Modularly assembled multiplex prime editors for simultaneous editing of agronomically important genes in rice

Recent Progress in Rice-Xanthomonas oryzae Interactions

Rice bacterial blight (BB) and bacterial leaf streak (BLS), caused by Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), respectively, are among the most devastating bacterial diseases threatening global rice production. The interactions between rice and Xanthomonas oryzae are complex and dynamic, involving recognition, attack, defense, and adaptation mechanisms enacted by both the rice host and the pathogens. This review summarizes recent advances in understanding rice-Xanthomonas oryzae interactions, focusing on infection models, pathogenic mechanisms, and immune responses elicited by Xanthomonas oryzae. Special attention is devoted to the roles of transcription activator-like effectors (TALEs) and non-TALE effectors in pathogenicity, the functions of resistance (R) genes in defense, and the interconnected molecular networks of interactions derived from multi-omics approaches. Understanding these interactions is essential for developing effective disease-resistance strategies and creating elite disease-resistant rice varieties.

Breeding herbicide-resistant rice 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.

Cas9-PE: a robust multiplex gene editing tool for simultaneous precise editing and site-specific random mutation in rice

In molecular design breeding, the simultaneous introduction of desired functional genes through specific nucleotide modifications and the elimination of genes regulating undesired phenotypic traits or agronomic components require advanced gene editing tools. Due to limited editing efficiency, even with the use of highly precise editing tools, such as prime editing (PE), simultaneous editing of multiple mutation types poses a challenge. Here, we replaced Cas9 nickase (nCas9) with Cas9 to construct a Cas9-mediated PE (Cas9-PE) system in rice. This system not only enables precise editing, but also allows for site-specific random mutation. Moreover, leveraging the precision of Cas9-PE, we established a transgene-free multiplex gene editing system using a co-editing strategy. This strategy involved the Agrobacterium-mediated transient expression of the precise editing rice endogenous acetolactate synthase gene ALSS627I to confer herbicide bispyribac-sodium (BS) resistance as a selection marker. This study provides a versatile and efficient multiplex gene editing tool for molecular design breeding.

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

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

Prime editing: A gene precision editing tool from inception to present

Genetic mutations significantly contribute to the onset of diseases, with over half of the cases caused by single-nucleotide mutations. Advances in gene editing technologies have enabled precise editing and correction of mutated genes, offering effective treatment methods for genetic disorders. CRISPR/Cas9, despite its power, poses risks of inducing gene mutations due to DNA double-strand breaks (DSB). The advent of base editing (BE) and prime editing (PE) has mitigated these risks by eliminating the hazards associated with DNA DSBs, allowing for more precise gene editing. This breakthrough lays a solid foundation for the clinical application of gene editing technologies. This review discusses the principles, development, and applications of PE gene editing technology in various genetic mutation-induced diseases.

Unleashing the Potential of CRISPR/Cas9 Genome Editing for Yield-Related Traits in Rice

Strategies to enhance rice productivity in response to global demand have been the paramount focus of breeders worldwide. Multiple factors, including agronomical traits such as plant architecture and grain formation and physiological traits such as photosynthetic efficiency and NUE (nitrogen use efficiency), as well as factors such as phytohormone perception and homeostasis and transcriptional regulation, indirectly influence rice grain yield. Advances in genetic analysis methodologies and functional genomics, numerous genes, QTLs (Quantitative Trait Loci), and SNPs (Single-Nucleotide Polymorphisms), linked to yield traits, have been identified and analyzed in rice. Genome editing allows for the targeted modification of identified genes to create novel mutations in rice, avoiding the unintended mutations often caused by random mutagenesis. Genome editing technologies, notably the CRISPR/Cas9 system, present a promising tool to generate precise and rapid modifications in the plant genome. Advancements in CRISPR have further enabled researchers to modify a larger number of genes with higher efficiency. This paper reviews recent research on genome editing of yield-related genes in rice, discusses available gene editing tools, and highlights their potential to expedite rice breeding programs.

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.