Identification and comparative analysis of cadmium tolerance-associated miRNAs and their targets in two soybean genotypes

Identification of miRNAs associated with Aspergillus flavus infection and their targets in groundnut (Arachis hypogaea L.)

BACKGROUND

The quality of groundnut produce is adversely impacted due to aflatoxin contamination by the fungus Aspergillus flavus. Although the transcriptomic control is not fully understood, the interaction between long non-coding RNAs and microRNAs in regulating A. flavus and aflatoxin contamination remains unclear. This study was carried out to identify microRNAs (miRNAs) to enhance the understanding of in vitro seed colonization (IVSC) resistance mechanism in groundnut.

RESULT

In this study, resistant (J 11) and susceptible (JL 24) varieties of groundnut were treated with toxigenic A. flavus (strain AF-11-4), and total RNA was extracted at 1 day after inoculation (1 DAI), 2 DAI, 3 DAI and 7 DAI. Seeds of JL 24 showed higher mycelial growth than J 11 at successive days after inoculation. A total of 208 known miRNAs belonging to 36 miRNA families, with length varying from 20-24 nucleotides, were identified, along with 27 novel miRNAs, with length varying from 20-22 nucleotides. Using psRNATarget server, 952 targets were identified for all the miRNAs. The targeted genes function as disease resistant proteins encoding, auxin responsive proteins, squamosa promoter binding like proteins, transcription factors, pentatricopeptide repeat-containing proteins and growth regulating factors. Through differential expression analysis, seven miRNAs (aly-miR156d-3p, csi-miR1515a, gma-miR396e, mtr-miR2118, novo-miR-n27, ptc-miR482d-3p and ppe-miR396a) were found common among 1 DAI, 2 DAI, 3 DAI and 7 DAI in J 11, whereas ten miRNAs (csi-miR159a-5p, csi-miR164a-3p, novo-miR-n17, novo-miR-n2, osa-miR162b, mtr-miR2118, ptc-miR482d-3p, ptc-miR167f-3p, stu-miR319-3p and zma-miR396b-3p) were found common among 1 DAI, 2 DAI, 3 DAI and 7 DAI in JL 24. Two miRNAs, ptc-miR482d-3p and mtr-miR2118, showed contrasting expression at different time intervals between J 11 and JL 24. These two miRNAs were found to target those genes with NBS-LRR function, making them potential candidates for marker development in groundnut breeding programs aimed at enhancing resistance against A. flavus infection.

CONCLUSION

This study enhances our understanding of the involvement of two miRNAs namely, ptc-miR482d-3p and mtr-miR2118, along with their NBS-LRR targets, in conferring resistance against A. flavus-induced aflatoxin contamination in groundnut under in vitro conditions.

miRNAs regulate the metabolic adaptation of Paracoccidioides brasiliensis during copper deprivation

Copper is an essential metal for cellular processes such as detoxification of reactive oxygen species, oxidative phosphorylation, and iron uptake. However, during infection, the host restricts the bioavailability of this micronutrient to the pathogen as a strategy to combat infection. Recently, we have shown the involvement of miRNAs as an adaptive strategy of P. brasiliensis upon metal deprivation such as iron and zinc. However, their role in copper limitation still needs to be elucidated. Our objective was to characterize the expression profile of miRNAs regulated during copper deprivation in P. brasiliensis and the putative altered processes. Through RNAseq analysis and bioinformatics, we identified 14 differentially expressed miRNAs, two of which putatively regulated oxidative stress response, beta-oxidation, glyoxylate cycle, and cell wall remodeling. Our results suggest that metabolic adaptations carried out by P. brasiliensis in copper deprivation are regulated by miRNAs.

Small RNA sequencing analysis provides novel insights into microRNA-mediated regulation of defense responses in chickpea against Fusarium wilt infection

MAIN CONCLUSION

Small RNA sequencing analysis in two chickpea genotypes, JG 62 (Fusarium wilt-susceptible) and WR 315 (Fusarium wilt-resistant), under Fusarium wilt stress led to identification of 544 miRNAs which included 406 known and 138 novel miRNAs. A total of 115 miRNAs showed differential expression in both the genotypes across different combinations. A miRNA, Car-miR398 targeted copper chaperone for superoxide dismutase (CCS) that, in turn, regulated superoxide dismutase (SOD) activity during chickpea-Foc interaction. Fusarium wilt (FW) of chickpea (Cicer arietinum L.) caused by Fusarium oxysporum f. sp. ciceris (Foc) is a destructive soil-borne disease that severely reduces the chickpea yield and quality globally. In the present study, we have investigated microRNAs and the microRNA/target gene crosstalk involved in chickpea resistance to FW. The control and stress samples from two genotypes, JG 62 (FW-susceptible) and WR 315 (FW-resistant), collected at 10 days post-inoculation (dpi), were selected for small RNA sequencing. A total of 12 libraries were constructed and sequenced using Illumina HiSeq 2500 platform. The sequencing and in silico analyses revealed the identification of 544 miRNAs which included 406 known and 138 novel miRNAs. A total of 50 miRNAs were physically co-localized with Foc-resistance QTLs present on chromosome 2 (also known as Foc hotspot). A total of 115 miRNAs showed differential expression in both the genotypes across different combinations. Prediction and functional annotation of miRNA targets revealed their role in transcription regulation, disease resistance, defense response, metabolism, etc. Ten miRNAs and their targets were validated using poly(A)-based qRT-PCR in two genotypes grown under lab and field conditions. Many miRNAs and their targets showed genotype-specific expression. The expression profiling also highlighted, both, similar and different expression patterns for the same sets of miRNA and mRNA at different stages of Foc infection. A high correlation in expression patterns of the miRNAs and their targets in lab- and field-grown plant samples was observed. Interestingly, Car-miR398 targeted copper chaperone for superoxide dismutase (CCS) that, in turn, regulated superoxide dismutase (SOD) activity during chickpea-Foc interaction. The cleavage site in targets was mapped for three miRNAs by analyzing publicly available degradome data for chickpea. The study, for the first time, provides novel insights into microRNA-mediated regulation of resistance and susceptibility mechanisms in chickpea against FW and opens up avenues for the development of the wilt-resistant cultivars in chickpea.

MiRNAs profiles among three poplar varieties provide insights into different molecular responses in resistance to newly emerging bacterial pathogen

Canker caused by Lonsdalea populi has seriously reduced the economic and ecological benefits of poplar. MicroRNAs play vital roles in the response of plants to biotic stress. However, there is little research about the regulatory mechanism of miRNAs among different tree varieties upon pathogen infection. To dissect miRNAs involved in L. populi resistance, three poplar varieties, 2025 (susceptible), 107 (moderately resistant) and Populus. tomentosa cv 'henan' (resistant) were selected to elucidate the expression profiles of miRNAs using small RNA-seq. A total of 227 miRNAs were identified from all varieties. Intriguingly, miR160, miR169, miR171 and miR482b-5p were only identified in the resistant variety P. tomentosa upon pathogen infection, and these miRNAs might be important candidates for future investigation to improve the tolerance of poplar to L. populi. Among all identified miRNAs, 174 were differentially expressed in all varieties. Functional annotation analysis indicated that an array of miRNAs, including miR482, miR472, miR169, miR481, and miR172, should be involved in disease resistance and phytohormone signal transduction. Furthermore, correlation analysis of small RNA-seq and RNA-seq identified a handful of L. populi-responsive miRNAs and target genes, which exhibited that miR159 and miR172 played key roles in resistant variety P. tomentosa by targeting MYB and ERF, while miR6462c-5p and miR828 were related to the susceptibility of 2025 by targeting MYB. The comprehensive integration analysis in this research provides new insights into the regulatory pathways involved in the defence response of poplar to L. populi and offers crucial candidate miRNAs-target genes modules for poplar resistance improvement.

Changes in microRNAs expression of flax (Linum usitatissimum L.) planted in a cadmium-contaminated soil following the inoculation with root symbiotic fungi

Cadmium is one of the most harmful heavy metals that harm agricultural products. Evaluating microRNAs expression is a new and accurate method to study plant response in various environmental conditions. So this study aimed to evaluate the contribution of two symbiotic fungi in improving flax tolerance in a Cd-polluted soil using microRNAs and their target gene expression. A factorial pot experiment in a completely randomized design was conducted with different levels of Cd (0, 20, and 40 mg kg-1) on non-inoculated and inoculated flax with Claroideoglomus etunicatum and Serendipita indica. The results presented that increasing Cd levels caused a constant decline of alkaline phosphatase of soil (from 243 to 210 and 153 μg PNP g-1 h-1), respectively, from control (Cd0) to 20 and 40 mg Cd kg-1. However, the inoculation of flax with fungi significantly enhanced these properties. A negative correlation was observed between the expression level of microRNA 167 and microRNA 398 with their corresponding target genes, auxin response factor 8 and superoxide dismutase zinc/copper 1, respectively. The expression level of both microRNAs and their targets indicated that the inoculation with symbiont fungi could diminish Cd stress and enhance the growth of flax.

