Prime editing technology, which functions as a highly precise genome modification tool, has been transformative since its introduction. However, its application in complex plant species, particularly dicots like soybean, has been hampered by inherently low editing efficiencies. This bottleneck arose from inefficiencies in the prime editor components and constraints in intracellular processes linked to plant physiology. The newly engineered GmPEplus system boldly addresses these challenges by meticulously optimizing multiple domains of the prime editor machinery.

At the core of GmPEplus is a deft modification of the reverse transcriptase (RT) domain, the crucial enzymatic engine responsible for synthesizing the edited DNA strand. The research team strategically excised the RNase H domain from the RT, which is known to degrade RNA-DNA hybrids, effectively preserving the stability of prime editing intermediates. Simultaneously, a point mutation, specifically the substitution of valine to alanine at position 223 (V223A), was introduced within the RT domain, which remarkably enhances the polymerase activity and overall editing precision.

Furthermore, the architecture of the fusion protein that couples the Cas9 nickase with RT was innovatively remodeled by inserting a viral nucleocapsid protein between them. This viral protein acts as a molecular chaperone, facilitating the correct folding and enhancing the interaction dynamics between the two domains. The result is a robust fusion complex that maintains activity and stability within soybean cells, vital for sustaining high-level editing efficiency.

Another layer of sophistication in the GmPEplus platform is the co-expression of a dominant-negative engineered allele of the endogenous soybean gene GmMLH1. The native GmMLH1, part of the mismatch repair system that typically counteracts prime editing outcomes by correcting mismatches, was effectively subverted by this engineered variant. By inhibiting this repair pathway, GmPEplus allows the retention of the desired edits, significantly boosting heritable editing frequencies.

These comprehensive genetic engineering strategies culminated in GmPEplus achieving unprecedented editing efficiencies, with reported rates soaring to as high as 81.3% in stable transgenic soybean lines. This level of precision and heritability provides an invaluable resource for breeding programs aiming to develop superior soybean cultivars, optimizing traits such as yield, disease resistance, and environmental resilience.

Building upon the enhanced GmPEplus system, the researchers further refined editing outcomes by employing a carefully orchestrated double nicking strategy. This involves the introduction of an additional single guide RNA (sgRNA) designed to nick the non-edited strand of the target DNA. Utilizing the plant’s endogenous transfer RNA (tRNA) processing system, this sgRNA is precisely processed and expressed, stimulating the cellular machinery to preferentially retain the intended edits on the opposite strand and thereby amplifying editing efficiency.

Not stopping there, the team innovated expression control by designing an independent U6 small nuclear RNA promoter cassette of Arabidopsis thaliana (AtU6) for the supplementary sgRNA. This optimized expression cassette ensures robust and consistent generation of the additional sgRNA, circumventing expression limitations seen in earlier systems. Remarkably, this modification propelled editing efficiencies by an impressive factor of 13.1 compared to prior methods, showcasing the critical role of regulatory element optimization in prime editing performance.

Despite these tremendous improvements in single-gene editing, complex traits in crops often require simultaneous manipulation of multiple genes. Recognizing this demand, the research introduced Csy4-mediated multiplex prime editing (CMMPE), a novel system harnessing the Csy4 endoribonuclease to process compound guide RNA arrays. This advance enables simultaneous prime editing of 2 to 12 genes within soybean hairy roots, a feat previously unattainable in the species due to technical constraints and cellular complexity.

Moreover, the CMMPE system demonstrated translatability from hairy root assays to stable transgenic soybean lines, achieving efficient multiplex editing of up to three genes concurrently. Multiplex genome editing in stable plants provides an unparalleled toolkit for functional genomics, breeding programs, and trait stacking—accelerating genetic gains in soybeans and potentially other dicot crops.

The implications of GmPEplus and CMMPE extend far beyond laboratory experimentation. By providing versatile, high-efficiency, and multiplex capable prime editing platforms, researchers and breeders can now envision precision breeding with unprecedented fidelity. These systems open avenues for targeted trait improvements that could lead to soybeans with improved nutrient profiles, enhanced tolerance to abiotic stresses like drought and salinity, and resistance to emerging pathogens threatening food security.

Importantly, the precise nature of prime editing, facilitated by these innovations, markedly reduces off-target effects and unintended mutations that are common pitfalls in traditional genome editing approaches such as CRISPR-Cas9-induced double-strand breaks. This precision not only reassures regulatory bodies and consumers about the safety of genome-edited crops but also accelerates the path to commercialization and field deployment.

From a methodological standpoint, the study showcases the power of combining protein engineering, regulatory element optimization, and exploiting endogenous plant molecular machinery to overcome barriers once thought insurmountable in plant genome editing. The integration of viral protein domains, fine-tuning of enzyme domains, and strategic suppression of DNA repair pathways exemplify a multidisciplinary approach that sets new standards in plant synthetic biology.

Looking forward, the scalability and adaptability of GmPEplus and CMMPE could revolutionize plant biotechnology workflows. Researchers could expand the scope of prime editing into other economically important dicot crops such as cotton, tomato, and potato, where similar efficiency challenges hamper genome editing applications. Furthermore, the modular design of these systems allows easy adaptation to emerging prime editor variants and guide RNA design tools.

The research also underscores the critical importance of stable heritable editing, ensuring that beneficial modifications persist across generations, a prerequisite for practical plant breeding programs. It bridges the gap between innovative genome editing technology and tangible agricultural applications, highlighting a future where tailor-made crop varieties emerge swiftly and safely.

