MicroRNA166 Modulates Cadmium Tolerance and Accumulation in Rice

Multiomics and biotechnologies for understanding and influencing cadmium accumulation and stress response in plants

Cadmium (Cd) is one of the most toxic heavy metals faced by plants and, additionally, via the food chain, threatens human health. It is principally dispersed through agro-ecosystems via anthropogenic activities and geogenic sources. Given its high mobility and persistence, Cd, although not required, can be readily assimilated by plants thereby posing a threat to plant growth and productivity as well as animal and human health. Thus, breeding crop plants in which the edible parts contain low to zero Cd as safe food stuffs and harvesting shoots of high Cd-containing plants as a route for decontaminating soils are vital strategies to cope with this problem. Recently, multiomics approaches have been employed to considerably enhance our understanding of the mechanisms underlying (i) Cd toxicity, (ii) Cd accumulation, (iii) Cd detoxification and (iv) Cd acquisition tolerance in plants. This information can be deployed in the development of the biotechnological tools for developing plants with modulated Cd tolerance and detoxification to safeguard cellular and genetic integrity as well as to minimize food chain contamination. The aim of this review is to provide a current update about the mechanisms involved in Cd uptake by plants and the recent developments in the area of multiomics approach in terms of Cd stress responses, as well as in the development of Cd tolerant and low Cd accumulating crops.

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.

Zero-valent iron (nZVI) nanoparticles mediate SlERF1 expression to enhance cadmium stress tolerance in tomato

Cadmium (Cd) pollution threatens plant physiological and biochemical activities and crop production. Significant progress has been made in characterizing how nanoparticles affect Cd stress tolerance; however, the molecular mechanism of nZVI nanoparticles in Cd stress remains largely uncharacterized. Plants treated with nZVI and exposed to Cd had increased antioxidant capacity and reduced Cd accumulation in plant tissues. The nZVI treatment differentially affected the expression of genes involved in plant environmental responses, including those associated with the ERF transcription factor. SlEFR1 was upregulated by Cd stress in nZVI-treated plants when compared with the control and the predicted protein-protein interactions suggested SlERF1 interacts with proteins associated with plant hormone signaling pathway and related to stress. Yeast overexpressing SlEFR1 grew faster after Cd exposure and significantly had higher Cd stress tolerance when compared with empty vector controls. These results suggest that nZVI induces Cd stress tolerance by activating SlERF1 expression to improve plant growth and nutrient accumulation. Our study reveals the molecular mechanism of Cd stress tolerance for improved plant growth and will support new research on overcoming Cd stress and improving vegetable crop production.

Mechanism of action of microRNA166 on nitric oxide in alfalfa (Medicago sativa L.) under drought stress

BACKGROUND

Alfalfa is a perennial forage crop of high importance, but its cultivation is often affected by drought stress. Currently, the investigation of drought-related small RNAs is a popular research topic to uncover plant drought resistance mechanisms. Among these small RNAs, microRNA166 (miR166) is associated with drought in numerous plant species. Initial small RNA sequencing studies have shown that miR166 is highly responsive to exogenous nitric oxide (NO) and drought. Therefore, analyzing the expression of Msa-miR166 under nitric oxide and drought treatment is significant.

RESULT

Bioinformatics analysis revealed that the miR166 family is widely distributed among plants, ranging from mosses to eudicots, with significant distribution differences between species. The evolutionary degree of Msa-miR166s is highly similar to that of Barrel medic (Medicago truncatula) and Soybean (Glycine max), but significantly different from the model plant Arabidopsis (Arabidopsis thaliana). It is suggested that there are no significant differences in miR166s within the species, and members of Msa-miR166s can form a typical stem-loop. The lowest level of exogenous nitric oxide was observed in Msa-miR166s under drought stress, followed by individual drought, and the highest level was observed after removing endogenous nitric oxide.

CONCLUSION

In response to short-term drought, Msa-miR166s down-regulate expression in alfalfa (Medicago sativa L.). Exogenous nitric oxide can reduce the expression of Msa-miR166s in response to short-term drought. These findings suggest that Msa-miR166e-5p is responsive to environmental changes. The expression levels of target genes showed an opposite trend to Msa-miR166s, verifying the accuracy of Degradome sequencing in the early stage. This suggests that alfalfa experiences drought stress when regulated by exogenous nitric oxide, targeting HD ZIP-III, FRI, and CoA ligase genes. Additionally, the expression of Msa-miR166s in response to drought stress varies between leaves and roots, indicating spatiotemporal specificity.

