1 Introduction

Weeds are among the most significant biotic constraints in rice cultivation, competing with rice plants for essential resources and leading to substantial reductions in both yield and grain quality (Olofsdotter et al., 2000; De Barreda et al., 2021; Sang et al., 2024). Effective weed management is therefore critical for sustaining rice productivity and ensuring food security in major rice-growing regions.

Traditional chemical weed control, primarily through the use of selective herbicides, has been the cornerstone of weed management in rice fields. However, the repeated and intensive application of herbicides has resulted in the evolution of herbicide-resistant weed populations, such as Echinochloa spp. and Cyperus difformis, and has contributed to rising costs for farmers (Olofsdotter et al., 2000; De Barreda et al., 2021). These challenges have diminished the long-term effectiveness of conventional chemical control and highlighted the need for innovative solutions.

In response, genetically modified (GM) herbicide-resistant rice technologies—such as glyphosate- and glufosinate-resistant rice—have been developed and introduced in several rice-producing countries (Sang et al., 2024). These transgenic rice varieties enable more efficient and selective control of problematic and herbicide-resistant weeds, and can potentially restore abandoned fields and reduce the environmental impact of traditional herbicides (Chhapekar et al., 2014). However, the adoption of GM herbicide-resistant rice also raises concerns, including the risk of gene flow to weedy rice, the evolution of herbicide-resistant weedy rice populations, and the need for integrated management strategies to sustain the effectiveness of these technologies (Olofsdotter et al., 2000; Gealy et al., 2003; Gressel and Valverde, 2009; Merotto et al., 2016; Zhang et al., 2018).

This study will evaluate the application effectiveness, potential problems and sustainable strategies of transgenic herbicide-resistant rice in weed management, explore the technical characteristics and mechanism of action of transgenic herbicide-resistant rice, and its specific impact on weed management, and introduce the comprehensive impact in agricultural ecosystems. This study provides practical suggestions and technical innovation directions for building a sustainable rice production system.

2 Development and Current Application Status of Herbicide-Resistant Rice

2.1 Common genetic engineering strategies for herbicide resistance

Several genetic engineering methods have been used to make rice resistant to herbicides. One way is to use the EPSPS gene to fight glyphosate. This gene, usually taken from bacteria, helps rice resist glyphosate. It is the key behind glyphosate-resistant rice kinds like Roundup Ready and is often used in real farming. Another method uses the bar and pat genes to resist glufosinate. These genes come from Streptomyces bacteria. They make an enzyme called phosphinothricin acetyltransferase, which breaks down glufosinate. This is how LibertyLink rice is made, and it has worked well to create rice lines that can handle glufosinate (Xiao et al., 2007).​

Scientists also develop rice that resists sulfonylurea herbicides by changing the AHAS/ALS gene. They use techniques like site-directed mutagenesis or gene editing (such as TALENs, CRISPR) to do this. This kind of rice can also handle imidazolinone herbicides. Clearfield rice is an example of this, and it has been tested and proven through both traditional mutagenesis and advanced genome editing (Sang et al., 2024). Other ways include changing HPPD or HIS1 genes to make rice resist β-triketone herbicides, and putting together multiple resistance genes to make rice able to handle more types of herbicides (Li et al., 2024).​

2.2 Global and chinese industrialization progress

Commercial Planting Cases in the U.S., Brazil, and Other Countries: Herbicide-resistant rice varieties such as Clearfield (imidazolinone-resistant), Roundup Ready (glyphosate-resistant), and LibertyLink (glufosinate-resistant) have been commercialized and adopted in the U.S., Brazil, and several other countries. These varieties have contributed to improved weed control and increased yields, but have also led to challenges such as the evolution of herbicide-resistant weedy rice through gene flow (Merotto et al., 2016; Li et al., 2024).

In China, research and field trials on GM herbicide-resistant rice are ongoing, with several varieties developed using both transgenic and gene-editing approaches. While some lines have demonstrated high resistance and agronomic stability in experimental settings, large-scale commercial approval and cultivation remain limited, primarily due to regulatory and public acceptance issues. Nonetheless, China continues to make significant advances in developing multi-resistance and high-yield rice varieties using multigene transformation and CRISPR/Cas9 editing (Li et al., 2024).