Unveiling novel anti-viral mechanisms of ε-poly-l-lysine on tobacco mosaic virus-infected Nicotiana tabacum through microRNA and transcriptome sequencing

MicroRNAs (miRNAs) play important roles in plant defense against various pathogens. ε-poly-l-lysine (ε-PL), a natural anti-microbial peptide produced by microorganisms, effectively suppresses tobacco mosaic virus (TMV) infection. To investigate the anti-viral mechanism of ε-PL, the expression profiles of miRNAs in TMV-infected Nicotiana tabacum after ε-PL treatment were analyzed. The results showed that the expression levels of 328 miRNAs were significantly altered by ε-PL. Degradome sequencing was used to identify their target genes. Integrative analysis of miRNAs target genes and gene-enriched GO/KEGG pathways indicated that ε-PL regulates the expression of miRNAs involved in critical pathways of plant hormone signal transduction, host defense response, and plant pathogen interaction. Subsequently, virus induced gene silencing combined with the short tandem targets mimic technology was used to analyze the function of these miRNAs and their target genes. The results indicated that silencing miR319 and miR164 reduced TMV accumulation in N. benthamiana, indicating the essential roles of these miRNAs and their target genes during ε-PL-mediated anti-viral responses. Collectively, this study reveals that microbial source metabolites can inhibit plant viruses by regulating crucial host miRNAs and further elucidate anti-viral mechanisms of ε-PL.

MicroRNA-encoded regulatory peptides modulate cadmium tolerance and accumulation in rice

MicroRNAs (miRNAs) are small noncoding RNAs that play a vital role in plant responses to abiotic and biotic stresses. Recently, it has been discovered that some primary miRNAs (pri-miRNAs) encode regulatory short peptides called miPEPs. However, the presence of miPEPs in rice, and their functions in response to abiotic stresses, particularly stress induced by heavy metals, remain poorly understood. Here, we identified a functional small peptide (miPEP156e) encoded by pri-miR156e that regulates the expression of miR156 and its target SPL genes, thereby affecting miR156-mediated cadmium (Cd) tolerance in rice. Overexpression of miPEP156e led to decreased uptake and accumulation of Cd and reactive oxygen species (ROS) levels in plants under Cd stress, resulting in improved rice Cd tolerance, as observed in miR156-overexpressing lines. Conversely, miPEP156e mutants displayed sensitivity to Cd stress due to the elevated accumulation of Cd and ROS. Transcriptome analysis further revealed that miPEP156e improved rice Cd tolerance by modulating Cd transporter genes and ROS scavenging genes. Our study provides insights into the regulatory mechanism of miPEP156e in rice response to Cd stress and demonstrates the potential of miPEPs as an effective tool for improving crop abiotic stress tolerance.

Unveiling Innovative Approaches to Mitigate Metals/Metalloids Toxicity for Sustainable Agriculture

Due to anthropogenic activities, environmental pollution of heavy metals/metalloids (HMs) has increased and received growing attention in recent decades. Plants growing in HM-contaminated soils have slower growth and development, resulting in lower agricultural yield. Exposure to HMs leads to the generation of free radicals (oxidative stress), which alters plant morpho-physiological and biochemical pathways at the cellular and tissue levels. Plants have evolved complex defense mechanisms to avoid or tolerate the toxic effects of HMs, including HMs absorption and accumulation in cell organelles, immobilization by forming complexes with organic chelates, extraction via numerous transporters, ion channels, signaling cascades, and transcription elements, among others. Nonetheless, these internal defensive mechanisms are insufficient to overcome HMs toxicity. Therefore, unveiling HMs adaptation and tolerance mechanisms is necessary for sustainable agriculture. Recent breakthroughs in cutting-edge approaches such as phytohormone and gasotransmitters application, nanotechnology, omics, and genetic engineering tools have identified molecular regulators linked to HMs tolerance, which may be applied to generate HMs-tolerant future plants. This review summarizes numerous systems that plants have adapted to resist HMs toxicity, such as physiological, biochemical, and molecular responses. Diverse adaptation strategies have also been comprehensively presented to advance plant resilience to HMs toxicity that could enable sustainable agricultural production.

miR397-LACs mediated cadmium stress tolerance in Arabidopsis thaliana

Cadmium (Cd) is a non-essential heavy metal, assimilated in plant tissue with other nutrients, disturbing the ions' homeostasis in plants. The plant develops different mechanisms to tolerate the hazardous environmental effects of Cd. Recently studies found different miRNAs that are involved in Cd stress. In the current study, miR397 mutant lines were constructed to explore the molecular mechanisms of miR397 underlying Cd tolerance. Compared with the genetically modified line of overexpressed miR397 (artificial miR397, amiR397), the lines of downregulated miR397 (Short Tandem Target Mimic miR397, STTM miR397) showed more substantial Cd tolerance with higher chlorophyll a & b, carotenoid and lignin content. ICP-OES revealed higher cell wall Cd and low total Cd levels in STTM miR397 than in the wild-type and amiR397 plants.Further, the STTM plants produced fewer reactive oxygen species (ROS) and lower activity of antioxidants enzymes (e.g., catalase [CAT], malondialdehyde [MDA]) compared with amiR397 and wild-type plants after stress, indicating that silencing the expression of miR397 can reduce oxidative damage. In addition, the different family transporters' gene expression was much higher in the amiR397 plants than in the wild type and STTM miRNA397. Our results suggest that miR397 plays a role in Cd tolerance in Arabidopsis thaliana. Overexpression of miR397 could decrease Cd tolerance in plants by regulating the expression of LAC 2/4/17, changing the lignin content, which may play an important role in inducing different stress-tolerant mechanisms and protecting the cell from a hazardous condition. This study provides a basis to elucidate the functions of miR397 and the Cd stress tolerance mechanism in Arabidopsis thaliana.

Natural variation of MS2 confers male fertility and drives hybrid breeding in soybean

A complete and genetically stable male sterile line with high outcrossing rate is a prerequisite for the development of commercial hybrid soybean. It was reported in the last century that the soybean male sterile ms2 mutant has the highest record with seed set. Here we report the cloning and characterization of the MS2 gene in soybean, which encodes a protein that is specifically expressed in the anther. MS2 functions in the tapetum and microspore by directly regulating genes involved in the biosynthesis of secondary metabolites and the lipid metabolism, which is essential for the formation of microspore cell wall. Through comparison of the field performance with the widely used male sterile mutants in the same genetic background, we demonstrated that the ms2 mutant conducts the best in outcrossing rate and makes it an ideal tool in building a cost-effective hybrid system for soybean.

The miRNA-mRNA Regulatory Modules of Pinus massoniana Lamb. in Response to Drought Stress

Masson pine (Pinus massoniana Lamb.) is a major fast-growing woody tree species and pioneer species for afforestation in barren sites in southern China. However, the regulatory mechanism of gene expression in P. massoniana under drought remains unclear. To uncover candidate microRNAs, their expression profiles, and microRNA-mRNA interactions, small RNA-seq was used to investigate the transcriptome from seedling roots under drought and rewatering in P. massoniana. A total of 421 plant microRNAs were identified. Pairwise differential expression analysis between treatment and control groups unveiled 134, 156, and 96 differential expressed microRNAs at three stages. These constitute 248 unique microRNAs, which were subsequently categorized into six clusters based on their expression profiles. Degradome sequencing revealed that these 248 differentially expressed microRNAs targeted 2069 genes. Gene Ontology enrichment analysis suggested that these target genes were related to translational and posttranslational regulation, cell wall modification, and reactive oxygen species scavenging. miRNAs such as miR482, miR398, miR11571, miR396, miR166, miRN88, and miRN74, along with their target genes annotated as F-box/kelch-repeat protein, 60S ribosomal protein, copper-zinc superoxide dismutase, luminal-binding protein, S-adenosylmethionine synthase, and Early Responsive to Dehydration Stress may play critical roles in drought response. This study provides insights into microRNA responsive to drought and rewatering in Masson pine and advances the understanding of drought tolerance mechanisms in Pinus.