Whole-transcriptome profiling and identification of cold tolerance-related ceRNA networks in japonica rice varieties

Introduction

Low-temperature stress negatively impacts rice yield, posing a significant risk to food security. While previous studies have explored the physiological and linear gene expression alterations in rice under low-temperature conditions, the changes in competing endogenous RNA (ceRNA) networks remain largely unexamined.

Methods

We conducted RNA sequencing on two japonica rice varieties with differing cold-tolerance capabilities to establish ceRNA networks. This enabled us to investigate the transcriptional regulatory network and molecular mechanisms that rice employs in response to low-temperature stress.

Results

We identified 364 differentially expressed circular RNAs (circRNAs), 224 differentially expressed microRNAs (miRNAs), and 12,183 differentially expressed messenger RNAs (mRNAs). WRKY family was the most prominent transcription factor family involved in cold tolerance. Based on the expression patterns and targeted relationships of these differentially expressed RNAs, we discerned five potential ceRNA networks related to low-temperature stress in rice: osa-miR166j-5p from the miR166 family was associated with cold tolerance; osa-miR528-3p and osa-miR156j-3p were linked to stress response; and osa-miR156j-3p was involved in the antioxidant system. In addition, Os03g0152000 in the antioxidant system, as well as Os12g0491800 and Os05g0381400, correlated with the corresponding stress response and circRNAs in the network. A gene sequence difference analysis and phenotypic validation of Os11g0685700 (OsWRKY61) within the WRKY family suggested its potential role in regulating cold tolerance in rice.

Discussion and conclusion

We identified Os11g0685700 (OsWRKY61) as a promising candidate gene for enhancing cold tolerance in japonica rice. The candidate miRNAs, mRNAs, and circRNAs uncovered in this study are valuable targets for researchers and breeders. Our findings will facilitate the development of cold-tolerant rice varieties from multiple angles and provide critical directions for future research into the functions of cold-tolerance-related miRNAs, mRNAs, and circRNAs in rice.

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.

Molecular-Assisted Breeding of Cadmium Pollution-Safe Cultivars

Cadmium (Cd) contamination in edible agricultural products, especially in crops intended for consumption, has raised worldwide concerns regarding food safety. Breeding of Cd pollution-safe cultivars (Cd-PSCs) is an effective solution to preventing the entry of Cd into the food chain from contaminated agricultural soil. Molecular-assisted breeding methods, based on molecular mechanisms for cultivar-dependent Cd accumulation and bioinformatic tools, have been developed to accelerate and facilitate the breeding of Cd-PSCs. This review summarizes the recent progress in the research of the low Cd accumulation traits of Cd-PSCs in different crops. Furthermore, the application of molecular-assisted breeding methods, including transgenic approaches, genome editing, marker-assisted selection, whole genome-wide association analysis, and transcriptome, has been highlighted to outline the breeding of Cd-PSCs by identifying critical genes and molecular biomarkers. This review provides a comprehensive overview of the development of Cd-PSCs and the potential future for breeding Cd-PSC using modern molecular technologies.

Synthetic biology tools for environmental protection

Synthetic biology transforms the way we perceive biological systems. Emerging technologies in this field affect many disciplines of science and engineering. Traditionally, synthetic biology approaches were commonly aimed at developing cost-effective microbial cell factories to produce chemicals from renewable sources. Based on this, the immediate beneficial impact of synthetic biology on the environment came from reducing our oil dependency. However, synthetic biology is starting to play a more direct role in environmental protection. Toxic chemicals released by industries and agriculture endanger the environment, disrupting ecosystem balance and biodiversity loss. This review highlights synthetic biology approaches that can help environmental protection by providing remediation systems capable of sensing and responding to specific pollutants. Remediation strategies based on genetically engineered microbes and plants are discussed. Further, an overview of computational approaches that facilitate the design and application of synthetic biology tools in environmental protection is presented.

