Plant non-coding RNAs: The new frontier for the regulation of plant development and adaptation to stress

Non-coding RNAs in plant stress responses: molecular insights and agricultural applications

Non-coding RNAs (ncRNAs) have emerged as crucial regulators in plant responses to environmental stress, orchestrating complex networks that finetune gene expression under both abiotic and biotic challenges. To elucidate this intricate ncRNA crosstalk, this review comprehensively summarizes recent advances in understanding the mechanisms of key regulatory ncRNAs including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), tRNA derived fragments (tRFs) and small interfering RNAs (siRNAs) in mediating plant adaptations to stress conditions. We discuss molecular insights into how these ncRNAs modulate stress signalling pathways, control hormonal responses and interact through elaborate crosstalk mechanisms. We also emphasize emerging biotechnological strategies that leverage both innate and artificial ncRNAs as well as potential approaches for finetuning ncRNA levels to engineer stress-resilient crops. Collectively, continued advances in high-throughput sequencing, functional genomics and computational modelling will deepen our understanding of ncRNA network mediated stress responses, ultimately guiding the design of robust climate-resilient crops.

Pre-mRNA Splicing Functions in Plant Sexual Reproduction Development

Precursor messenger RNA (pre-mRNA) splicing is a critical post-transcriptional regulatory mechanism in gene expression. The precise splicing of pre-mRNAs is essential for plant development and responding to genetic and environmental signals. In plant sexual reproduction, gene expression regulation relies on the accurate processing of pre-mRNAs, which is fundamental for coordinating developmental programs. The alternation of generations in plants involves two key phases: gametophyte development, which produces gametes, and fertilization, which leads to the formation of a diploid sporophyte. Gametophyte and embryo development represent essential processes in plant sexual reproduction. This review focuses on summarizing and analyzing the current evidence regarding the role of pre-mRNA splicing in plant sexual reproduction, with an emphasis on its involvement in gametophyte formation and embryo development. Future challenges in understanding RNA splicing regulation in plant sexual reproduction are also discussed, particularly in modulating splicing factor levels and activities and identifying target mRNAs and non-coding RNAs regulated by these factors. This review provides crucial insights into the molecular mechanisms of plant reproductive development and offers a theoretical basis for improving plant fertility and adaptability via RNA splicing regulation.

Drought stress memory in maize: understanding and harnessing the past for future resilience

Maize (Zea mays L.), a cornerstone of global food security, faces significant challenges due to drought stress, which disrupts its growth, development, and productivity. This review synthesizes advances in our understanding of drought stress memory, a mechanism that enables maize to "remember" prior drought exposure through transcriptional, epigenetic, and physiological pathways. Key regulators, including transcription factors (ZmEREB24 and ZmNF-YC12) and epigenetic modifications (DNA methylation and histone acetylation), orchestrate stress-responsive pathways that ensure rapid adaptation to recurrent drought events. Complementing these molecular mechanisms, physiological adaptations, such as optimized root and leaf architecture, enhanced water-use efficiency, and antioxidant defenses, further strengthen drought tolerance. Practical applications, including molecular priming techniques (e.g., osmopriming, hydropriming, nanoparticles) and advanced genetic tools (CRISPR/Cas9, GWAS), promise scalable solutions for breeding drought-resilient maize varieties. Despite this progress, challenges remain, including genotype-specific variability, scalability, and trade-offs between resilience and yield. This review provides a roadmap for integrating laboratory discoveries with field-level practices, bridging molecular and agronomic innovations to address climate variability and ensure sustainable maize production and global food security.

Deciphering the Vulnerability of Pollen to Heat Stress for Securing Crop Yields in a Warming Climate

