MicroRNA172b-5p/trehalose-6-phosphate synthase module stimulates trehalose synthesis and microRNA172b-3p/AP2-like module accelerates flowering in barley upon drought stress

Non-coding RNAs and their role in plants: prospective omics-tools for improving growth, development and stress tolerance in field crops

Plants, as sessile organisms, must adapt to dynamic environmental changes through a range of response strategies that confer phenotypic flexibility. Breakthroughs in next-generation sequencing technologies have led to significant improvements in our understanding of the genomic and molecular mechanisms underlying plant growth, development and stress responses. Non-coding RNAs (ncRNAs), have emerged as pivotal regulators in these processes. This article reviews the roles of regulatory ncRNAs in plant stress responses and development, highlighting their intricate molecular interactions. It presents a comprehensive atlas of differentially regulated ncRNAs across key crop genomes, enhancing our understanding of their roles in stress responses, growth, and development. The atlas presented herein offers a foundation for further research in agronomically important crops, paving the way for crop improvement through genetic engineering and sustainable agricultural practices. Additionally, we discuss the role of ncRNAs that have already been functionally characterized in growth, development and stress tolerance, providing insights into their potential for developing stress-resistant and high-yielding crops.

Study of the Drug Resistance Function of Ivermectin-Resistance-Related miRNAs in Haemonchus contortus

Haemonchus contortus has caused significant economic losses in many regions. The emergence of drug resistance has created new difficulties for the prevention and control of parasitic diseases in cattle and sheep. The mechanism of drug resistance to ivermectin in H. contortus is not clear; therefore, it is of great significance to study it. Non-coding RNAs, especially microRNAs (miRNAs), play important roles in drug resistance in some human tumors and insects. However, few studies have investigated whether miRNAs are involved in the regulation of drug resistance to ivermectin. In the early stages of this study, four miRNAs that may be involved in the regulation of ivermectin resistance in H. contortus were identified by high-throughput sequencing analysis of ivermectin-sensitive and -resistant strains of H. contortus. To verify whether these miRNAs are indeed related to ivermectin resistance in H. contortus, RNA interference (RNAi) experiments were performed on these miRNAs. The expression of candidate drug-resistance-related miRNA target genes before and after RNAi was detected by quantitative polymerase chain reaction. The resistance of the third-stage larvae (L3s) of H. contortus before and after RNAi was detected using 0.5% dimethyl sulfoxide and 100 µg/mL ivermectin treatment. The locomotion behavior of the L3s of H. contortus before and after RNAi was detected by counting the frequency of head thrashes and body bending. Finally, we confirmed that miR-10,025-y, miR-5960-z, miR-27-y, and miR-276-y were involved in and regulate ivermectin resistance in H. contortus.

Genome-wide analysis of miR172-mediated response to heavy metal stress in chickpea (Cicer arietinum L.): physiological, biochemical, and molecular insights

BACKGROUND

Chickpea (Cicer arietinum L.), a critical diploid legume in the Fabaceae family, is a rich source of protein, vitamins, and minerals. However, heavy metal toxicity severely affects its growth, yield, and quality. MicroRNAs (miRNAs) play a crucial role in regulating plant responses to both abiotic and biotic stress, including heavy metal exposure, by suppressing the expression of target genes. Plants respond to heavy metal stress through miRNA-mediated regulatory mechanisms at multiple physiological, biochemical, and molecular levels. Although the Fabaceae family is well represented in miRNA studies, chickpeas have been notably underrepresented. This study aimed to investigate the effects of heavy metal-induced stress, particularly from 100 µM concentrations of cadmium (Cd), chromium (Cr), nickel (Ni), lead (Pb), and 30 µM arsenic (As), on two chickpea varieties: ILC 482 (sensitive) and Azkan (tolerant). The assessment focused on physiological, biochemical, and molecular parameters. Furthermore, a systematic characterization of the miR172 gene family in the chickpea genome was conducted to better understand the plant's molecular response to heavy metal stress.

