mutations, and retaining the positively charged loop of S. anginosus Cas9. The SpcRN++ variant exhibits a higher genome editing capacity and wider target range than the Sc++ variant in rice protoplasts and stable transgenic plants. Further evidence indicates that nSpcRN++-based A3A/Y130F and TadA8e exhibit enhanced cytosine and adenine editing efficiency in plants. Finally, herbicide-resistant rice germplasms are produced by targeting the OsACC gene using nSpcRN++-based adenine base editors. These results demonstrate that SpcRN++ is a powerful tool for genome editing in plants, and this integrative protein engineering strategy holds promise for engineering other Cas9 proteins.

Development and optimization of base editors and its application in crops

Genome editing technologies hold significant potential for targeted mutagenesis in crop development, aligning with evolving agricultural needs. Point mutations, or single nucleotide polymorphisms (SNPs), define key agronomic traits in various crop species and play a pivotal role. The implementation of single nucleotide variations through genome editing-based base editing offers substantial promise in expediting crop improvement by inducing advantageous trait variations. Among many genome editing techniques, base editing stands out as an advanced next-generation technology, evolved from the CRISPR/Cas9 system.Base editing, a recent advancement in genome editing, enables precise DNA modification without the risks associated with double-strand breaks. Base editors, designed as precise genome editing tools, enable the direct and irreversible conversion of specific target bases. Base editors consist of catalytically active CRISPR-Cas9 domains, including Cas9 variants, fused with domains like cytidine deaminase, adenine deaminase, or reverse transcriptase. These fusion proteins enable the introduction of specific point mutations in target genomic regions. Currently developed are cytidine base editors (CBEs), mutating C to T; adenine base editors (ABEs), changing A to G; and prime editors (PEs), enabling arbitrary base conversions, precise insertions, and deletions. In this review, the research, development, and progress of various base editing systems, along with their potential applications in crop improvement, were intended to be summarized. The limitations of this technology will also be discussed. Finally, an outlook on the future of base editors will be provided.

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.

CRISPR-Cas systems and applications for crop bioengineering

CRISPR-Cas technologies contribute to enhancing our understanding of plant gene functions, and to the precise breeding of crop traits. Here, we review the latest progress in plant genome editing, focusing on emerging CRISPR-Cas systems, DNA-free delivery methods, and advanced editing approaches. By illustrating CRISPR-Cas applications for improving crop performance and food quality, we highlight the potential of genome-edited crops to contribute to sustainable agriculture and food security.

Breeding herbicide-resistant rice (Oryza sativa) using CRISPR-Cas gene editing and other technologies

The emergence of herbicide-resistant weeds in crop fields and the extensive use of herbicides have led to a decrease in rice (Oryza sativa) yields and an increase in production costs. To address these challenges, researchers have focused on the discovery of new germplasm resources with herbicide resistance. The most promising candidate genes have been functionally studied and applied in rice breeding. Here, we review recent progress in the breeding of herbicide-resistant rice. We provide examples of various techniques used to breed herbicide-resistant rice, such as physical and chemical mutagenesis, genetic transformation, and CRISPR-Cas-mediated gene editing. We highlight factors involved in the breeding of herbicide-resistant rice, including target genes, rice varieties, degrees of herbicide resistance, and research tools. Finally, we suggest methods for breeding herbicide-resistant rice that could potentially be used for weed management in direct-seeding farm systems.

Targeted genome-modification tools and their advanced applications in crop breeding

Crop improvement by genome editing involves the targeted alteration of genes to improve plant traits, such as stress tolerance, disease resistance or nutritional content. Techniques for the targeted modification of genomes have evolved from generating random mutations to precise base substitutions, followed by insertions, substitutions and deletions of small DNA fragments, and are finally starting to achieve precision manipulation of large DNA segments. Recent developments in base editing, prime editing and other CRISPR-associated systems have laid a solid technological foundation to enable plant basic research and precise molecular breeding. In this Review, we systematically outline the technological principles underlying precise and targeted genome-modification methods. We also review methods for the delivery of genome-editing reagents in plants and outline emerging crop-breeding strategies based on targeted genome modification. Finally, we consider potential future developments in precise genome-editing technologies, delivery methods and crop-breeding approaches, as well as regulatory policies for genome-editing products.

