The scale of RNA activity in plant cells is staggering. Eukaryotic genomes undergo pervasive, genome-wide transcription, generating far more RNA than is needed to encode proteins. These molecules are anything but silent players, the authors emphasize. Their activities are determined not only by their nucleotide sequences but also by multiple regulatory layers, including processing, turnover, chemical modifications, and three-dimensional folding, each contributing critically to how a plant ultimately looks and performs. Over the past decade, high-throughput sequencing, single-molecule sequencing, and precise genome editing have propelled plant RNA biology forward, deepening understanding of RNA regulatory mechanisms and functional networks to a degree that would have been unthinkable a generation ago.

The research paradigm itself has shifted. Plant RNA biology long centered on the model plant Arabidopsis thaliana, a small weed in the mustard family that has served as the workhorse of plant genetics for decades. The review documents how the field has now expanded to a wide range of vital crops, including rice, maize, and wheat. This migration from model organism to staple crop matters enormously for agriculture, because insights into RNA regulatory networks translate directly into genetic resources for crop improvement, including stress-resistant breeding, quality enhancement, and yield promotion. In-depth dissection of these intricate networks, the authors argue, improves the theoretical framework of plant molecular biology while providing critical foundations for applied breeding programs.

The review is structured into eight progressive modules that trace the regulatory mechanisms and agricultural potential of plant RNAs step by step. The first section follows the life cycle of messenger RNA, from its birth through splicing and 3-prime end formation to its eventual degradation. Alternative splicing, particularly intron retention, and 3-prime end processing emerge as key mechanisms shaping transcriptome diversity in plants. The authors also detail the 5-prime-to-3-prime and 3-prime-to-5-prime decay pathways that precisely regulate transcript stability, along with the sophisticated quality control systems that safeguard protein synthesis. These include nonsense-mediated decay, no-go decay, and nonstop decay, surveillance mechanisms that eliminate aberrant transcripts before they can wreak havoc on the cell.

Perhaps the most conceptually striking section redefines the biological functions of classical housekeeping non-coding RNAs, including ribosomal RNAs, transfer RNAs, small nucleolar RNAs, and small nuclear RNAs. For years, these molecules were viewed as humble infrastructure, participating only in translation and splicing. The review confirms that they do far more: they can respond to environmental signals, generate functional small RNAs, and participate in plant developmental regulation, stress adaptation, chromatin remodeling, and gene silencing. This reframing suggests that even the most familiar RNA species in the cell harbor regulatory capacities that remain largely untapped in crop science, a finding with significant implications for how researchers screen for agriculturally useful RNA functions.

Small RNAs and long non-coding RNAs receive their own dedicated treatments. The small RNA section elucidates the biogenesis pathways and action modes of microRNAs and various classes of small interfering RNAs, revealing that these molecules regulate plant growth, development, and stress responses through target cleavage, translational repression, and DNA methylation. The non-cell-autonomous movement of small RNAs between cells, and their cross-kingdom transport, are identified as core links connecting developmental regulation with stress adaptation. The long non-coding RNA section overturns the early perception of these transcripts as transcriptional noise, concluding that they participate in flowering, reproduction, root development, and stress responses through multiple strategies, including recruiting chromatin modification complexes, sequestering microRNAs, modulating protein activity, and even encoding functional small peptides.

Two emerging fields receive forward-looking coverage. The first is RNA higher-order structure, where cutting-edge in vivo structural profiling technologies are uncovering how RNA secondary structures influence splicing, translational regulation, and temperature sensing. The review highlights the value of TPP riboswitches and ribosnitches, sequence-variation-mediated RNA structural remodeling elements, in regulating crop agronomic traits. The second is the rapidly expanding field of RNA chemical modifications. The authors systematically summarize non-canonical cap structures such as m7G and NAD, and internal modifications including m6A, m5C, and ac4C, elaborating the writer, eraser, and reader protein systems that install, remove, and recognize these chemical tags. RNA modifications, they conclude, constitute a crucial post-transcriptional regulatory layer that extensively modulates plant development, immunity, and stress responses.

The agricultural payoff is where the review becomes most concrete. Artificial modification of microRNAs and long non-coding RNAs can effectively enhance crop yield, stress tolerance, and nutrient use efficiency. Beyond endogenous RNA manipulation, RNA interference technologies offer innovative and eco-friendly strategies for protecting crops from diseases and pests. Spray-induced gene silencing allows farmers to apply double-stranded RNA directly to plants, while microbe-induced gene silencing harnesses beneficial microorganisms to deliver silencing signals. Cross-kingdom RNAi mechanisms, in which small RNAs move between species, underpin these approaches. Together, they provide green alternatives to traditional chemical pesticides, overcoming the environmental limitations of conventional crop protection methods at a time when sustainable agriculture has become an urgent global priority.