Negative regulators of grain yield and mineral contents in rice: potential targets for CRISPR-Cas9-mediated genome editing

Rice is a major global staple food crop, and improving its grain yield and nutritional quality has been a major thrust research area since last decades. Yield and nutritional quality are complex traits which are controlled by multiple signaling pathways. Sincere efforts during past decades of research have identified several key genetic and molecular regulators that governed these complex traits. The advent of clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-mediated gene knockout approaches has accelerated the development of improved varieties; however, finding out target gene with negative regulatory function in particular trait without giving any pleiotropic effect remains a challenge. Here, we have reviewed past and recent literature and identified important negative regulators of grain yield and mineral contents which could be potential targets for CRISPR-Cas9-mediated gene knockout. Additionally, we have also compiled a list of microRNAs (miRNAs), which target positive regulators of grain yield, plant stress tolerance, and grain mineral contents. Knocking out these miRNAs could help to increase expression of such positive regulators and thus improve the plant trait. The knowledge presented in this review would help to further accelerate the CRISPR-Cas9-mediated trait improvement in rice.

Intronic microRNA-directed regulation of mitochondrial reactive oxygen species enhances plant stress tolerance in Arabidopsis

MicroRNAs (miRNAs) play crucial roles in regulating plant development and stress responses. However, the functions and mechanism of intronic miRNAs in plants are poorly understood. This study reports a stress-responsive RNA splicing mechanism for intronic miR400 production, whereby miR400 modulates reactive oxygen species (ROS) accumulation and improves plant tolerance by downregulating its target expression. To monitor the intron splicing events, we used an intronic miR400 splicing-dependent luciferase transgenic line. Luciferase activity was observed to decrease after high cadmium concentration treatment due to the retention of the miR400-containing intron, which inhibited the production of mature miR400. Furthermore, we demonstrated that under Cd treatments, Pentatricopeptide Repeat Protein 1 (PPR1), the target of miR400, acts as a positive regulator by inducing ROS accumulation. Ppr1 mutation affected the Complex III activity in the electron transport chain and RNA editing of the mitochondrial gene ccmB. This study illustrates intron splicing as a key step in intronic miR400 production and highlights the function of intronic miRNAs as a 'signal transducer' in enhancing plant stress tolerance.

MicroRNA2871b of Dongxiang Wild Rice (Oryza rufipogon Griff.) Negatively Regulates Cold and Salt Stress Tolerance in Transgenic Rice Plants

Cold and salt stresses are major environmental factors that constrain rice production. Understanding their mechanisms is important to enhance cold and salt stress tolerance in rice. MicroRNAs (miRNAs) are a class of non-coding RNAs with only 21-24 nucleotides that are gene regulators in plants and animals. Previously, miR2871b expression was suppressed by cold stress in Dongxiang wild rice (DXWR, Oryza rufipogon Griff.). However, its biological functions in abiotic stress responses remain elusive. In the present study, miR2871b of DWXR was overexpressed to investigate its function under stress conditions. When miR2871b of DWXR was introduced into rice plants, the transgenic lines were more sensitive to cold and salt stresses, and their tolerance to cold and salt stress decreased. The increased expression of miR2871b in rice plants also increased the levels of reactive oxygen species (ROS) and malondialdehyde (MDA); however, it markedly decreased the activities of peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT) and the contents of proline (Pro) and soluble sugar (SS). These data suggested that miR2871b of DXWR has negative regulatory effects on cold and salt stress tolerance. Meanwhile, 412 differentially expressed genes (DEGs) were found in rice transgenic plants using transcriptome sequencing, among which 266 genes were up-regulated and 146 genes were down-regulated. Furthermore, the upstream cis-acting elements and downstream targets of miR2871b were predicted and analyzed, and several critical acting elements (ABRE and TC-rich repeats) and potential target genes (LOC_Os03g41200, LOC_Os07g47620, and LOC_Os04g30260) were obtained. Collectively, these results generated herein further elucidate the vital roles of miR2871b in regulating cold and salt responses of DXWR.

Revitalizing miRNAs mediated agronomical advantageous traits improvement in rice

One of the key enigmas in conventional and modern crop improvement programmes is how to introduce beneficial traits without any penalty impairment. Rice (Oryza sativa L.), among the essential staple food crops grown and utilized worldwide, needs to improve genotypes in multifaceted ways. With the global view to feed ten billion under the climatic perturbation, only a potent functional master regulator can withstand with hope for the next green revolution and food security. miRNAs are such, miniature, fine tuners for crop improvement and provide a value addition in emerging technologies, namely large-scale genotyping, phenotyping, genome editing, marker-assisted selection, and genomic selection, to make rice production feasible. There has been surplus research output generated since the last decade on miRNAs in rice, however, recent functional knowledge is limited to reaping the benefits for conventional and modern improvements in rice to avoid ambiguity and redundancy in the generated data. Here, we present the latest functional understanding of miRNAs in rice. In addition, their biogenesis, intra- and inter-kingdom signaling and communication, implication of amiRNAs, and consequences upon integration with CRISPR-Cas9. Further, highlights refer to the application of miRNAs for rice agronomical trait improvements, broadly classified into three functional domains. The majority of functionally established miRNAs are responsible for growth and development, followed by biotic and abiotic stresses. Tabular cataloguing reveals and highlights two multifaceted modules that were extensively studied. These belong to miRNA families 156 and 396, orchestrate multifarious aspects of advantageous agronomical traits. Moreover, updated and exhaustive functional aspects of different supplemental miRNA modules that would strengthen rice improvement are also being discussed.