Cadmium induced a non-coding RNA microRNA535 mediates Cd accumulation in rice

Identifying key regulators related to cadmium (Cd) tolerance and accumulation is the main factor for genetic engineering to improve plants for bioremediation and ensure crop food safety. MicroRNAs (miRNAs), as fine-tuning regulators of genes, participate in various abiotic stress processes. MiR535 is an ancient conserved non-coding small RNA in land plants, positively responding to Cd stress. We investigated the effects of knocking out (mir535) and overexpressing miR535 (mir535 and OE535) under Cd stress in rice plants in this study. The mir535 plants showed better Cd tolerance than wild type (WT), whereas the OE535 showed the opposite effect. Cd accumulated approximately 71.9% and 127% in the roots of mir535 and OE535 plants, respectively, compared to WT, after exposure to 2 µmol/L Cd. In brown rice, the total Cd accumulation of OE535 and mir535 was about 78% greater and 35% lower than WT. When growing in 2 mg/kg Cd of soil, the Cd concentration was significantly lower in mir535 and higher in OE535 than in the WT; afterward, we further revealed the most possible target gene SQUAMOSA promoter binding-like transcription factor 7(SPL7) and it negatively regulates Nramp5 expression, which in turn regulates Cd metabolism. Therefore, the CRISPR/Cas9 technology may be a valuable strategy for creating new rice varieties to ensure food safety.

Identifying the Soybean microRNAs Related to Phytophthora sojae Based on RNA Sequencing and Bioinformatics Analysis

Phytophthora root rot in soybeans is caused by a pathogen called Phytophthora sojae (P. sojae), which results in a significant decrease in soybean production within affected regions. MicroRNAs (miRNAs) are a class of small non-coding RNA molecules that play a key post-transcriptional regulatory role in eukaryotes. In this paper, the miRNAs that respond to P. sojae were analyzed from the gene level to complement the study of molecular resistance mechanisms in soybean. The study utilized high-throughput sequencing of soybean data to predict miRNAs that respond to P. sojae, analyze their specific functions, and verify regulatory relationships using qRT-PCR. The results showed that the miRNAs in soybean respond to P. sojae infection. MiRNAs can be transcribed independently, suggesting the presence of transcription factor binding sites in the promoter regions. Additionally, we performed an evolutionary analysis on conserved miRNAs that respond to P. sojae. Finally, we investigated the regulatory relationships among miRNAs, genes, and transcription factors, and identified five regulatory patterns. These findings lay the groundwork for future studies on the evolution of miRNAs responsive to P. sojae.

MicroRNA miR171b Positively Regulates Resistance to Huanglongbing of Citrus

Huanglongbing (HLB) is one of the most severe citrus diseases in the world, causing huge economic losses. However, efficient methods of protecting citrus from HLB have not yet been developed. microRNA (miRNA)-mediated regulation of gene expression is a useful tool to control plant diseases, but the miRNAs involved in regulating resistance to HLB have not yet been identified. In this study, we found that miR171b positively regulated resistance to HLB in citrus. Upon infection with HLB bacteria, the bacteria were detected in the second month in the control plants. However, in the miR171b-overexpressing transgenic citrus plants, the bacteria could not be detected until the 24th month. RNA-seq data indicated that multiple pathways, such as photosynthesis, plant–pathogen interaction, the MAPK signaling pathway, etc., might be involved in improving the resistance to HLB in miR171b-overexpressing plants compared with the control. Finally, we determined that miR171b could target SCARECROW-like (SCL) genes to downregulate their expression, which then led to promoted resistance to HLB stress. Collectively, our results demonstrate that miR171b plays a positive regulatory role in resistance to citrus HLB, and provides a new insight into the role of miRNAs in the adaptation of citrus to HLB stress.

Small RNA and Degradome Sequencing in Floral Bud Reveal Roles of miRNAs in Dormancy Release of Chimonanthus praecox

Chimonanthus praecox (wintersweet) is highly valued ornamentally and economically. Floral bud dormancy is an important biological characteristic in the life cycle of wintersweet, and a certain period of chilling accumulation is necessary for breaking floral bud dormancy. Understanding the mechanism of floral bud dormancy release is essential for developing measures against the effects of global warming. miRNAs play important roles in low-temperature regulation of flower bud dormancy through mechanisms that are unclear. In this study, small RNA and degradome sequencing were performed for wintersweet floral buds in dormancy and break stages for the first time. Small RNA sequencing identified 862 known and 402 novel miRNAs; 23 differentially expressed miRNAs (10 known and 13 novel) were screened via comparative analysis of breaking and other dormant floral bud samples. Degradome sequencing identified 1707 target genes of 21 differentially expressed miRNAs. The annotations of the predicted target genes showed that these miRNAs were mainly involved in the regulation of phytohormone metabolism and signal transduction, epigenetic modification, transcription factors, amino acid metabolism, and stress response, etc., during the dormancy release of wintersweet floral buds. These data provide an important foundation for further research on the mechanism of floral bud dormancy in wintersweet.

Identification of microRNA and analysis of target genes in Panax ginseng

Objective

Ginsenosides, polysaccharides and phenols, the main active ingredients in Panax ginseng, are not different significantly in content between 3 and 5 years old of ginsengs called Yuan ginseng and more than ten years old ones called Shizhu ginseng. The responsible chemical compounds cannot fully explain difference in efficacy between them. According to reports in Lonicerae Japonicae Flos (Jinyinhua in Chinese) and Glycyrrhizae Radix et Rhizoma (Gancao in Chinese), microRNA may play a role in efficacy, so we identified microRNAs in P. ginseng at the different growth years and analyzed their target genes.

Methods

Using high-throughput sequencing, the RNA-Seq, small RNA-Seq and degradome databases of P. ginseng were constructed. The differentially expressed microRNAs was identified by qRT-PCR.

Results

A total of 63,875 unigenes and 24,154,579 small RNA clean reads were obtained from the roots of P. ginseng. From these small RNAs, 71 miRNA families were identified by bioinformatics target prediction software, including 34 conserved miRNAs, 37 non-conserved miRNA families, as well as 179 target genes of 17 known miRNAs. Through degradome sequencing and computation, we finally verified 13 targets of eight miRNAs involved in transcription, energy metabolism, biological stress and disease resistance, suggesting the significance of miRNAs in the development of P. ginseng. Consistently, major miRNA targets exhibited tissue specificity and complexity in expression patterns.

Conclusion

Differential expression microRNAs were found in different growth years of ginsengs (Shizhu ginseng and Yuan ginseng), and the regulatory roles and functional annotations of miRNA targets in P. ginseng need further investigation.

Plant responses to metals stress: microRNAs in focus

Metal toxicity can largely affect the growth and yield of numerous plant species. Plants have developed specific mechanisms to withstand the varying amounts of metals. One approach involves utilization of microRNAs (miRNAs) that are known for cleaving transcripts or inhibiting translation to mediate post-transcriptional control. Use of transcription factors (TFs) or gene regulation in metal detoxification largely depends on metal-responsive miRNAs. Moreover, systemic signals and physiological processes for plants response to metal toxicities are likewise controlled by miRNAs. Therefore, it is necessary to understand miRNAs and their regulatory networks in relation to metal stress. The miRNA-based approach can be important to produce metal-tolerant plant species. Here, we have reviewed the importance of plant miRNAs and their role in mitigating metal toxicities. The current review also discusses the specific advances that have occurred as a result of the identification and validation of several metal stress-responsive miRNAs.

microRNAs: Key Players in Plant Response to Metal Toxicity

Environmental metal pollution is a common problem threatening sustainable and safe crop production. Heavy metals (HMs) cause toxicity by targeting key molecules and life processes in plant cells. Plants counteract excess metals in the environment by enhancing defense responses, such as metal chelation, isolation to vacuoles, regulating metal intake through transporters, and strengthening antioxidant mechanisms. In recent years, microRNAs (miRNAs), as a small non-coding RNA, have become the central regulator of a variety of abiotic stresses, including HMs. With the introduction of the latest technologies such as next-generation sequencing (NGS), more and more miRNAs have been widely recognized in several plants due to their diverse roles. Metal-regulated miRNAs and their target genes are part of a complex regulatory network. Known miRNAs coordinate plant responses to metal stress through antioxidant functions, root growth, hormone signals, transcription factors (TF), and metal transporters. This article reviews the research progress of miRNAs in the stress response of plants to the accumulation of HMs, such as Cu, Cd, Hg, Cr, and Al, and the toxicity of heavy metal ions.