The final module looks ahead, identifying the core challenges and opportunities that will define the next phase of plant RNA biology. The authors propose the necessity of dissecting the synergistic mechanisms among diverse RNA regulatory pathways, since no single RNA class operates in isolation. They call for advancing single-cell-level research on RNA dynamics, which would reveal how regulatory networks differ across the specialized cell types that make up plant tissues. They also point to ncRNA editing, RNA synthetic biology, novel RNAi technologies, and multi-tool combined gene editing systems as sources of brand-new technical support for precision plant breeding and the development of green, sustainable agriculture.

Taken as a whole, the review bridges a persistent gap between fundamental theoretical research on plant RNAs and practical agricultural application. It provides important theoretical references and frontier directions for deciphering plant RNA regulatory networks, addressing food security, and promoting the high-quality development of sustainable agriculture. The collaboration of sixteen experts across institutions including Tsinghua University, Sun Yat-sen University, Southern University of Science and Technology, the Chinese Academy of Sciences, Peking University, and Fudan University reflects the maturity the field has reached. As climate change intensifies pressure on global crop production, the ability to read, understand, and ultimately engineer the RNA regulatory landscape of plants may prove one of the most consequential tools in modern agricultural science.

Subject of Research: RNA regulatory mechanisms in plants and their application to crop improvement

Article Title: New comprehensive review maps the RNA regulatory landscape in plants

Article References: New comprehensive review maps the RNA regulatory landscape in plants. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: plant RNA biology, non-coding RNAs, microRNAs, RNA modifications, m6A, RNA interference, alternative splicing, lncRNAs, small RNAs, crop improvement, food security, sustainable agriculture

The core of the story lies in RNA interference, or RNAi, a gene-regulation system shared across much of life. Small interfering RNAs and microRNAs can be loaded into Argonaute proteins to form silencing complexes that seek out and destroy matching messenger RNAs. What has stunned researchers is that these molecules do not respect species barriers. A fungal pathogen can ship its own small RNAs into a plant cell, where they hijack the host’s Argonaute machinery and switch off immunity genes. Conversely, a plant can package its small RNAs into extracellular vesicles and send them into an invading fungus, where they silence the very genes the pathogen needs to cause disease.

The evidence is strikingly specific. The gray mold fungus Botrytis cinerea secretes small RNAs such as Bc-siR3.1 and Bc-siR5 into plant cells, where they co-opt the host AGO1 complex to suppress immunity-related genes. The wheat rust pathogen Puccinia striiformis delivers a microRNA-like RNA called Pst-milR1 that silences PR2, a gene encoding beta-1,3-glucanase involved in degrading fungal cell walls. In the banana-wilting Fusarium oxysporum system, fungal milRNAs target banana transcription factors and receptor-like kinases, dismantling early defense signaling. Rhizoctonia solani deploys a battery of milRNAs against rice, suppressing vacuolar sorting receptors, NB-ARC immune receptors, and F-box proteins to blunt the hypersensitive response. Even Valsa mali, the apple canker pathogen, uses a single milRNA to silence two receptor-like kinases and reduce reactive oxygen accumulation and callose deposition in host tissue.

Crucially, the traffic runs both ways. Plants selectively load small RNAs into extracellular vesicles with the help of RNA-binding proteins including AGO1, the helicases RH11 and RH37, and the annexins ANN1 and ANN2, which sort, stabilize, and transport the cargo. Encapsulation shields the RNA from extracellular nucleases during the journey. In the Brachypodium distachyon and Fusarium graminearum system, researchers identified 258 plant-derived small RNAs that target fungal messenger RNAs and significantly reduce pathogenicity. Wheat roots even send microRNAs into the beneficial fungus Clonostachys rosea, where they fine-tune fungal secondary metabolism rather than triggering defense, showing that RNA exchange also shapes cooperative relationships, not just conflict.

Bacteria play this game too, though the evidence is younger. The rice pathogen Xanthomonas oryzae pv. oryzicola packages a small RNA called Xosr001 into outer membrane vesicles, which deliver it into rice cells to silence OsJMT1, a jasmonate metabolism gene, thereby suppressing stomatal immunity. In the opposite direction, Arabidopsis plants have been shown to silence virulence genes of Pseudomonas syringae, reducing bacterial colonization and impairing stomatal reopening, with the silencing RNAs exported through both vesicle-associated and non-vesicular routes. Plant-derived small RNAs can also suppress gene expression in Ralstonia pseudosolanacearum, the agent of bacterial wilt. Even mutualistic partnerships show RNA crosstalk: Bradyrhizobium japonicum produces tRNA-derived fragments that accumulate in soybean nodules and use the host AGO1 machinery to regulate plant transcripts involved in nodulation.

