Microscopic view of wheat seedlings protected by glowing RNA strands against fungal pathogens.

Can RNAi Technology Revolutionize Fungicide Use in Agriculture?

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Nico Varela in Tech & Innovation November 2026 • 5 min read.

"A New Study Shows Promise in Combating Fungal Resistance and Enhancing Plant Immunity"


In a world grappling with a growing population and shrinking farmland, ensuring food security is more critical than ever. Fungal diseases wreak havoc on crops, causing approximately 30% loss in global crop production before and after harvest (Majumdar et al., 2013). Traditional methods of combating these pathogens are increasingly challenged by the emergence of fungicide resistance, making the quest for new agricultural solutions essential.

Among the notorious fungal offenders, Magnaporthe oryzae, Botrytis cinerea, Fusarium spp., and Colletotrichum spp. top the list of scientifically and economically significant pathogens (Dean et al., 2012). These pathogens inflict severe damage on essential crops like rice, wheat, maize, soybeans, tomatoes, and bananas, not to mention the threat posed by mycotoxins they produce, endangering both human and animal health (Woloshuk and Shim, 2013).

For decades, chemical pesticides have been the go-to defense against fungal pathogens. However, the extended use of these agents has led to significant problems, notably the rise of fungicide resistance (Brent, 1995; Jorgensen et al., 2017; van den Bosch and Gilligan, 2008; Vleeshouwers and Oliver, 2014). The potential harm caused by chemicals and their persistence in the environment raises serious concerns about future human and ecological safety (Karaborklu et al., 2017). There is an urgent need for safer, eco-friendly, and widely applicable fungal control methods.

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Resistance Lessons for RNAi

The review reports that evolutionary insights arrived too late to preserve the efficacy of historical fungicide classes. It argues that those lessons may help prevent or delay resistance to newer fungicides and emerging methods such as RNAi-based crop protection. The supplied sources give no numerical statistics on fungicide resistance or RNAi impact.

Resistance and the Search for New Strategies

The source describes rapid fungicide-resistance evolution, the continuing appearance of new pathogens, and legislation against chemical pesticides over human-health and environmental concerns as reasons new crop-protection strategies are urgently needed. It also identifies a March 21, 2014 PLOS One model describing the emergence of resistance in crop-pathogen populations. The source notes that resistance can be detected and tracked, and connects lessons from fungicide resistance with genome-sequencing discoveries in fungal evolution.

How Does RNAi Technology Offer a Solution?

Microscopic view of wheat seedlings protected by glowing RNA strands against fungal pathogens.

RNA interference (RNAi) presents a groundbreaking approach to crop protection. This natural genetic regulation mechanism involves processing double-stranded RNA (dsRNA) molecules into small interfering RNAs (siRNAs) by Dicer enzymes (Fire et al., 1998). Over the past decade, RNAi has become a robust genetic tool for silencing specific genes, altering phenotypes in various eukaryotic organisms, including insects, mammals, and fungi (Tomoyasu et al., 2008; Huvenne and Smagghe, 2010; Belles and Drosophila, 2010).

In agriculture, RNAi technology has been harnessed to protect crops from viruses, insects, oomycetes, and fungi through a method called host-induced gene silencing (HIGS) (Baulcombe and VIGS, 2015; Baum et al., 2007a; Pooggin et al., 2003). RNA-based pesticides are emerging as a new frontier in biological pest control, initially studied in insects (Zhang et al., 2017). Recent studies have expanded this approach to fungi, demonstrating its potential in controlling B. cinerea and F. graminearum (Wang et al., 2016; Koach et al., 2016).