A Multi-Level Iterative Bi-Clustering Method for Discovering miRNA Co-regulation Network of Abiotic Stress Tolerance in Soybeans

Although growing evidence shows that microRNA (miRNA) regulates plant growth and development, miRNA regulatory networks in plants are not well understood. Current experimental studies cannot characterize miRNA regulatory networks on a large scale. This information gap provides an excellent opportunity to employ computational methods for global analysis and generate valuable models and hypotheses. To address this opportunity, we collected miRNA-target interactions (MTIs) and used MTIs from Arabidopsis thaliana and Medicago truncatula to predict homologous MTIs in soybeans, resulting in 80,235 soybean MTIs in total. A multi-level iterative bi-clustering method was developed to identify 483 soybean miRNA-target regulatory modules (MTRMs). Furthermore, we collected soybean miRNA expression data and corresponding gene expression data in response to abiotic stresses. By clustering these data, 37 MTRMs related to abiotic stresses were identified, including stress-specific MTRMs and shared MTRMs. These MTRMs have gene ontology (GO) enrichment in resistance response, iron transport, positive growth regulation, etc. Our study predicts soybean MTRMs and miRNA-GO networks under different stresses, and provides miRNA targeting hypotheses for experimental analyses. The method can be applied to other biological processes and other plants to elucidate miRNA co-regulation mechanisms.

Comprehensive Genomic Survey, Evolution, and Expression Analysis of GIF Gene Family during the Development and Metal Ion Stress Responses in Soybean

The GIF gene family is one of the plant transcription factors specific to seed plants. The family members are expressed in all lateral organs produced by apical and floral meristems and contribute to the development of leaves, shoots, flowers, and seeds. This study identified eight GIF genes in the soybean genome and clustered them into three groups. Analyses of Ka/Ks ratios and divergence times indicated that they had undergone purifying selection during species evolution. RNA-sequence and relative expression patterns of these GmGIF genes tended to be conserved, while different expression patterns were also observed between the duplicated GIF members in soybean. Numerous cis-regulatory elements related to plant hormones, light, and stresses were found in the promoter regions of these GmGIF genes. Moreover, the expression patterns of GmGIF members were confirmed in soybean roots under cadmium (Cd) and copper (Cu) stress, indicating their potential functions in the heavy metal response in soybean. Our research provides valuable information for the functional characterization of each GmGIF gene in different legumes in the future.

The elemental defense effect of cadmium on Alternaria brassicicola in Brassica juncea

BACKGROUND

The elemental defense hypothesis states a new defensive strategy that hyperaccumulators defense against herbivores or pathogens attacks by accumulating heavy metals. Brassica juncea has an excellent ability of cadmium (Cd) accumulation. However, the elemental defense effect and its regulation mechanism in B. juncea remain unclear.

RESULTS

In this study, we profiled the elemental defense effect and the molecular regulatory mechanism in Cd-accumulated B. juncea after Alternaria brassicicola infection. B. juncea treated with 180 mg Kg^- 1 DW CdCl₂ 2.5H₂O exhibited obvious elemental defense effect after 72 h of infection with A. brassicicola. The expression of some defense-related genes including BjNPR1, BjPR12, BjPR2, and stress-related miRNAs (miR156, miR397, miR398a, miR398b/c, miR408, miR395a, miR395b, miR396a, and miR396b) were remarkably elevated during elemental defense in B. juncea.

CONCLUSIONS

The results indicate that Cd-accumulated B. juncea may defend against pathogens by coordinating salicylic acid (SA) and jasmonic acid (JA) mediated systemic acquired resistance (SAR) and elemental defense in a synergistic joint effect. Furthermore, the expression of miRNAs related to heavy metal stress response and disease resistance may regulate the balance between pathogen defense and heavy metal stress-responsive in B. juncea. The findings provide experimental evidence for the elemental defense hypothesis in plants from the perspectives of phytohormones, defense-related genes, and miRNAs.

Integration of Small RNA and Degradome Sequencing Reveals the Regulatory Network of Al-Induced Programmed Cell Death in Peanut

Peanut is one of the most important oil crops in the world. In China, the peanut is highly produced in its southern part, in which the arable land is dominated by acid soil. At present, miRNAs have been identified in stress response, but their roles and mechanisms are not clear, and no miRNA studies have been found related to aluminum (Al)-induced programmed cell death (PCD). In the present study, transcriptomics, sRNAs, and degradome analysis in the root tips of two peanut cultivars ZH2 (Al-sensitive, S) and 99-1507 (Al-tolerant, T) were carried out. Here, we generated a comprehensive resource focused on identifying key regulatory miRNA-target circuits that regulate PCD under Al stress. Through deep sequencing, 2284 miRNAs were identified and 147 miRNAs were differentially expressed under Al stress. Furthermore, 19237 target genes of 749 miRNAs were validated by degradome sequencing. GO and KEGG analyses of differential miRNA targets showed that the pathways of synthesis and degradation of ketone bodies, citrate cycle (TCA cycle), and peroxisome were responded to Al stress. The combined analysis of the degradome data sets revealed 89 miRNA-mRNA interactions that may regulate PCD under Al stress. Ubiquitination may be involved in Al-induced PCD in peanut. The regulatory networks were constructed based on the differentially expressed miRNAs and their targets related to PCD. Our results will provide a useful platform to research on PCD induced by Al and new insights into the genetic engineering for plant stress response.

Trophic Transfer without Biomagnification of Cadmium in a Soybean-Dodder Parasitic System

Cadmium (Cd) is among the most available and most toxic heavy metals taken up by plants from soil. Compared to the classic plant-animal food chains, the host-parasitic plant food chains have, thus far, been largely overlooked in the studies of Cd trophic transfer. To investigate the pattern of Cd transfer during the infection of parasitic plants on Cd-contaminated hosts, we conducted a controlled experiment that grew soybeans parasitized by Chinese dodders (Cuscuta chinensis) in soil with different levels of Cd treatment, and examined the concentration, accumulation, allocation and transfer coefficients of Cd within this parasitic system. Results showed that among all components, dodders accounted for more than 40% biomass of the whole system but had the lowest Cd concentration and accumulated the least amount of Cd. The transfer coefficient of Cd between soybean stems and dodders was much lower than 1, and was also significantly lower than that between soybean stems and soybean leaves. All these features were continuously strengthened with the increase of Cd treatment levels. The results suggested no evidence of Cd biomagnification in dodders parasitizing Cd-contaminated hosts, and implied that the Cd transfer from hosts to dodders may be a selective process.

Non-Coding RNAs in Response to Drought Stress

Drought stress causes changes in the morphological, physiological, biochemical and molecular characteristics of plants. The response to drought in different plants may vary from avoidance, tolerance and escape to recovery from stress. This response is genetically programmed and regulated in a very complex yet synchronized manner. The crucial genetic regulations mediated by non-coding RNAs (ncRNAs) have emerged as game-changers in modulating the plant responses to drought and other abiotic stresses. The ncRNAs interact with their targets to form potentially subtle regulatory networks that control multiple genes to determine the overall response of plants. Many long and small drought-responsive ncRNAs have been identified and characterized in different plant varieties. The miRNA-based research is better documented, while lncRNA and transposon-derived RNAs are relatively new, and their cellular role is beginning to be understood. In this review, we have compiled the information on the categorization of non-coding RNAs based on their biogenesis and function. We also discuss the available literature on the role of long and small non-coding RNAs in mitigating drought stress in plants.

MicroRNAs: Tiny, powerful players of metal stress responses in plants

Metal contamination of the environment is a widespread problem threatening sustainable and safe crop production. Physio-biochemical and molecular mechanisms of plant responses to metal exposure have been studied to establish the best possible agronomical or biotechnological methods to tackle metal contamination. Metal stress tolerance is regulated by several molecular effectors among which microRNAs are one of the key master regulators of plant growth and stress responses in plants. MicroRNAs are known to coordinate multitude of plant responses to metal stress through antioxidant functions, root growth, hormonal signalling, transcription factors and metal transporters. The present review discusses integrative functions of microRNAs in the regulation of metal stress in plants, which will be useful for engineering stress tolerance traits for improved plant growth and productivity in metal stressed situations.