3 Weed Damage and Limitations of Traditional Weed Control

3.2 Main weed species in rice fields and their impact

Common problematic weeds in rice cultivation include barnyardgrass (Echinochloa crus-galli), weedy rice (Oryza sativa f. spontanea), Monochoria vaginalis, and various sedges. These weeds possess biological traits such as rapid growth, high seed production, and adaptability, making them highly competitive against rice for light, nutrients, and water . For example, barnyardgrass and weedy rice can significantly reduce rice plant height, tiller number, leaf area, and ultimately grain yield. Weedy rice biotypes often exhibit greater height, tiller number, and biomass than cultivated rice, intensifying competition and yield loss. Monochoria and sedges also contribute to yield reductions by competing for resources and reducing rice quality (Karn et al., 2020; Shrestha et al., 2020; Pala et al., 2023).

Weed competition can cause substantial yield losses, with studies reporting reductions ranging from 15% to over 80%, depending on weed species, density, and duration of infestation. In severe cases, whole-season weed competition can reduce rice grain yield by up to 90% (Karn et al., 2020; Islam et al., 2021; Pala et al., 2023). Weeds not only lower yield but also negatively affect grain quality by reducing the percentage of filled grains and overall kernel quality.

3.2 Limitations of traditional weed control methods​

Manual weeding works well, but it needs a lot of people and costs much. This is a bigger problem as many rice-growing areas have fewer workers . The money needed for manual weeding often makes it hard to use on large rice farms (Tomita et al., 2003). Chemical herbicides are used a lot because they work fast, but using too much of them pollutes the environment. They can also harm rice plants and be bad for people’s health (Akbar et al., 2011).

These leftover herbicides stay in the environment, messing up soil and water quality. Using the same herbicides over and over has made some weeds resistant. For example, barnyardgrass and weedy rice that don’t get killed by herbicides are now common. This makes weed control harder and makes chemical sprays less useful (Pala et al., 2023). To fix these issues and keep rice yields steady, more and more people suggest using integrated weed management. This includes planting rice types that can compete with weeds and using the right number of seeds (Akbar et al., 2011; Islam et al., 2021).

4 Technical Characteristics and Mechanisms of GM Herbicide-Resistant Rice

4.1 R&D strategies for herbicide-resistant GM rice

The genes most often used to make rice resistant to herbicides are these: EPSPS (5-enolpyruvylshikimate-3-phosphate synthase) helps rice resist glyphosate, letting the plant handle doses of this wide-range herbicide that would normally kill it (Chhapekar et al., 2014; Ramzi et al., 2020). PAT/bar (phosphinothricin acetyltransferase) gives resistance to glufosinate by breaking down the herbicide, allowing the plant to survive when glufosinate is used (Fartyal et al., 2018b). AHAS/ALS (acetohydroxyacid synthase/acetolactate synthase) mutants, with changes or missing parts in the gene, make rice resistant to sulfonylurea and imidazolinone herbicides, letting it survive these commonly used weed killers (Endo et al., 2007; Fartyal et al., 2018a; Fang et al., 2020; Zhang et al., 2020).

Herbicide resistance genes are usually put into rice using Agrobacterium-mediated transformation, which lets the new gene join the rice’s genes stably and work properly. Changing codons to fit better and using strong, always-active promoters (like CaMV35S) help the gene work better. Some methods involve putting together multiple resistance genes to make rice tolerate two or more types of herbicides (Chhapekar et al., 2014; Fartyal et al., 2018a; Fartyal et al., 2018b).

4.2 Mechanisms of herbicide tolerance in GM rice

Transgenic rice expressing modified or synthetic EPSPS genes can tolerate high concentrations of glyphosate. The EPSPS enzyme is less sensitive to glyphosate inhibition, allowing the shikimate pathway to function normally even in the presence of the herbicide. Co-expression with glyphosate-detoxifying genes (e.g., igrA or glyphosate oxidase) further enhances tolerance and reduces glyphosate residues in plant tissues (Chhapekar et al., 2014; Fartyal et al., 2018b).