Climate change is leading to more frequent and severe extreme temperature events, negatively impacting agricultural productivity and threatening global food security. Plant reproduction, the process fundamental to crop yield, is highly susceptible to heatwaves, which disrupt pollen development and ultimately affect seed-set and crop yields. Recent research has increasingly focused on understanding how pollen grains from various crops react to heat stress at the molecular and cellular levels. This surge in interest over the last decade has been driven by advances in genomic technologies, such as single-cell RNA sequencing, which holds significant potential for revealing the underlying regulatory reprogramming triggered by heat stress throughout the various stages of pollen development. This review focuses on how heat stress affects gene regulatory networks, including the heat stress response, the unfolded protein response, and autophagy, and discusses the impact of these changes on various stages of pollen development. It highlights the potential of pollen selection as a key strategy for improving heat tolerance in crops by leveraging the genetic variability among pollen grains. Additionally, genome-wide association studies and population screenings have shed light on the genetic underpinnings of traits in major crops that respond to high temperatures during male reproductive stages. Gene-editing tools like CRISPR/Cas systems could facilitate precise genetic modifications to boost pollen heat resilience. The information covered in this review is valuable for selecting traits and employing molecular genetic approaches to develop heat-tolerant genotypes.

Overexpression of lncRNA22524 from Dongxiang Wild Rice Reduces Drought and Salt Stress Tolerance in Cultivated Rice

Drought and salt stresses are major challenges to rice production, and a deep understanding of the mechanisms for tolerance could help deal with the challenges. Long non-coding RNAs (lncRNAs) play crucial roles in gene regulation. Previously, lncRNA22524 has been identified as a drought stress-responsive lncRNA from Dongxiang wild rice (DXWR). Nevertheless, its reactions to abiotic stresses in genetics and physiology remained unclear. In this study, we employed a rapid amplification of cDNA ends (RACE) to obtain the full-length cDNA of lncRNA22524 from DXWR, analyzed its cellular localization, built an overexpression vector to generate transgenic lines of cultivated rice and evaluated its impact in genetics and physiology. After treated with drought and salt stress, the overexpressed lines exhibited much more injuries and lower rates of survival, more reactive oxygen species (ROS) and malondialdehyde (MDA), lower antioxidant enzymes and lower proline (Pro) and soluble sugar (SS) than their wild-type (WT). Furthermore, transcriptome analysis of overexpressed lines with weaker tolerance than WT revealed 1,233 differentially expressed genes (DEGs), where most DEGs were involved in phenylpropanoid biosynthesis, photosynthesis and glutathione metabolism. These findings demonstrated that lncRNA22524 negatively regulated rice responses to drought and salt stress, which clear way of working from transcription to metabolic products should be worth of further study.

Small Interfering RNAs as Critical Regulators of Plant Life Process: New Perspectives on Regulating the Transcriptomic Machinery

Small interfering RNAs (siRNAs) are a distinct class of regulatory RNAs in plants and animals. Gene silencing by small interfering RNAs is one of the fundamental mechanisms for regulating gene expression. siRNAs are critical regulators during developmental processes. siRNAs have similar structures and functions to small RNAs but are derived from double-stranded RNA and may be involved in directing DNA methylation of target sequences. siRNAs are a less well-studied class than the miRNA group, and researchers continue to identify new classes of siRNAs that appear at specific developmental stages and in particular tissues, revealing a more complex mode of siRNA action than previously thought. This review characterizes the siRNA classes and their biogenesis process and focuses on presenting their known functions in the regulation of plant development and responses to biotic and abiotic stresses. The review also highlights the exciting potential for future research in this field, proposing methods for detecting plant siRNAs and a bioinformatic pathway for identifying siRNAs and their functions.

Elucidating circRNA-miRNA-mRNA competing endogenous regulatory RNA network during leaf rust pathogenesis in wheat (Triticum aestivum L.)