MS1 is essential for male fertility by regulating the microsporocyte cell plate expansion in soybean

Male sterility is an essential trait in hybrid seed production, especially for monoclinous and autogamous food crops. Soybean male-sterile ms1 mutant has been known for more than 50 years and could be instrumental in making hybrid seeds. However, the gene responsible for the male-sterile phenotype has remained unknown. Here, we report the map-based cloning and characterization of the MS1 gene in soybean. MS1 encodes a kinesin protein and localizes to the nucleus, where it is required for the male meiotic cytokinesis after telophase II. We further substantiated that MS1 colocalizes with microtubules and is essential for cell plate formation in soybean male gametogenesis through immunostaining. Both ms1 and CRISPR/Cas9 knockout mutants show complete male sterility but are otherwise phenotypically normal, making them perfect tools for producing hybrid seeds. The identification of MS1 has the practical potential for assembling the sterility system and speeding up hybrid soybean breeding.

miRNAs play critical roles in response to abiotic stress by modulating cross-talk of phytohormone signaling

One of the most interesting signaling molecules that regulates a wide array of adaptive stress responses in plants are the micro RNAs (miRNAs) that are a unique class of non-coding RNAs constituting novel mechanisms of post-transcriptional gene regulation. Recent studies revealed the role of miRNAs in several biotic and abiotic stresses by regulating various phytohormone signaling pathways as well as by targeting a number of transcription factors (TFs) and defense related genes. Phytohormones are signal molecules modulating the plant growth and developmental processes by regulating gene expression. Studies concerning miRNAs in abiotic stress response also show their vital roles in abiotic stress signaling. Current research indicates that miRNAs may act as possible candidates to create abiotic stress tolerant crop plants by genetic engineering. Yet, the detailed mechanism governing the dynamic expression networks of miRNAs in response to stress tolerance remains unclear. In this review, we provide recent updates on miRNA-mediated regulation of phytohormones combating various stress and its role in adaptive stress response in crop plants.

Title: Hypermethylation of miRNA Genes During Nodule Development

DNA methylation has recently emerged as a powerful regulatory mechanism controlling the expression of key regulators of various developmental processes, including nodulation. However, the functional role of DNA methylation in regulating the expression of microRNA (miRNA) genes during the formation and development of nitrogen-fixing nodules remains largely unknown. In this study, we profiled DNA methylation patterns of miRNA genes during nodule formation, development, and early senescence stages in soybean (Glycine max) through the analysis of methylC-seq data. Absolute DNA methylation levels in the CG, CHH, and CHH sequence contexts over the promoter and primary transcript regions of miRNA genes were significantly higher in the nodules compared with the corresponding root tissues at these three distinct nodule developmental stages. We identified a total of 82 differentially methylated miRNAs in the nodules compared with roots. Differential DNA methylation of these 82 miRNAs was detected only in the promoter (69), primary transcript region (3), and both in the promoter and primary transcript regions (10). The large majority of these differentially methylated miRNAs were hypermethylated in nodules compared with the corresponding root tissues and were found mainly in the CHH context and showed stage-specific methylation patterns. Differentially methylated regions in the promoters of 25 miRNAs overlapped with transposable elements, a finding that may explain the vulnerability of miRNAs to DNA methylation changes during nodule development. Gene expression analysis of a set of promoter-differentially methylated miRNAs pointed to a negative association between DNA methylation and miRNA expression. Gene Ontology and pathways analyses indicate that changes in DNA methylation of miRNA genes are reprogrammed and contribute to nodule development through indirect regulation of genes involved in cellular processes and pathways with well-established roles in nodulation.

Biotechnological strategies for enhancing heavy metal tolerance in neglected and underutilized legume crops: A comprehensive review

Contamination of agricultural land and water by heavy metals due to rapid industrialization and urbanization including various natural processes have become one of the major constraints to crop growth and productivity. Several studies have reported that to counteract heavy metal stress, plants should be able to maneuver various physiological, biochemical and molecular processes to improve their growth and development under heavy metal stress. With the advent of modern biotechnological tools and techniques it is now possible to tailor legume and other plants overexpressing stress-induced genes, transcription factors, proteins, and metabolites that are directly involved in heavy metal stress tolerance. This review provides an in-depth overview of various biotechnological approaches and/or strategies that can be used for enhancing detoxification of the heavy metals by stimulating phytoremediation processes. Synthetic biology tools involved in the engineering of legume and other crop plants against heavy metal stress tolerance are also discussed herewith some pioneering examples where synthetic biology tools that have been used to modify plants for specific traits. Also, CRISPR based genetic engineering of plants, including their role in modulating the expression of several genes/ transcription factors in the improvement of abiotic stress tolerance and phytoremediation ability using knockdown and knockout strategies has also been critically discussed.

MicroRNA-Mediated Responses to Cadmium Stress in Arabidopsis thaliana

In recent decades, the presence of cadmium (Cd) in the environment has increased significantly due to anthropogenic activities. Cd is taken up from the soil by plant roots for its subsequent translocation to shoots. However, Cd is a non-essential heavy metal and is therefore toxic to plants when it over-accumulates. MicroRNA (miRNA)-directed gene expression regulation is central to the response of a plant to Cd stress. Here, we document the miRNA-directed response of wild-type Arabidopsis thaliana (Arabidopsis) plants and the drb1, drb2 and drb4 mutant lines to Cd stress. Phenotypic and physiological analyses revealed the drb1 mutant to display the highest degree of tolerance to the imposed stress while the drb2 mutant was the most sensitive. RT-qPCR-based molecular profiling of miRNA abundance and miRNA target gene expression revealed DRB1 to be the primary double-stranded RNA binding (DRB) protein required for the production of six of the seven Cd-responsive miRNAs analyzed. However, DRB2, and not DRB1, was determined to be required for miR396 production. RT-qPCR further inferred that transcript cleavage was the RNA silencing mechanism directed by each assessed miRNA to control miRNA target gene expression. Taken together, the results presented here reveal the complexity of the miRNA-directed molecular response of Arabidopsis to Cd stress.

Identification of Differentially Methylated miRNA Genes During Compatible and Incompatible Interactions Between Soybean and Soybean Cyst Nematode

DNA methylation is a widespread epigenetic mark that affects gene expression and transposon mobility during plant development and stress responses. However, the role of DNA methylation in regulating the expression of microRNA (miRNA) genes remains largely unexplored. Here, we analyzed DNA methylation changes of miRNA genes using a pair of soybean (Glycine max) near-isogenic lines (NILs) differing in their response to soybean cyst nematode (SCN; Heterodera glycines). Differences in global DNA methylation levels over miRNA genes in response to SCN infection were observed between the isogenic lines. miRNA genes with significant changes in DNA methylation levels in the promoter and primary transcript-coding regions were detected in both lines. In the susceptible isogenic line (NIL-S), 82 differentially methylated miRNAs were identified in response to SCN infection whereas, in the resistant isogenic line (NIL-R), only 16 differentially methylated miRNAs were identified. Interestingly, gma-miR5032, gma-miR5043, gma-miR1520b, and gma-2107-ch16 showed opposite methylation patterns in the isogenic lines. In addition, the miRNA paralogs gma-miR5770a and gma-miR5770b showed hypermethylation and hypomethylation in NIL-S and NIL-R, respectively. Gene expression quantification of gma-miR5032, gma-miR5043, gma-miR1520b, and gma-miR5770a/b and their confirmed targets indicated a role of DNA methylation in regulating miRNA expression and, thus, their targets upon SCN infection. Furthermore, overexpression of these four miRNAs in NIL-S using transgenic hairy root system enhanced plant resistance to SCN to various degrees with a key role observed for miR5032. Together, our results provide new insights into the role of epigenetic mechanisms in controlling miRNA regulatory function during SCN-soybean interactions.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Modulation of Plant and Fungal Gene Expression Upon Cd Exposure and Symbiosis in Ericoid Mycorrhizal Vaccinium myrtillus

The success of Ericaceae in stressful habitats enriched in heavy metals has been ascribed to the distinctive abilities of their mycorrhizal fungal partners to withstand heavy metal stress and to enhance metal tolerance in the host plant. Whereas heavy metal tolerance has been extensively investigated in some ericoid mycorrhizal (ERM) fungi, the molecular and cellular mechanisms that extend tolerance to the host plant are currently unknown. Here, we show a reduced Cd content in Cd-exposed mycorrhizal roots of Vaccinium myrtillus colonized by a metal tolerant isolate of the fungus Oidiodendron maius as compared to non-mycorrhizal roots. To better understand this phenotype, we applied Next Generation Sequencing technologies to analyze gene expression in V. myrtillus and O. maius Zn grown under normal and Cd-stressed conditions, in the free living and in the mycorrhizal status. The results clearly showed that Cd had a stronger impact on plant gene expression than symbiosis, whereas fungal gene expression was mainly regulated by symbiosis. The higher abundance of transcripts coding for stress related proteins in non-mycorrhizal roots may be related to the higher Cd content. Regulated plant metal transporters have been identified that may play a role in reducing Cd content in mycorrhizal roots exposed to this metal.