The PAT/bar gene encodes an enzyme that acetylates and inactivates glufosinate, preventing its toxic effects on glutamine synthetase and enabling the plant to survive herbicide application. Transgenic rice lines with the bar gene show robust glufosinate tolerance at various developmental stages without significant yield penalties (Fartyal et al., 2018a).

Site-directed mutagenesis or base editing of the AHAS/ALS gene (e.g., P171, G628, W548 mutations or deletions) results in enzymes that are no longer inhibited by sulfonylurea or imidazolinone herbicides. These modifications confer resistance to multiple herbicide families, and some engineered lines show tolerance to several herbicides simultaneously (Endo et al., 2007; Fartyal et al., 2018a; Fang et al., 2020; Zhang et al., 2020).

Recent studies confirm that transgenic rice lines can maintain high and stable expression of herbicide resistance genes across multiple generations, with consistent phenotypic resistance and no significant agronomic penalties (Chhapekar et al., 2014). Dual or stacked gene approaches further improve the robustness and spectrum of herbicide tolerance (Fartyal et al., 2018a; Fartyal et al., 2018b).

5 Impact of GM Herbicide-Resistant Rice on Weed Management

5.1 Enhanced weed control effectiveness and efficiency

The introduction of GM herbicide-resistant rice varieties—such as those resistant to imidazolinone, glufosinate, and glyphosate—has significantly improved the effectiveness and efficiency of weed management in rice cultivation. These technologies enable selective, in-crop control of problematic and hard-to-kill weed species, including weedy rice and Echinochloa spp., which are often resistant to conventional herbicides. The adoption of herbicide-resistant rice has allowed for more efficient post-emergence weed control, reduced labor and fuel costs, and the potential to reclaim fields previously abandoned due to severe weed infestations. Additionally, these systems can facilitate longer crop rotations and reduce reliance on more environmentally harmful herbicides, contributing to more sustainable production systems (Olofsdotter et al., 2000; Sang et al., 2024).

5.2 The issue of herbicide resistance in weeds

Despite these benefits, the widespread use of GM herbicide-resistant rice has accelerated the evolution of herbicide-resistant weed populations. Gene flow from herbicide-resistant rice to weedy rice (red rice) and other wild relatives can result in the rapid emergence of herbicide-resistant weedy rice, undermining the effectiveness of these technologies. Studies have documented that hybridization and introgression of resistance traits can occur within a few generations, leading to distinct populations of herbicide-resistant weedy rice with altered morphology and phenology. The stacking of multiple resistance traits may further increase the risk of multiple-resistant weed populations if not managed carefully. These developments highlight the need for integrated weed management and stewardship practices to delay resistance evolution and preserve the utility of herbicide-resistant rice technologies (Olofsdotter et al., 2000; Gealy et al., 2003; Owen and Zelaya, 2005; Burgos et al., 2014; Merotto et al., 2016; Dauer et al., 2018; De Barreda et al., 2021).

5.3 Agronomic management changes in rice cultivation systems

The adoption of GM herbicide-resistant rice has led to notable changes in agronomic management. Farmers have shifted toward reduced tillage and direct-seeded rice systems, which are more compatible with herbicide-based weed control and offer labor and cost savings. Crop rotation practices have also evolved, with some systems incorporating soybeans or other crops to diversify weed management strategies and reduce selection pressure for resistance. However, these changes require careful management to prevent the buildup of resistant weed populations and to address new challenges, such as volunteer herbicide-resistant rice and shifts in weed community composition. Integrated approaches that combine chemical, cultural, and mechanical control methods are increasingly recommended to sustain the benefits of GM herbicide-resistant rice (Olofsdotter et al., 2000; Dauer et al., 2018; Mascanzoni et al., 2018).

6 Integrated Impacts on Agricultural Ecosystems

6.1 Changes in herbicide usage and environmental risks

The adoption of GM herbicide-resistant rice often leads to an initial reduction in the diversity and total amount of herbicides used, as broad-spectrum herbicides like glyphosate or glufosinate can replace multiple selective herbicides. However, over time, reliance on a single herbicide mode of action can result in increased application rates and frequency due to the evolution of resistant weed populations, leading to long-term dependence and potential dosage escalation (Sondhia, 2014).