Diverse nucleotide substitutions in rice base editing mediated by novel TadA variants

CRISPR-mediated base editors have been widely used to correct defective alleles and create novel alleles by artificial evolution for the rapid genetic improvement of crops. The editing capabilities of base editors strictly rely on the performance of various nucleotide modification enzymes. Compared with the well-developed adenine base editors (ABEs), cytosine base editors (CBEs) and dual base editors suffer from unstable editing efficiency and patterns at different genomic loci in rice, significantly limiting their application. Here, we comprehensively examined the base editing activities of multiple evolved TadA8e variants in rice. We found that both TadA-CDd and TadA-E27R/N46L achieved more robust C-to-T editing than previously reported hyperactive hAID∗Δ, and TadA-CDd outperformed TadA-E27R/N46L. A C-to-G base editor (CGBE) engineered with TadA-CDd and OsUNG performed highly efficient C-to-G editing in rice compared with that of TadA-N46P. In addition, a dual base editor constructed with a single protein, TadDE, enabled simultaneous, highly efficient C-to-T and A-to-G editing in rice. Collectively, our results demonstrate that TadA8e derivatives improve both CBEs and dual base editors in rice, providing a powerful way to induce diverse nucleotide substitutions for plant genome editing.

Creating large-scale genetic diversity in Arabidopsis via base editing-mediated deep artificial evolution

BACKGROUND

Base editing is a powerful tool for artificial evolution to create allelic diversity and improve agronomic traits. However, the great evolutionary potential for every sgRNA target has been overlooked. And there is currently no high-throughput method for generating and characterizing as many changes in a single target as possible based on large mutant pools to permit rapid gene directed evolution in plants.

RESULTS

In this study, we establish an efficient germline-specific evolution system to screen beneficial alleles in Arabidopsis which could be applied for crop improvement. This system is based on a strong egg cell-specific cytosine base editor and the large seed production of Arabidopsis, which enables each T1 plant with unedited wild type alleles to produce thousands of independent T2 mutant lines. It has the ability of creating a wide range of mutant lines, including those containing atypical base substitutions, and as well providing a space- and labor-saving way to store and screen the resulting mutant libraries. Using this system, we efficiently generate herbicide-resistant EPSPS, ALS, and HPPD variants that could be used in crop breeding.

CONCLUSIONS

Here, we demonstrate the significant potential of base editing-mediated artificial evolution for each sgRNA target and devised an efficient system for conducting deep evolution to harness this potential.

High performance TadA-8e derived cytosine and dual base editors with undetectable off-target effects in plants

Cytosine base editors (CBEs) and adenine base editors (ABEs) enable precise C-to-T and A-to-G edits. Recently, ABE8e, derived from TadA-8e, enhances A-to-G edits in mammalian cells and plants. Interestingly, TadA-8e can also be evolved to confer C-to-T editing. This study compares engineered CBEs derived from TadA-8e in rice and tomato cells, identifying TadCBEa, TadCBEd, and TadCBEd_V106W as efficient CBEs with high purity and a narrow editing window. A dual base editor, TadDE, promotes simultaneous C-to-T and A-to-G editing. Multiplexed base editing with TadCBEa and TadDE is demonstrated in transgenic rice, with no off-target effects detected by whole genome and transcriptome sequencing, indicating high specificity. Finally, two crop engineering applications using TadDE are shown: introducing herbicide resistance alleles in OsALS and creating synonymous mutations in OsSPL14 to resist OsMIR156-mediated degradation. Together, this study presents TadA-8e derived CBEs and a dual base editor as valuable additions to the plant editing toolbox.

A Critical Review of Conventional and Modern Approaches to Develop Herbicide-Resistance in Rice

Together with rice, weeds strive for nutrients and space in farmland, resulting in reduced rice yield and quality. Planting herbicide-resistant rice varieties is one of the effective ways to control weeds. In recent years, a series of breakthroughs have been made to generate herbicide-resistant germplasm, especially the emergence of biotechnological tools such as gene editing, which provides an inherent advantage for the knock-out or knock-in of the desired genes. In order to develop herbicide-resistant rice germplasm resources, gene manipulation has been conducted to enhance the herbicide tolerance of rice varieties through the utilization of techniques such as physical and chemical mutagenesis, as well as genome editing. Based on the current research and persisting problems in rice paddy fields, research on the generation of herbicide-resistant rice still needs to explore genetic mechanisms, stacking multiple resistant genes in a single genotype, and transgene-free genome editing using the CRISPR system. Current rapidly developing gene editing technologies can be used to mutate herbicide target genes, enabling targeted genes to maintain their biological functions, and reducing the binding ability of target gene encoded proteins to corresponding herbicides, ultimately resulting in herbicide-resistant crops. In this review article, we have summarized the utilization of conventional and modern approaches to develop herbicide-resistant cultivars in rice as an effective strategy for weed control in paddy fields, and discussed the technology and research directions for creating herbicide-resistant rice in the future.

CRISPR-mediated acceleration of wheat improvement: advances and perspectives

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