Emerging Roles of microRNAs in Plant Heavy Metal Tolerance and Homeostasis

Heavy metal stress is a major growth- and yield-limiting factor for plants. Heavy metals include essential metals (copper, iron, zinc, and manganese) and non-essential metals (cadmium, mercury, aluminum, arsenic, and lead). Plants use complex mechanisms of gene regulation under heavy metal stress. MicroRNAs are 21-nucleotide non-coding small RNAs as important modulators of gene expression post-transcriptionally. Recently, high-throughput sequencing has led to the identification of an increasing number of heavy-metal-responsive microRNAs in plants. Metal-regulated microRNAs and their target genes are part of a complex regulatory network that controls various biological processes, including heavy metal uptake and transport, protein folding and assembly, metal chelation, scavenging of reactive oxygen species, hormone signaling, and microRNA biogenesis. In this review, we summarize the recent molecular studies that identify heavy-metal-regulated microRNAs and their roles in the regulation of target genes as part of the microRNA-associated regulatory network in response to heavy metal stress in plants.

MicroRNA expression patterns unveil differential expression of conserved miRNAs and target genes against abiotic stress in safflower

Environmental stresses influence the growth and development of plants by influencing patterns of gene expression. Different regulators control gene expression, including transcription factors (TFs) and microRNAs. MicroRNAs (miRNAs: ~21 nucleotides long) are encoded by miRNA genes transcribed by RNA polymerase II (RNP-II) and play key roles in plant development and physiology. There is little knowledge currently available on miRNAs and their function in response to environmental stresses in safflower. To obtain more information on safflower miRNAs, we initially used a comparative genomics approach and succeeded in identifying 126 miRNAs belonging to 29 conserved families, along with their target genes. In this study, we investigated the expression profiles of seven conserved miRNAs related to drought, salinity, heat, and Cd stress in the leaf and root organs using qRT-PCR, for the first time. Gene Ontology (GO) analysis found that target genes of miRNAs are often TFs such as AP2/ERF and HD-ZIP as well as NAC domain-containing proteins. Expression analyses confirmed that miRNAs can play a vital role in keeping safflower stress-tolerant. Differential expression of miR156, miR162, miR164, miR166, miR172, miR398, and miR408 regulate the expression of their respective target genes. These genes activate several pathways leading to physiological and biochemical responses to abiotic stresses. Some conserved miRNAs were regulated by abiotic stresses. Our finding provides valuable information to understand miRNAs in relation to different abiotic stresses in safflower.

Determination of the MiRNAs Related to Bean Pyralid Larvae Resistance in Soybean Using Small RNA and Transcriptome Sequencing

Soybean is one of the most important oil crops in the world. Bean pyralid is a major leaf-feeding insect of soybean. In order to screen out the functional genes and regulatory pathways related to the resistance for bean pyralid larvae, the small RNA and transcriptome sequencing were performed based on the highly resistant material (Gantai-2-2) and highly susceptible material (Wan 82-178) of soybean. The results showed that, when comparing 48 h feeding with 0 h feeding, 55 differentially expressed miRNAs were identified in Gantai-2-2 and 58 differentially expressed miRNAs were identified in Wan82-178. When comparing Gantai-2-2 with Wan82-178, 77 differentially expressed miRNAs were identified at 0 h feeding, and 70 differentially expressed miRNAs were identified at 48 h feeding. The pathway analysis of the predicted target genes revealed that the plant hormone signal transduction, RNA transport, protein processing in the endoplasmic reticulum, zeatin biosynthesis, ubiquinone and other terpenoid-quinone biosynthesis, and isoquinoline alkaloid biosynthesis may play important roles in soybean's defense against the stress caused by bean pyralid larvae. According to conjoint analysis of the miRNA/mRNA, a total of 20 differentially expressed miRNAs were negatively correlated with 26 differentially expressed target genes. The qRT-PCR analysis verified that the small RNA sequencing results were credible. According to the analyses of the differentially expressed miRNAs, we speculated that miRNAs are more likely to play key roles in the resistance to insects. Gma-miR156q, Gma-miR166u, Gma-miR166b, Gma-miR166j-3p, Gma-miR319d, Gma-miR394a-3p, Gma-miR396e, and so on-as well as their negatively regulated differentially expressed target genes-may be involved in the regulation of soybean resistance to bean pyralid larvae. These results laid a foundation for further in-depth research regarding the action mechanisms of insect resistance.

Integrated transcriptome, small RNA and degradome sequencing approaches provide insights into Ascochyta blight resistance in chickpea

Ascochyta blight (AB) is one of the major biotic stresses known to limit the chickpea production worldwide. To dissect the complex mechanisms of AB resistance in chickpea, three approaches, namely, transcriptome, small RNA and degradome sequencing were used. The transcriptome sequencing of 20 samples including two resistant genotypes, two susceptible genotypes and one introgression line under control and stress conditions at two time points (3rd and 7th day post inoculation) identified a total of 6767 differentially expressed genes (DEGs). These DEGs were mainly related to pathogenesis-related proteins, disease resistance genes like NBS-LRR, cell wall biosynthesis and various secondary metabolite synthesis genes. The small RNA sequencing of the samples resulted in the identification of 651 miRNAs which included 478 known and 173 novel miRNAs. A total of 297 miRNAs were differentially expressed between different genotypes, conditions and time points. Using degradome sequencing and in silico approaches, 2131 targets were predicted for 629 miRNAs. The combined analysis of both small RNA and transcriptome datasets identified 12 miRNA-mRNA interaction pairs that exhibited contrasting expression in resistant and susceptible genotypes and also, a subset of genes that might be post-transcriptionally silenced during AB infection. The comprehensive integrated analysis in the study provides better insights into the transcriptome dynamics and regulatory network components associated with AB stress in chickpea and, also offers candidate genes for chickpea improvement.

Stress-responsive miRNAome of Glycine max (L.) Merrill: molecular insights and way forward

MAIN CONCLUSION

Analysis of stress-associated miRNAs of Glycine max (L.) Merrill reveals wider ramifications of small RNA-mediated (conserved and legume-specific miRNAs) gene regulatory foot prints in molecular adaptive responses. MicroRNAs (miRNAs) are indispensable components of gene regulatory mechanism of plants. Soybean is a crop of immense commercial potential grown worldwide for its edible oil and soy meal. Intensive research efforts, using the next generation sequencing and bioinformatics techniques, have led to the identification and characterization of numerous small RNAs, especially microRNAs (miRNAs), in soybean. Furthermore, studies have unequivocally demonstrated the significance of miRNAs during the developmental processes and various stresses in soybean. In this review, we summarize the current state of understanding of miRNA-based abiotic and biotic stress responses in soybean. In addition, the molecular insights gained from the stress-related soybean miRNAs have been compared to the miRNAs of other crops, especially legumes, and the core commonalities have been highlighted, though differences among them were not ignored. Nature of response of soybean-derived conserved miRNAs during various stresses was also analyzed to gain deeper insights regarding sRNAome-based defense responses. This review further provides way forward in legume small RNA transcriptomics based on the adaptive responses of soybean and other legume-derived miRNAs.