Herbicide residues are frequently detected in agricultural soils, surface waters, and sediments, with concentrations varying by region, crop type, and management practices (Sondhia, 2014; Froger et al., 2023). These residues can pose ecological risks, particularly in water bodies, where herbicide mixtures often exceed risk thresholds for aquatic organisms. Persistent herbicide residues contribute to water pollution and can negatively affect aquatic plant diversity and microbial communities, with surface waters generally more contaminated than groundwater (Sondhia, 2014).

6.2 Effects on non-target plants and soil systems

Herbicide residues can have toxic effects on neighboring crops and field-edge vegetation, especially when sensitive species are present or when herbicide drift and runoff occur. Non-target plant damage may manifest as reduced seedling emergence, stunted growth, or altered community composition, particularly for species sensitive to residual herbicide activity.

In soil systems, herbicide residues influence microbial community structure and soil enzyme activities. Some studies report that high concentrations of herbicide residues reduce microbial richness and alter the abundance of key microbial genera, which can disrupt nutrient cycling and soil multifunctionality. For example, long-term herbicide accumulation can inhibit soil enzyme activities and decrease beneficial microbial populations, while lower concentrations may have less pronounced or even stimulatory effects (Bhardwaj et al., 2024; Wang et al., 2024). The persistence of herbicides like glyphosate and their transformation products can also negatively impact mutualistic plant-microbe interactions, reducing plant resilience and ecosystem services (Ruuskanen et al., 2022).

7 Case Studies of GM Herbicide-Resistant Rice Application

7.1 Glyphosate-resistant rice: application results and experience

Field and laboratory studies across multiple regions have demonstrated that glyphosate-resistant rice, developed through targeted mutations in the EPSPS gene or by introducing glyphosate-detoxifying genes, provides robust resistance to glyphosate and enables effective weed management. For example, CRISPR/Cas9-edited rice lines with specific EPSPS mutations (GATIPS) exhibited high glyphosate resistance in both in vitro and field conditions, with treated lines showing a 20%~22% increase in grain yield compared to wild type, and no yield penalty under glyphosate application (Figure 1) (Sony et al., 2023). Overexpression of improved EPSPS variants (TIPS-OsEPSPS and GATIPS-OsEPSPS) under strong promoters resulted in tolerance to up to three times the recommended glyphosate dose, with transgenic lines producing 17–19% more grain than wild type even without glyphosate application (Achary et al., 2020).

Figure 1 Construction of CRISPR-Cas9–based plant expression cassette and molecular analysis of edited rice plants (Adopted from Sony et al., 2023) Image caption: (A) The structures of pCAMBIA1300-based NICTK-1_pCRISPR-Cas9 binary vector. Nuclear localization sequence (NLS), essential sequences, and restriction sites required for the cloning. (B) Schematic representation of OsEPSPS-sgRNA expression cassettes. (C) Schematic representation of OsEPSPS-HDR template with desired mutation sites. (D) Different stages of edited plant development following tissue culture, where (i) embryogenic callus formation in callus induction media; (ii) biolistic transformation; (iii) shoot initiation in shooting media; (iv) regeneration of well-developed shoot; (v) root initiation; (vi) acclimatization of plant in green house; and (vii) developed regenerated plantlets (Adopted from Sony et al., 2023)

Co-expression of bacterial EPSPS and glyphosate oxidase genes in rice not only conferred high glyphosate tolerance but also significantly reduced glyphosate residues in plant tissues, addressing food safety concerns. Additionally, glyphosate-resistant rice has shown potential for integrated weed and disease management, as glyphosate application suppressed both weeds and fungal blast disease in transgenic lines (Mehta et al., 2021). Field studies in Colombia confirmed that glyphosate effectively controls weedy rice populations, including those resistant to other herbicides, supporting its use in diverse rice production systems.