  • Targeted Gene Silencing: RNAi acts with high specificity, relying on precise base-pairing between small RNAs (20-25 nt) and target mRNA, making it a gene-specific drug development tool (Liu et al., 2014; Mohr and Perrimon, 2012).
  • Addressing Genomic Diversity: RNAi technology must overcome the challenge that fungal genomes vary greatly even within the same genus, which can limit the broad applicability of highly specific RNAi approaches. For example, the genus Fusarium includes over 90 species or varieties, often causing diseases through multiple species (Gerlach and Nirenberg, 1982; Mesterhazy, 1995).
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Review of Spray-Induced RNAi

A review published April 1, 2026, surveys recent applications of RNAi to control phytopathogenic fungi. It focuses on RNAi’s mechanism of action, biological barriers that affect efficiency, and delivery strategies. These include transgenic approaches and non-transgenic approaches such as spray-induced gene silencing (SIGS).

Variable Efficiency and Uptake Barriers

A meta-analysis reports that RNAi protection efficiencies against fungal diseases vary greatly, while the factors behind that variation remain incompletely understood. The resistance review notes that some fungi do not take up environmental dsRNA, including Z. tritici, Trichoderma virens, and Colletotrichum gloeosporioides. These findings point to variability and uptake as challenges for applying RNAi-based crop protection across fungal pathogens.

Different dsRNA Experiments, Different Outcomes

In a wheat study on Fusarium graminearum, leaves sprayed with pairs of dsRNAs targeting chitin synthase, glucan synthase, and protein kinase had lesion areas of 5.18% to 7.43%, a 62%–70% reduction compared with controls. Separately, a study of toxigenic F. graminearum reported that dsRNA treatment of fungal liquid cultures silenced FgVe1 expression 19.78-fold and reduced DON accumulation. The two reported outcomes concern different experimental settings and are not a direct head-to-head comparison.

A recent study has focused on using a conserved gene across multiple fungal species to broaden the impact of RNAi. Researchers targeted the β2-tubulin gene from Fusarium asiaticum, conserved among various fungal pathogens, to develop an RNAi strategy that controls diverse fungal species. Segments of the β2-tubulin gene were tested for their efficacy in suppressing fungal growth. The segment Faβ2Tub-3 was found to be particularly effective, inhibiting growth and causing abnormalities in mycelia across several species, including Fusarium asiaticum, Fusarium graminearum, Fusarium tricinctum, Fusarium oxysporum, Fusarium fujikuroi, Botrytis cinerea, Magnaporthe oryzae, and Colletotrichum truncatum. Additionally, Faβ2Tub-3 dsRNA increased the sensitivity of F. asiaticum to carbendazim (MBC), suggesting its potential as a fungicide resistance-reducing agent. This offers a novel strategy for controlling multiple fungal pathogens without inducing resistance or tolerance.

Looking Ahead: The Future of RNAi in Agriculture

The implications of this research are significant for the future of agriculture. By leveraging RNAi technology, specifically through agents like Faβ2Tub-3 dsRNA, there is potential to develop more sustainable and effective methods for plant protection. This approach not only broadens the spectrum of fungal control but also addresses the pressing issue of fungicide resistance, marking a promising step towards safer and more environmentally friendly agricultural practices.

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RNAi Can Involve Plant Transport

A study of spray-induced control of Fusarium graminearum infections found that effective control in distal tissue involved passage of CYP3-dsRNA through the plant vascular system. After the pathogen took up the dsRNA, fungal DICER-LIKE 1 (FgDCL-1) processed it into small interfering RNAs. The reported result links control in distant tissue to both plant transport and the fungal silencing machinery.

Environmental Questions and Agricultural Change

A review of RNAi-biofungicides for tree diseases says the environmental fate of RNAi molecules and their potential effects on non-target organisms require extensive investigation on a case-by-case basis. Another source describes escalating fungicide resistance and the ecological impact of conventional agrochemicals as critical challenges for modern agriculture. It calls for a shift beyond simple product substitution toward an integrated technological platform.

About this Article -

Written with AI assistance from published research, and reviewed by the Mystum team. See our About page for more information.