Homeostasis in the soybean miRNA396-GRF network is essential for productive soybean cyst nematode infections

Heterodera glycines, the soybean cyst nematode, penetrates soybean roots and migrates to the vascular cylinder where it forms a feeding site called the syncytium. MiRNA396 (miR396) targets growth-regulating factor (GRF) genes, and the miR396-GRF1/3 module is a master regulator of syncytium development in model cyst nematode H. schachtii infection of Arabidopsis. Here, we investigated whether this regulatory system operates similarly in soybean roots and is likewise important for H. glycines infection. We found that a network involving nine MIR396 and 23 GRF genes is important for normal development of soybean roots and that GRF function is specified in the root apical meristem by miR396. All MIR396 genes are down-regulated in the syncytium during its formation phase while, specifically, 11 different GRF genes are up-regulated. The switch to the syncytium maintenance phase coincides with up-regulation of MIR396 and down-regulation of the 11 GRF genes specifically via post-transcriptional regulation by miR396. Furthermore, interference with the miR396-GRF6/8-13/15-17/19 regulatory network, through either overexpression or knockdown experiments, does not affect the number of H. glycines juveniles that enter the vascular cylinder to initiate syncytia, but specifically inhibits efficient H. glycines development to adult females. Therefore, homeostasis in the miR396-GRF6/8-13/15-17/19 regulatory network is essential for productive H. glycines infections.

Photoelectrochemical biosensor for microRNA detection based on a MoS2/g-C3N4/black TiO2 heterojunction with Histostar@AuNPs for signal amplification

Herein, a novel photoelectrochemical (PEC) biosensor was developed for the ultrasensitive detection of microRNA-396a based on a MoS₂/g-C₃N₄/black TiO₂ heterojunction as the photoactive material and gold nanoparticles carrying Histostar antibodies (Histostar@AuNPs) for signal amplification. Briefly, MoS₂/g-C₃N₄/black TiO₂ was deposited on an indium tin oxide (ITO) electrode surface, after which gold nanoparticles (AuNPs) and probe DNA were assembled on the modified electrode. Hybridization with miRNA-396a resulted in a rigid DNA: RNA hybrid being formed, which was recognized by the S9.6 antibody. The captured antibody can further conjugate with the secondary IgG antibodies of Histostar@AuNPs, thereby leading to the immobilization of horse radish peroxidase (HRP). In the presence of HRP, the oxidation of 4-chloro-1-naphthol (4-CN) by H₂O₂ was accelerated, producing the insoluble product benzo-4-chlorohexadienone on the electrode surface and causing a significant decrease in the photocurrent. The developed biosensor could detect miRNA-396a at concentrations from 0.5 fM to 5000 fM, with a detection limit of 0.13 fM. Further, the proposed method can also be used to investigate the effect of heavy metal ions on the expression level of miRNAs. Results suggest that the biosensor developed herein offers a promising platform for the ultrasensitive detection of miRNA.

Ectopic Overexpression of bol-miR171b Increases Chlorophyll Content and Results in Sterility in Broccoli ( Brassica oleracea L var. italica)

MiR171 plays pleiotropic roles in the growth and development of several plant species. However, the mechanism underlying the miR171-mediated regulation of organ development in broccoli remains unknown. In this study, bol-miR171b was characterized and found to be differentially expressed in various broccoli organs. The ectopic overexpression of bol-miR171b in Arabidopsis affected the leaf and silique development of transgenic lines. In particular, the chlorophyll content of leaves from overexpressed bol-miR171b transgenic Arabidopsis was higher than that of the vector controls. The fertility and seed yield of Arabidopsis with overexpressed bol-miR171b were markedly lower than those of the vector controls. Similarly, overexpressed bol-miR171b transgenic broccoli exhibited dark green leaves with high chlorophyll content, and nearly all of the flowers were sterile. These results demonstrated that overexpression of bol-miR171b could increase the chlorophyll content of transgenic plants. Degradome sequencing was conducted to identify the targets of bol-miR171b. Two members of the GRAS gene family, BolSCL6 and BolSCL27, were cleaved by bol-miR171b-3p in broccoli. In addition to the genes targeted by bol-miR171b-3p, adenylylsulfate reductase 3 ( APSR3), which played important roles in plant sulfate assimilation and reduction, was speculated to be cleaved by bol-miR171b-5p, suggesting that the star sequence of bol-miR171b may also have functions in broccoli. Comparative transcriptome analysis further revealed that the genes involved in chloroplast development and sulfate homeostasis should participate in the bol-miR171b -mediated regulatory network. Taken together, these findings provided new insights into the function and regulation of bol-miR171b in broccoli and indicated the potential of bol-miR171b as a small RNA molecule that increased leaf chlorophyll in plants by genetic engineering.

MicroRNA166 Modulates Cadmium Tolerance and Accumulation in Rice

MicroRNAs (miRNAs) are 20- to 24-nucleotide small noncoding RNAs that regulate gene expression in eukaryotic organisms. Several plant miRNAs, such as miR166, have vital roles in plant growth, development and responses to environmental stresses. One such environmental stress encountered by crop plants is exposure to cadmium (Cd), an element highly toxic to most organisms, including humans and plants. In this study, we analyzed the role of miR166 in Cd accumulation and tolerance in rice (Oryza sativa). The expression levels of miR166 in both root and leaf tissues were significantly higher in the reproductive stage than in the seedling stage in rice. The expression of miR166 in the roots of rice seedlings was reduced after Cd treatment. Overexpression of miR166 in rice improved Cd tolerance, a result associated with the reduction of Cd-induced oxidative stress in transgenic rice plants. Furthermore, overexpression of miR166 reduced both Cd translocation from roots to shoots and Cd accumulation in the grains. miR166 targets genes encoding the class-III homeodomain-Leu zipper (HD-Zip) family proteins in plants. In rice, HOMEODOMAIN CONTAINING PROTEIN4 (OsHB4) gene (Os03g43930), which encodes an HD-Zip protein, was up-regulated by Cd treatment but down-regulated by overexpression of miR166 in transgenic rice plants. Overexpression of OsHB4 increased Cd sensitivity and Cd accumulation in the leaves and grains of transgenic rice plants. By contrast, silencing OsHB4 by RNA interference enhanced Cd tolerance in transgenic rice plants. These results indicate a critical role for miR166 in Cd accumulation and tolerance through regulation of its target gene, OsHB4, in rice.

Down-regulation of genes coding for core RNAi components and disease resistance proteins via corresponding microRNAs might be correlated with successful Soybean mosaic virus infection in soybean

Plants protect themselves from virus infections by several different defence mechanisms. RNA interference (RNAi) is one prominent antiviral mechanism, which requires the participation of AGO (Argonaute) and Dicer/DCL (Dicer-like) proteins. Effector-triggered immunity (ETI) is an antiviral mechanism mediated by resistance (R) genes, most of which encode nucleotide-binding site-leucine-rich repeat (NBS-LRR) family proteins. MicroRNAs (miRNAs) play important regulatory roles in plants, including the regulation of host defences. Soybean mosaic virus (SMV) is the most common virus in soybean and, in this work, we identified dozens of SMV-responsive miRNAs by microarray analysis in an SMV-susceptible soybean line. Amongst the up-regulated miRNAs, miR168a, miR403a, miR162b and miR1515a predictively regulate the expression of AGO1, AGO2, DCL1 and DCL2, respectively, and miR1507a, miR1507c and miR482a putatively regulate the expression of several NBS-LRR family disease resistance genes. The regulation of target gene expression by these seven miRNAs was validated by both transient expression assays and RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE) experiments. Transcript levels for AGO1, DCL1, DCL2 and five NBS-LRR family genes were repressed at different time points after SMV infection, whereas the corresponding miRNA levels were up-regulated at these same time points. Furthermore, inhibition of miR1507a, miR1507c, miR482a, miR168a and miR1515a by short tandem target mimic (STTM) technology compromised SMV infection efficiency in soybean. Our results imply that SMV can counteract soybean defence responses by the down-regulation of several RNAi pathway genes and NBS-LRR family resistance genes via the induction of the accumulation of their corresponding miRNA levels.

Identification of virus-derived siRNAs and their targets in RBSDV-infected rice by deep sequencing

RNA interference (RNAi) is a conserved mechanism against viruses in plants and animals. It is thought to inactivate the viral genome by producing virus-derived small interfering RNAs (vsiRNAs). Rice black-streaked dwarf virus (RBSDV) is transmitted to plants by the small brown planthopper (Laodelphax striatellus), and seriously threatens production of rice in East Asia, particularly Oryza sativa japonica subspecies. Through deep sequencing, genome-wide comparisons of RBSDV-derived vsiRNAs were made between the japonica variety Nipponbare, and the indica variety 9311. Four small RNA libraries were constructed from the leaves and shoots of each variety. We found 659,756 unique vsiRNAs in the four samples, and only 43,485 reads were commonly shared. The size distributions of vsiRNAs were mostly 21- and 22-nt long, and A/U bias (66-68%) existed at the first nucleotide of vsiRNAs. Additionally, vsiRNAs were continuously but heterogeneously distributed along S1-S10 segments of the RBSDV genome. Distribution profiles of vsiRNA hotspots were similar in different hosts and tissues, and the 5'- and 3'-terminal regions of S4, S5, and S8 had more hotspots. Distribution and abundance of RBSDV vsiRNAs could be useful in designing efficient targets for exploiting RNA interference for virus resistance. Degradome analysis found 25 and 11 host genes appeared to be targeted by vsiRNAs in 9311 and Nipponbare. We report for the first time vsiRNAs derived from RBSDV-infected rice.