Advancements in bioinformatic tools and breakthroughs in high throughput RNA sequencing have unveiled the potential role of non-coding RNAs in influencing the overall expression of disease-responsive genes. Owing to the increasing need to develop resilient crop varieties against environmental constraints, our study explores the functional relationship of various non-coding RNAs in wheat during leaf rust pathogenesis. MicroRNAs (miRNAs) and circular RNAs (circRNAs) were retrieved from SAGE and RNA-Seq libraries, respectively, in the susceptible (HD2329) and resistant (HD2329 + Lr28) wheat Near-Isogenic Lines (NILs). Here we explored the previously published circRNAs for their differential expression and correlated the data with the differentially expressed miRNAs (DEMs) through various in silico methods to acquire the target miRNAs of circRNAs and the downstream target mRNAs of miRNAs. Finally, a competing endogenous RNA (ceRNAs) regulatory network was constructed and validated through RT-qPCR method. We have identified the ceRNA regulatory network of four differentially expressed circRNAs (DECs) and five DEMs to highlight their crucial roles in the robust enhancement of the temporal expression profiles of five defense responsive genes (mRNAs) in wheat NILs against leaf rust infection. The study confirms the synergistic expression of circRNAs and mRNAs with an antagonistic correlation with the expression profile of the corresponding miRNAs. The vital role of leaf rust-resistant gene Lr28 has also been highlighted for driving the efficiency of the circRNAs to upregulate target gene expression. Thus, understanding the circRNA-miRNA-target gene interaction during leaf rust pathogenesis can help to identify stress-specific regulatory biomarkers to enhance defense responses in wheat for improved resilience through multi-omics integration of transcriptomics, proteomics and metabolomics.

Insights into lncRNA-mediated regulatory networks in Hevea brasiliensis under anthracnose stress

In recent years, long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have emerged as critical regulators in plant biology, governing complex gene regulatory networks. In the context of disease resistance in Hevea brasiliensis, the rubber tree, significant progress has been made in understanding its response to anthracnose disease, a serious threat posed by fungal pathogens impacting global rubber tree cultivation and latex quality. While advances have been achieved in unraveling the genetic and molecular foundations underlying anthracnose resistance, gaps persist in comprehending the regulatory roles of lncRNAs and miRNAs under such stress conditions. The specific contributions of these non-coding RNAs in orchestrating molecular responses against anthracnose in H. brasiliensis remain unclear, necessitating further exploration to uncover strategies that increase disease resistance. Here, we integrate lncRNA sequencing, miRNA sequencing, and degradome sequencing to decipher the regulatory landscape of lncRNAs and miRNAs in H. brasiliensis under anthracnose stress. We investigated the genomic and regulatory profiles of differentially expressed lncRNAs (DE-lncRNAs) and constructed a competitive endogenous RNA (ceRNA) regulatory network in response to pathogenic infection. Additionally, we elucidated the functional roles of HblncRNA29219 and its antisense hbr-miR482a, as well as the miR390-TAS3-ARF pathway, in enhancing anthracnose resistance. These findings provide valuable insights into plant-microbe interactions and hold promising implications for advancing agricultural crop protection strategies. This comprehensive analysis sheds light on non-coding RNA-mediated regulatory mechanisms in H. brasiliensis under pathogen stress, establishing a foundation for innovative approaches aimed at enhancing crop resilience and sustainability in agriculture.

Crossing a CRISPR/Cas9 transgenic tomato plant with a wild-type plant yields diverse mutations in the F1 progeny

Generating CRISPR/Cas9-mediated mutants in tomato (Solanum lycopersicum L.) involves screening shoots regenerated from cultured cells transformed with a T-DNA harboring sequences encoding Cas9 and single guide RNAs (sgRNAs). Production of transformants can be inconsistent and obtaining transformants in large numbers may be difficult, resulting in a limited variety of mutations. Here, I report a method for generating various types of mutations from one transgenic plant harboring the CRISPR/Cas9 system. In this method, a wild-type plant was crossed with a T0 biallelic mutant expressing two sgRNAs targeting the RIPENING INHIBITOR (RIN) gene, and the resulting F1 seedlings were classified using a kanamycin resistance marker on the T-DNA. Genotyping of the RIN locus revealed that kanamycin-sensitive F1 seedlings, which carried no T-DNA, always harbored the wild-type allele and a mutant allele from the transgenic parent. Kanamycin-resistant F1 seedlings, which do carry the T-DNA, harbored a variety of novel mutant alleles, but not the wild-type allele, suggesting that it was mutated during crossing. The novel mutations included one-base insertions or short deletions at each target site, or large deletions across the two target sites. This method was also successfully applied to produce mutations in Geranylgeranyl pyrophosphate synthase 2 (GGPS2). Because this method involves crossing rather than transformation, it can be readily scaled up to produce numerous novel mutations, even in plant species or cultivars for which transformation is inefficient. Therefore, when initial transgene experiments fail to induce the desired mutation, this method provides additional opportunities for generating mutants.