RESULTS

Variance analysis indicated significant effects of genotype (G), treatment (T), and genotype-by-treatment (GxT) interactions on plant growth, physiological, and biochemical parameters. Heavy metal stress negatively impacted plant growth in chickpea genotypes ILC 482 and Azkan. A reduction in chlorophyll content and relative leaf water content was observed, along with increased cell membrane damage. In ILC 482, the highest hydrogen peroxide (H₂O₂) levels in shoot tissue were recorded under As, Cd, and Ni treatments, while in Azkan, peak levels were observed with Pb treatment. Malondialdehyde (MDA) levels in root tissue were highest in ILC 482 under Cd and Ni exposure and in Azkan under As, Cr, and Cd treatments. Antioxidant enzyme activities, including superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX), were significantly elevated under heavy metal stress in both genotypes. Gene expression analysis revealed upregulation of essential antioxidant enzyme genes, such as SOD, CAT, and APX, with APX showing notable increases in both shoot and root tissues compared to the control. Additionally, seven miR172 genes (miR172a, miR172b, miR172c, miR172d, miR172e, miR172f, and miR172g) were identified in the chickpea genome, distributed across five chromosomes. All genes exhibited conserved hairpin structures essential for miRNA functionality. Phylogenetic analysis grouped these miR172 genes into three clades, suggesting strong evolutionary conservation with other plant species. The expression analysis of miR172 and its target genes under heavy metal stress showed varied expression patterns, indicating their role in enhancing heavy metal tolerance in chickpea.

CONCLUSIONS

Heavy metal stress significantly impaired plant growth and physiological and biochemical parameters in chickpea genotypes, except for cell membrane damage. The findings underscore the critical role of miR172 and its target genes in modulating chickpea's response to heavy metal stress. These insights provide a foundational understanding for developing stress-tolerant chickpea varieties through miRNA-based genetic engineering approaches.

Arabidopsis class II TPS controls root development and confers salt stress tolerance through enhanced hydrophobic barrier deposition

KEY MESSAGE

The mechanism of conferring salt tolerance by AtTPS9 involves enhanced deposition of suberin lamellae in the Arabidopsis root endodermis, resulting in reduction of Na+ transported to the leaves. Members of the class I trehalose-6-phosphate synthase (TPS) enzymes are known to play an important role in plant growth and development in Arabidopsis. However, class II TPSs and their functions in salinity stress tolerance are not well studied. We characterized the function of a class II TPS gene, AtTPS9, to understand its role in salt stress response and root development in Arabidopsis. The attps9 mutant exhibited significant reduction of soluble sugar levels in the leaves and formation of suberin lamellae (SL) in the endodermis of roots compared to the wild type (WT). The reduction in SL deposition (hydrophobic barriers) leads to increased apoplastic xylem loading, resulting in enhanced Na+ content in the plants, which explains salt sensitivity of the mutant plants. Conversely, AtTPS9 overexpression lines exhibited increased SL deposition in the root endodermis along with increased salt tolerance, showing that regulation of SL deposition is one of the mechanisms of action of AtTPS9 in conferring salt tolerance to Arabidopsis plants. Our data showed that besides salt tolerance, AtTPS9 also regulates seed germination and root development. qRT-PCR analyses showed significant downregulation of selected SNF1-RELATED PROTEIN KINASE2 genes (SnRK2s) and ABA-responsive genes in the mutant, suggesting that AtTPS9 may regulate the ABA-signaling intermediates as part of the mechanism conferring salinity tolerance.

MiRNAs differentially expressed in vegetative and reproductive organs of Marchantia polymorpha - insights into their expression pattern, gene structures and function

MicroRNAs regulate gene expression affecting a variety of plant developmental processes. The evolutionary position of Marchantia polymorpha makes it a significant model to understand miRNA-mediated gene regulatory pathways in plants. Previous studies focused on conserved miRNA-target mRNA modules showed their critical role in Marchantia development. Here, we demonstrate that the differential expression of conserved miRNAs among land plants and their targets in selected organs of Marchantia additionally underlines their role in regulating fundamental developmental processes. The main aim of this study was to characterize selected liverwort-specific miRNAs, as there is a limited knowledge on their biogenesis, accumulation, targets, and function in Marchantia. We demonstrate their differential accumulation in vegetative and generative organs. We reveal that all liverwort-specific miRNAs examined are encoded by independent transcriptional units. MpmiR11737a, MpmiR11887 and MpmiR11796, annotated as being encoded within protein-encoding genes, have their own independent transcription start sites. The analysis of selected liverwort-specific miRNAs and their pri-miRNAs often reveal correlation in their levels, suggesting transcriptional regulation. However, MpmiR11796 shows a reverse correlation to its pri-miRNA level, suggesting post-transcriptional regulation. Moreover, we identify novel targets for selected liverwort-specific miRNAs and demonstrate an inverse correlation between their expression and miRNA accumulation. In the case of one miRNA precursor, we provide evidence that it encodes two functional miRNAs with two independent targets. Overall, our research sheds light on liverwort-specific miRNA gene structure, provides new data on their biogenesis and expression regulation. Furthermore, identifying their targets, we hypothesize the potential role of these miRNAs in early land plant development and functioning.