Regulation of Isoflavone Biosynthesis by miRNAs in Two Contrasting Soybean Genotypes at Different Seed Developmental Stages

Owing to the presence of nutritionally important, health-promoting bioactive compounds, especially isoflavones, soybean has acquired the status of a functional food. miRNAs are tiny riboregulator of gene expression by either decreasing and/or increasing the expression of their corresponding target genes. Despite several works on identification and functional characterization of plant miRNAs, the role of miRNAs in the regulation of isoflavones metabolism is still a virgin field. In the present study, we identified a total of 31 new miRNAs along with their 245 putative target genes from soybean seed-specific ESTs using computational approach. The Kyoto Encyclopedia of Genes and Genomes pathway analyses indicated that miRNA putatively regulates metabolism and genetic information processing. Out of that, a total of 5 miRNAs (Gma-miRNA12, Gma-miRNA24, Gma-miRNA26, Gma-miRNA28, and Gma-miRNA29) were predicted and validated for their probable role during isoflavone biosynthesis. We also validated their five target genes using RA-PCR, which is as good as 5'RLM-RACE. Temporal regulation [35 days after flowering, 45, 55, and 65 DAF] of miRNAs and their targets showed differential expression schema. Differential expression of Gma-miR26 and Gma-miRNA28 along with their corresponding target genes (Glyma.10G197900 and Glyma.09G127200) showed a direct relationship with the total isoflavone content. Therefore, understanding the miRNA-based genetic regulation of isoflavone pathway would assist in selection and manipulation to get high-performing soybean genotypes with better isoflavone yield.

miRNA-based heavy metal homeostasis and plant growth

Plants have been naturally gifted with mechanisms to adjust under very high or low nutrient concentrations. Heavy metal toxicity is considered as a major growth and yield-limiting factor for plants. This stress includes essential as well as non-essential metals. MicroRNAs (miRNAs) are known for mediating post-transcriptional regulation by cleaving transcripts or translational inhibition. It is commonly agreed that an extensive understanding of plant miRNAs will significantly help in the induction of tolerance against environmental stresses. With the introduction of the latest technology like next generation sequencing (NGS), a growing figure of miRNAs has been productively recognized in several plants for their diverse roles. These miRNAs are well-known modulators of plant responses to heavy metal (HM) stress. Data regarding metal-responsive miRNAs point out the vital role of plant miRNAs in supplementing metal detoxification by means of transcription factors (TF) or gene regulation. Acting as systemic signals, miRNAs also synchronize different physiological processes for plant responses to metal toxicities. In contrast to practicing techniques, using miRNA is a greatly helpful, pragmatic, and feasible approach. The earlier findings point towards miRNAs as a prospective target to engineer heavy metal tolerance in plants. Therefore, there is a need to augment our knowledge about the orchestrated functions of miRNAs during HM stress. We reviewed the deterministic significance of plant miRNAs in heavy metal tolerance and their role in mediating plant responses to HM toxicities. This review also summarized the topical developments by identification and validation of different metal stress-responsive miRNAs.

Variation in accumulation and translocation of di-n-butyl phthalate (DBP) among rice (Oryza sativa L.) genotypes and selection of cultivars for low DBP exposure

Di-n-butyl phthalate (DBP) is a typical endocrine-disrupting chemical with higher detection frequency and concentration in agricultural soil (particularly in paddy-field soil of Guangdong Province) of China. In this study, a greenhouse experiment was conducted to investigate variation in uptake and accumulation of DBP by 20 rice cultivars and to screen low DBP-accumulating cultivars. DBP concentrations in plants varied greatly with rice cultivars, growth stages, and tissues. The highest DBP concentrations in both roots and shoots were observed at the ripening stage, with concentrations 2-100-fold higher than those at tillering, jointing, and flowering stages. At the ripening stage, DBP concentrations decreased in the order of leaf > root > stem > grain, and significant differences of DBP concentrations were observed among various rice cultivars. Moreover, the magnitude of variation in DBP concentrations among various cultivars was greater in stems and grains than in roots and leaves. The translocation factors of DBP from roots to stems and from shoots to grains were <1.0, and those from stems to leaves were almost >1.0. Overall, cultivars Yuxiangyouzhan, Jinnongsimiao, Tianyou 122, and Wuyou 380 accumulated relatively lower DBP in grains, resulting in lower DBP exposure. The DBP uptake and translocation pathways in rice require further investigation. Graphical abstract ᅟ.

Tissue-Specific Regulation of Gma-miR396 Family on Coordinating Development and Low Water Availability Responses

Previously, it was reported that miR396s interact with growth-regulating factors (GRFs) to modulate plant growth, development, and stress resistance. In soybean, 11 gma-miR396 precursors (Pre-miR396a-k) were found, and 24 GmGRFs were predicted as targets of seven mature gma-miR396s (gma-miR396a/b/c/e/h/i/k). To explore the roles of the miR396-GRF module in low water availability response of soybean, we analyzed the expression of Pre-miR396a-k, and found that Pre-miR396a/i/bdgk/e/h were up-regulated in leaves and down-regulated in roots; on the contrary, GmGRF5/6/7/8/15/17/21 were down-regulated in leaves and GmGRF1/2/17/18/19/20/21/22/23/24 were up-regulated in roots of low water potential stressed soybean. Any one of gma-miR396a/b/c/e/h/i/k was able to interact with 20 GmGRFs (GmGRF1/2/6-11/13-24), confirming that this module represents a multi-to-multi network interaction. We generated Arabidopsis plants over-expressing each of the 11 gma-miR396 precursors (Pre-miR396a-k), and seven of them (miR396a/b/c/e/h/i/k-OE transgenic Arabidopsis) showed altered development. The low water availability of miR396a/b/c/e/h/i/k-OE was enhanced in leaves but reduced in seeds and roots. Contrary to previous reports, miR396a/b/c/i-OE seedlings showed lower survival rate than WT when recovering after rewatering under soil drying. In general, we believe our findings are valuable to understand the role of gma-miR396 family in coordinating development and low water availability responses, and can provide potential strategies and directions for soybean breeding programs to improve seed yield and plant drought tolerance.

Integration of small RNAs, degradome and transcriptome sequencing in hyperaccumulator Sedum alfredii uncovers a complex regulatory network and provides insights into cadmium phytoremediation

The hyperaccumulating ecotype of Sedum alfredii Hance is a cadmium (Cd)/zinc/lead co-hyperaccumulating species of Crassulaceae. It is a promising phytoremediation candidate accumulating substantial heavy metal ions without obvious signs of poisoning. However, few studies have focused on the regulatory roles of miRNAs and their targets in the hyperaccumulating ecotype of S. alfredii. Here, we combined analyses of the transcriptomics, sRNAs and the degradome to generate a comprehensive resource focused on identifying key regulatory miRNA-target circuits under Cd stress. A total of 87 721 unigenes and 356 miRNAs were identified by deep sequencing, and 79 miRNAs were differentially expressed under Cd stress. Furthermore, 754 target genes of 194 miRNAs were validated by degradome sequencing. A gene ontology (GO) enrichment analysis of differential miRNA targets revealed that auxin, redox-related secondary metabolism and metal transport pathways responded to Cd stress. An integrated analysis uncovered 39 pairs of miRNA targets that displayed negatively correlated expression profiles. Ten miRNA-target pairs also exhibited negative correlations according to a real-time quantitative PCR analysis. Moreover, a coexpression regulatory network was constructed based on profiles of differentially expressed genes. Two hub genes, ARF4 (auxin response factor 4) and AAP3 (amino acid permease 3), which might play central roles in the regulation of Cd-responsive genes, were uncovered. These results suggest that comprehensive analyses of the transcriptomics, sRNAs and the degradome provided a useful platform for investigating Cd hyperaccumulation in S. alfredii, and may provide new insights into the genetic engineering of phytoremediation.