Heritable Wheat Genome Editing via RNA Virus Delivery

In a groundbreaking advancement poised to revolutionize the future of crop genetic engineering, scientists have unveiled a novel method for delivering CRISPR–Cas9 genome-editing tools into wheat plants using an RNA virus-based vector. This technological breakthrough addresses a major bottleneck in plant biotechnology — the efficient and heritable delivery of gene-editing components into monocot species, which include important cereal crops such as wheat, rice, and maize. The study leverages the unique biology of barley yellow striate mosaic virus (BYSMV), transforming it into a robust delivery system capable of reaching the growing points of wheat axillary meristems and generating stable, heritable genome modifications without the need for transgenic constructs or tissue culture procedures.

Conventional approaches to plant genome editing face numerous challenges, especially in monocots, where transformation techniques are often inefficient, genotype-dependent, and labor-intensive. Traditional methods typically require the insertion of foreign DNA through tissue culture regeneration, which can induce somaclonal variations and prolong breeding timelines. The newly engineered BYSMV vector circumvents these limitations by employing a negative-strand RNA virus platform, which naturally infects monocot species and propagates systematically within host plants. By repurposing the virus as a gene delivery vehicle, the research team succeeded in introducing both the Cas9 endonuclease and the specific single guide RNAs (sgRNAs) into wheat cells in a tissue culture- and transgene-free manner.

At the heart of this innovative system lies a sophisticated molecular strategy that dramatically enhances the mobility and targeting of genome-editing reagents. The researchers discovered that fusing a mobile transfer RNA (tRNA) sequence to the mRNA encoding Cas9, as well as to the sgRNAs, enables efficient transport of these molecules into the axillary meristems — the critical growth regions responsible for producing tillers, or side shoots, in wheat plants. This ingenious fusion trick ensures that the gene-editing components arrive precisely where heritable changes can occur prior to tiller generation, a step crucial for passing mutations on to subsequent progeny.

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The ability to edit multiple homoeoalleles simultaneously was another remarkable aspect of this methodology. Wheat is a hexaploid species containing three distinct genomes, each harboring homologous gene copies known as homoeoalleles. Targeting all three alleles in one go is notoriously difficult due to genetic redundancy and sequence similarities. However, the BYSMV-based delivery system achieved simultaneous mutations across all targeted homoeoalleles, thereby producing nascent tillers bearing compound edits — a feat that significantly accelerates functional genomics analysis as well as breeding programs aiming to introduce complex traits.

Importantly, the progeny plants derived from infected parents were confirmed to be virus-free, eliminating concerns about viral persistence or off-target effects stemming from prolonged virus infection. Moreover, the mutations identified in these seedlings were either bi-allelic or homozygous, signifying stable inheritance of edits and the potential for immediate use in breeding efforts without the necessity for further backcrossing or selection. This outcome reflects the high precision and reliability of the viral delivery platform, which could represent a transformative step toward non-transgenic crop improvement.

The use of BYSMV as a gene delivery vector is particularly strategic given its natural host range, which spans an impressive 26 monocot species. This broad infectivity hints at the versatility of the system beyond wheat alone, opening avenues for genome editing across a diverse array of cereal crops and grasses. Such scalability is crucial in modern agriculture, where rapid adaptation to climate change, pest pressure, and evolving consumer demands require swift and flexible breeding solutions.

While previous efforts in virus-mediated delivery have typically involved positive-strand RNA viruses, the current study illustrates the effective engineering of a negative-strand RNA virus backbone, expanding the viral toolbox available for plant biotechnology. Negative-strand RNA viruses present unique benefits including their replication mechanisms and genomic architectures, which can be harnessed for stable expression and accurate delivery of genome editing components. This methodological innovation broadens the horizons of plant genome engineering by providing alternative viral vectors with diverse properties suited to varying crop species and experimental objectives.

The integration of a mobile tRNA fusion sequence into the Cas9 and sgRNA transcripts harnesses the plant’s intrinsic intercellular trafficking mechanisms, an elegant exploitation of host biology to enhance delivery efficiency. By co-opting the endogenous pathways for RNA mobility, the technology ensures that editing machinery not only reaches proliferating cells but also persists long enough to enact heritable genome modifications. Such deep understanding of molecular plant biology combined with viral vector engineering exemplifies the sophisticated, interdisciplinary approach required to push the boundaries of crop genome editing.

This RNA virus-based delivery system also addresses major regulatory and public acceptance hurdles associated with transgenic and tissue culture-based genetic modifications. Since the method results in virus-free progeny devoid of foreign DNA integration, the edited plants are effectively non-transgenic, thereby simplifying regulatory pathways and potentially reducing public resistance to genome-edited crops. By enabling non-transgenic, heritable genome editing that bypasses classical genetic engineering bottlenecks, the BYSMV vector system emerges as a powerful tool for next-generation crop breeding.

Beyond fundamental research, the implications for global food security and sustainable agriculture are profound. Wheat is a staple crop feeding billions worldwide, and innovations that accelerate its genetic improvement will have ripple effects throughout the agri-food sector. By facilitating rapid and precise editing of crucial agronomic traits — including yield components, disease resistance, and stress tolerance — this technology has the potential to enhance productivity and resilience, particularly under challenging environmental conditions driven by climate variability.

Moreover, the system’s broad host range and adaptability may enable rapid deployment in orphan crops and regionally important cereals where conventional transformation methods remain elusive. This democratization of genome editing technology could empower breeders and researchers in developing countries, fostering agricultural innovation tailored to local challenges and resource constraints.

Despite these promising advances, further research will be essential to optimize the delivery efficiency across different genotypes and environmental conditions. Understanding the interplay between viral infection dynamics, plant immune responses, and editing outcomes will aid in refining this platform and broadening its applicability. Additionally, comprehensive off-target analyses and long-term field evaluations will help validate the safety and stability of edited plants produced via this approach.

The demonstration of heritable, non-transgenic genome editing via a negative-strand RNA virus vector marks a significant milestone in plant biotechnology. By marrying advanced viral vector engineering with the precision of CRISPR–Cas systems and the natural mobility of tRNA sequences, the researchers have created a versatile, highly efficient platform that could fundamentally transform crop improvement strategies worldwide. This innovation exemplifies how leveraging sophisticated biological knowledge and molecular tools converges to overcome longstanding challenges, paving the way for a new era of sustainable, precise, and accessible plant genome editing.

As the global community faces escalating demands for food and environmental pressures, such pioneering work underscores the vital role of cutting-edge biotechnology in securing future agricultural resilience. The deployment of BYSMV-based genome editing in wheat is more than a technological breakthrough; it represents a paradigm shift toward rapid, non-transgenic, heritable trait modification with enormous potential to reshape how crops are bred in the decades to come.

Subject of Research: Genome editing in wheat using a negative-strand RNA virus vector system.

Article Title: Transgene- and tissue culture-free heritable genome editing using RNA virus-based delivery in wheat.

Article References:
Qiao, JH., Zang, Y., Gao, Q. et al. Transgene- and tissue culture-free heritable genome editing using RNA virus-based delivery in wheat. Nat. Plants (2025). https://doi.org/10.1038/s41477-025-02023-8

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