Viruses occupy a special place in this landscape. Because viral RNA replicates continuously inside host cells, the review’s authors treat plant-virus systems as a closely related but mechanistically distinct model rather than classical cross-kingdom transfer. Still, the dynamics are instructive. Plants process viral double-stranded RNA with Dicer-like enzymes into virus-derived small interfering RNAs that guide sequence-specific degradation of viral genomes. Viruses fight back with silencing suppressor proteins such as the NS3 protein of Rice stripe virus, which binds small RNAs and interferes with microRNA biogenesis. Virus-derived siRNAs from Rice black-streaked dwarf virus directly target host genes in rice and maize, while virally activated siRNAs extend RNA regulation to endogenous plant transcripts during infection, creating layered, bidirectional control networks.

These discoveries have crystallized into three agricultural technologies that share a common RNAi mechanism but differ in delivery. Spray-induced gene silencing, or SIGS, applies double-stranded RNAs directly onto plant surfaces, where they are taken up by tissues and silence invading pathogens. It is non-transgenic, rapid, and flexible, and has been shown to suppress gray mold, Fusarium head blight, stem rot, powdery mildew, and late blight across cereals, vegetables, fruits, and ornamentals. Artificial vesicles and nanocarriers such as layered double-hydroxide nanosheets dramatically extend the persistence of sprayed RNAs, with encapsulated double-stranded RNAs protecting tomato and grape tissues for up to ten days and grape leaves for up to twenty-one days.

Host-induced gene silencing, or HIGS, takes the opposite approach: the plant itself is genetically engineered to continuously produce silencing RNAs directed at pathogen genes. Stable HIGS lines have delivered durable resistance in sugarcane against Pokkah boeng and smut, in rice against Bakanae disease and blast, in potato against late blight, and in apple against ring rot. In one notable strategy, transgenic Arabidopsis expressing short tandem target mimics effectively blocked the immune-suppressing small RNAs of Botrytis cinerea, reducing gray mold infection. HIGS offers long-lasting, tissue-specific protection, but it inherits the regulatory hurdles, biosafety debates, and public concerns that surround genetically modified crops, and it demands years of development time.

The newest and perhaps most intriguing strategy is microbe-induced gene silencing, or MIGS, which recruits beneficial microorganisms as living RNA delivery vehicles. Engineered Trichoderma harzianum strains colonizing the rhizosphere produce small RNAs that silence virulence genes in Verticillium dahliae and Fusarium oxysporum. Even more remarkably, engineered Bacillus subtilis and Pseudomonas putida can package double-stranded RNAs into extracellular vesicles and deliver them across kingdoms to fungal pathogens, suppressing Botrytis and Verticillium infections in Arabidopsis and tomato. Because microbes protect their RNA cargo from environmental degradation and can be produced at relatively low cost, MIGS could overcome the two biggest weaknesses of sprayed RNA: instability and expense.

The field is moving from laboratory proof-of-concept toward commercial reality. RNA-based pesticides are a rapidly growing industry, and China has officially released the first batch of registered RNA pesticide products, targeting Tobacco Mosaic Virus. The review argues that the safest and most effective targets will come from cross-kingdom small RNAs themselves, molecules already filtered through millions of years of co-evolution, whose natural trafficking suggests low off-target risk and environmental compatibility. Pairing these evolutionarily optimized sequences with microbial bio-factories for production and delivery, the authors contend, could dissolve the techno-economic barriers that have slowed RNA biopesticides. Significant questions remain, including how RNAs are packaged and recognized by recipient cells, how stable they are under field conditions, and what ecological effects engineered microbes might have on soil biodiversity. But the direction is clear: the quiet molecular conversation between plants and microbes is becoming a blueprint for agriculture that protects crops with the precision of a key in a lock rather than the blunt force of a chemical spray.

Subject of Research: Cross-kingdom RNA communication between plants and microbes and its application in RNA interference-based crop protection

Article Title: Cross-kingdom RNA in plant–microbe interactions: from molecular interactions to next-generation crop protection

Article References: Cross-kingdom RNA in plant–microbe interactions: from molecular interactions to next-generation crop protection. (n.d.). https://doi.org/10.1007/s44154-026-00337-x

Image Credits: AI Generated

DOI: 10.1007/s44154-026-00337-x

Keywords: cross-kingdom RNA, RNA interference, plant-microbe interactions, spray-induced gene silencing, host-induced gene silencing, microbe-induced gene silencing, small RNAs, extracellular vesicles, RNA pesticides, fungal pathogens, plant immunity, sustainable agriculture