7.2 Glufosinate-resistant rice: field practice and evaluation

Glufosinate-resistant rice, typically developed by introducing the PAT/bar gene, has demonstrated high efficacy in controlling a broad spectrum of weeds under field conditions. These transgenic lines maintain stable resistance across generations and show no significant agronomic penalties compared to conventional rice. Field evaluations indicate that glufosinate-resistant rice enables efficient post-emergence weed control, reduces labor and input costs, and can improve overall economic returns for farmers. However, long-term ecological monitoring is necessary to assess potential impacts on non-target organisms and the risk of resistance evolution in weed populations.

8 Sustainable Weed Management Strategies and Resistance Mitigation

8.1 Strategies for delaying resistance evolution

Rotating and mixing herbicides with different modes of action are among the most effective strategies for delaying resistance. Simulation studies show that complex rotation patterns can delay resistance two- to three-fold, while well-designed herbicide mixtures can delay resistance up to six-fold compared to single-herbicide use. Mixtures are particularly effective at delaying both monogenic (single-gene) and polygenic (multi-gene) resistance, especially when used at full recommended rates and as part of a broader management program (Evans et al., 2015). However, over-reliance on mixtures may increase the risk of generalist (broad-spectrum) resistance, highlighting the need for careful design and monitoring (Comont et al., 2020). Reducing the intensity and frequency of herbicide applications, avoiding repeated use of the same herbicide, and using recommended dosages are also critical to minimize selection pressure and slow resistance evolution (Hicks et al., 2018).

8.2 Integrated weed management (IWM) with multiple strategies

IWM combines chemical, cultural, mechanical, and biological control methods to reduce weed pressure and delay resistance. Diversifying weed control techniques—such as crop rotation, altering planting dates, using competitive crop varieties, and minimizing weed seed return to the soil—can significantly extend the effective lifespan of herbicides. Large-scale and landscape-level approaches, including limiting gene flow and seed dispersal, are also important for managing resistance spread. IWM reduces reliance on herbicides alone, thereby lowering the risk of resistance and supporting more sustainable weed management (Evans et al., 2015).

8.3 Integration of herbicide-resistant rice with green agriculture

Integrating herbicide-resistant rice into green agriculture requires balancing effective weed control with environmental stewardship. This involves adopting best management practices that combine herbicide-resistant crops with non-chemical weed control, minimizing herbicide use, and monitoring for resistance development (Evans et al., 2015). Emphasizing ecological and evolutionary principles in management decisions—such as maintaining biodiversity, protecting non-target organisms, and preserving soil health—supports the long-term sustainability of both weed control and agricultural ecosystems (Neve et al., 2014).

9 Concluding Remarks

Herbicide-resistant genetically modified (GM) rice has brought significant advances in weed management, offering improved control efficiency, higher yields, and the ability to manage problematic and herbicide-resistant weed species. These technologies have enabled more effective post-emergence weed control, reduced labor and input costs, and allowed for the reclamation of fields previously lost to severe weed infestations, contributing to more sustainable rice production systems.

However, the widespread adoption of herbicide-resistant rice also introduces ecological and agronomic challenges. The most pressing concern is the potential for gene flow from GM rice to weedy rice and related species, which can rapidly lead to the emergence of herbicide-resistant weedy rice populations. This gene flow, combined with increased selection pressure from repeated herbicide use, can accelerate the evolution of resistant weeds and reduce the long-term effectiveness of these technologies. Additionally, the persistence of herbicide residues in the environment raises concerns about water pollution, impacts on non-target organisms, and changes in soil microbial communities.

To address these challenges, it is essential to strengthen ecological risk assessment and implement robust resistance monitoring systems. Coordinated development of resistant rice varieties, ecological regulation, and integrated agronomic management—including crop rotation, herbicide rotation, and stewardship practices—are key to achieving a green and sustainable weed control system in rice paddies. These measures will help maximize the benefits of GM herbicide-resistant rice while minimizing ecological risks and ensuring the long-term sustainability of rice production.

Acknowledgments

I sincerely thank the anonymous peer reviewers for their valuable comments and constructive suggestions.

Conflict of Interest Disclosure

The author affirms that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.

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