In conclusion, the optimized GmPEplus system coupled with the Csy4-mediated multiplex editing strategy marks a pivotal advance in plant genome editing technology. By overcoming efficiency bottlenecks, enhancing multiplexing capabilities, and enabling heritable edits, these tools provide a powerful platform for next-generation precision breeding in soybean and potentially many other crops. As the global population grows and agricultural challenges intensify, such breakthroughs in biotechnology hold promise for sustainable and resilient food systems worldwide. The future of crop improvement is now not only feasible but imminent, driven by cutting-edge molecular innovation.

Subject of Research:
Genome editing optimization and multiplex prime editing technology in soybean for heritable precision breeding.

Article Title:
Efficient prime editors for heritable multiplex precision genome editing in soybean.

Article References:
Su, F., Dong, Y., Guo, R. et al. Efficient prime editors for heritable multiplex precision genome editing in soybean. Nat. Plants (2026). https://doi.org/10.1038/s41477-026-02315-7

Image Credits: AI Generated

DOI:
https://doi.org/10.1038/s41477-026-02315-7

Addressing this critical bottleneck, a pioneering research group from China has unveiled an innovative and highly efficient visualization system tailored for soybean genome editing. This system, termed the Visual Soybean Editing System (VSES), promises to transform the selection process by allowing real-time, straightforward screening of edited plants from the earliest developmental stages. The VSES aims to eliminate the dependence on costly and specialized diagnostic equipment by introducing a visual marker that is observable under natural light conditions.

At the heart of VSES is the enhanced expression of DsRed2, a red fluorescent protein that, unlike conventional fluorescence requiring UV or blue light, manifests vividly in seeds under ambient lighting. This development means researchers and breeders can instantly discern Cas9-containing seeds without resort to complex instrumentation. The ability to differentiate such seeds by naked-eye observation streamlines large-scale screening and accelerates downstream applications, significantly reducing labor and resource input.

Extending beyond seed identification, VSES exhibits an intriguing capacity to mark transgenic plants during early seedling stages through visible pigmentation changes in the stem and leaves. Such phenotypic indicators provide a practical and rapid phenotyping method that helps in distinguishing edited plants from non-edited counterparts soon after germination. This early-stage discrimination is a game-changer for plant breeding, as it removes ambiguity long before the plants reach maturity, allowing selective cultivation of desirable lines with minimal guesswork.

Crucially, the VSES does not compromise the core genome editing efficiency of CRISPR/Cas9 systems. Maintaining high mutation rates and precise gene targeting alongside these visual markers underscores its potential as a robust tool for plant molecular biology. The molecule’s integration into the editing construct ensures that the visual selection is inherently linked to the genome editing event, fostering consistency and reliability in modified plant populations.

The development of VSES reflects meticulous optimization of genetic constructs and functional testing to balance robust reporter gene expression without adversely affecting plant physiology or gene editing outcomes. Under the guidance of Professor Xiangguo Liu and Professor Dongquan Guo at the Jilin Academy of Agricultural Sciences, China, the team has demonstrated the system’s applicability in practical agricultural research scenarios, moving closer to scalable deployment.

The implications of this visual marker system extend well beyond soybeans. Researchers envision adapting and tailoring VSES for use across a broad spectrum of crop species, allowing diverse agricultural communities worldwide to benefit from swift, cost-effective genome editing selection methods. This cross-species adaptability is supported by the conserved mechanisms underlying reporter gene expression and the modularity of genome editing platforms.

Looking ahead, the researchers emphasize their commitment to further refine the VSES, enhancing its color range, marker stability, and ease of use. Such advancements will cement its role not only in academic research but also in commercial crop breeding, where rapid, reliable identification of transgenic plants is vital for regulatory compliance and product development timelines.

The introduction of VSES aligns with a broader movement towards democratizing genome editing technologies, lowering barriers, and fostering innovation in crop biotechnology. By simplifying visual screening protocols, it bridges the gap between cutting-edge molecular tools and pragmatic field application, bolstering global efforts to meet increasing food demand sustainably.

This groundbreaking work has been documented in the Journal of Integrative Agriculture, a respected platform showcasing interdisciplinary advances in agricultural sciences. The study illustrates the seamless integration of molecular genetics and plant developmental biology towards improving agricultural methodologies pragmatically.

As genome editing technologies continue to evolve, complementary tools like VSES are integral to their translational success. By enabling visual confirmation from seed to plant, this system renders genome editing more accessible to plant breeders, molecular biologists, and agronomists alike, accelerating the development of next-generation crops.

The research team has publicly declared no conflicts of interest, underscoring their commitment to transparent and unbiased scientific progress. Supported by multiple funding bodies from the Jilin province, this work embodies collaboration between government research programs and academic excellence.

In summary, the Visual Soybean Editing System marks a significant leap in plant biotechnology, bringing together visual biology and genome editing to revolutionize the way researchers and breeders select gene-edited plants. Its simplicity and efficiency herald a new era of innovation in crop improvement strategies worldwide.

Subject of Research: Cells

Article Title: From seed to whole plant: An innovative visual marker system to enhance selection efficiency in soybean genome editing

Web References: http://dx.doi.org/10.1016/j.jia.2025.06.010

Image Credits: Xiangguo Liu et al.

Keywords: Agriculture, Cell biology, Genetics, Molecular biology, Plant sciences