Everything You Need To Know

1

What exactly is RNA interference (RNAi), and why is it considered a significant advancement in agriculture?

RNA interference, or RNAi, is a natural process where double-stranded RNA (dsRNA) is used to silence specific genes. Enzymes called Dicers process the dsRNA into small interfering RNAs (siRNAs). These siRNAs then target messenger RNA (mRNA) with a matching sequence, preventing the production of the protein that the mRNA would normally produce. This is significant because it can be used to control specific traits or functions in organisms by selectively turning off certain genes. Host-induced gene silencing (HIGS) is a specific application in agriculture, where plants are engineered to produce dsRNA that targets essential genes in pests or pathogens that attack them. When the pest consumes the plant, it also ingests the dsRNA, triggering gene silencing and ultimately controlling the pest. The specificity of RNAi makes it a powerful tool for targeted pest control, reducing reliance on broad-spectrum pesticides.

2

Why is fungicide resistance such a big deal in agriculture, and how does RNAi technology address this problem?

Fungicide resistance is a growing problem in agriculture because many fungal pathogens have developed the ability to withstand the effects of traditional fungicides. This happens through various mechanisms, such as mutations in the genes targeted by the fungicides or increased production of enzymes that break down the fungicides. The extended use of chemical pesticides has accelerated the rise of fungicide resistance, making it harder to control fungal diseases and threatening crop yields. Because of this, alternative strategies like RNAi are required. RNAi offers a different approach by targeting the genes of the fungus directly, rather than relying on chemicals that the fungus can develop resistance to.

3

What makes the β2-tubulin gene such an important target for controlling fungal diseases?

The β2-tubulin gene is important because it is a highly conserved gene across many different fungal species. This means that the sequence of this gene is very similar in a wide range of fungi. By targeting the β2-tubulin gene with RNAi, it's possible to disrupt the growth and development of multiple fungal pathogens at once. For example, the segment Faβ2Tub-3 dsRNA, which targets the β2-tubulin gene from Fusarium asiaticum, has been shown to inhibit growth and cause abnormalities in several fungal species, including Fusarium graminearum, Botrytis cinerea, and Magnaporthe oryzae. Also, Faβ2Tub-3 dsRNA can increase the sensitivity of F. asiaticum to carbendazim (MBC). Targeting such a conserved gene allows for a broader spectrum of fungal control, making RNAi a more versatile and effective approach.

4

What is Faβ2Tub-3 dsRNA, and how does it work to control fungal pathogens?

Faβ2Tub-3 dsRNA is a specific double-stranded RNA molecule designed to target a segment of the β2-tubulin gene in fungi. It works by triggering the RNAi pathway in fungal cells, leading to the degradation of the β2-tubulin mRNA and inhibiting the production of the β2-tubulin protein. This protein is essential for the formation of microtubules, which are critical for cell division, cell shape, and intracellular transport. By disrupting the production of β2-tubulin, Faβ2Tub-3 dsRNA can inhibit fungal growth and cause abnormalities in the mycelia. This is significant because it offers a targeted way to control fungal pathogens without harming other organisms. Its effectiveness against multiple fungal species makes it a valuable tool for crop protection.

5

Can you explain what host-induced gene silencing (HIGS) is and why it's important?

Host-induced gene silencing, or HIGS, is a method of using RNAi technology to protect plants from pests and pathogens. In HIGS, the plant is genetically modified to produce dsRNA that targets essential genes in the pest or pathogen. When the pest feeds on the plant, it ingests the dsRNA, which is then processed into siRNAs and triggers the RNAi pathway in the pest's cells. This leads to the silencing of the targeted genes, disrupting essential functions and ultimately controlling the pest. HIGS is important because it offers a targeted and environmentally friendly approach to pest control, reducing the need for chemical pesticides. The lack of discussion about the delivery method of RNAi (spraying vs. genetic modification) is a gap in understanding the practical implementation of this strategy.

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