Noncoding RNAs and their roles in regulating the agronomic traits of crops

Molecular breeding is one of the most effective methods for improving the performance of crops. Understanding the genome features of crops, especially the physiological functions of individual genes, is of great importance to molecular breeding. Evidence has shown that genomes of both animals and plants transcribe numerous non-coding RNAs, which are involved in almost every aspect of development. In crops, an increasing number of studies have proven that non-coding RNAs are new genetic resources for regulating crop traits. In this review, we summarize the current knowledge of non-coding RNAs, which are potential crop trait regulators, and focus on the functions of long non-coding RNAs (lncRNAs) in determining crop grain yield, phased small-interfering RNAs (phasiRNAs) in regulating fertility, small interfering RNAs (siRNAs) and microRNAs (miRNAs) in facilitating plant immune response and disease resistance, and miRNAs mediating nutrient and metal stress. Finally, we also discuss the next-generation method for ncRNA application in crop domestication and breeding.

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.

miRNAs for crop improvement

Climate change significantly impacts crop production by inducing several abiotic and biotic stresses. The increasing world population, and their food and industrial demands require focused efforts to improve crop plants to ensure sustainable food production. Among various modern biotechnological tools, microRNAs (miRNAs) are one of the fascinating tools available for crop improvement. miRNAs belong to a class of small non-coding RNAs playing crucial roles in numerous biological processes. miRNAs regulate gene expression by post-transcriptional target mRNA degradation or by translation repression. Plant miRNAs have essential roles in plant development and various biotic and abiotic stress tolerance. In this review, we provide propelling evidence from previous studies conducted around miRNAs and provide a one-stop review of progress made for breeding stress-smart future crop plants. Specifically, we provide a summary of reported miRNAs and their target genes for improvement of plant growth and development, and abiotic and biotic stress tolerance. We also highlight miRNA-mediated engineering for crop improvement and sequence-based technologies available for the identification of miRNAs associated with stress tolerance and plant developmental events.

Toxic effects of cadmium on the physiological and biochemical attributes of plants, and phytoremediation strategies: A review

Anthropogenic activities pose a more significant threat to the environment than natural phenomena by contaminating the environment with heavy metals. Cadmium (Cd), a highly poisonous heavy metal, has a protracted biological half-life and threatens food safety. Plant roots absorb Cd due to its high bioavailability through apoplastic and symplastic pathways and translocate it to shoots through the xylem with the help of transporters and then to the edible parts via the phloem. The uptake and accumulation of Cd in plants pose deleterious effects on plant physiological and biochemical processes, which alter the morphology of vegetative and reproductive parts. In vegetative parts, Cd stunts root and shoot growth, photosynthetic activities, stomatal conductance, and overall plant biomass. Plants' male reproductive parts are more prone to Cd toxicity than female reproductive parts, ultimately affecting their grain/fruit production and survival. To alleviate/avoid/tolerate Cd toxicity, plants activate several defense mechanisms, including enzymatic and non-enzymatic antioxidants, Cd-tolerant gene up-regulations, and phytohormonal secretion. Additionally, plants tolerate Cd through chelating and sequestering as part of the intracellular defensive mechanism with the help of phytochelatins and metallothionein proteins, which help mitigate the harmful effects of Cd. The knowledge on the impact of Cd on plant vegetative and reproductive parts and the plants' physiological and biochemical responses can help selection of the most effective Cd-mitigating/avoiding/tolerating strategy to manage Cd toxicity in plants.

Genome-wide survey of catalase genes in Brassica rapa, Brassica oleracea, and Brassica napus: identification, characterization, molecular evolution, and expression profiling of BnCATs in response to salt and cadmium stress

Catalase (CAT, EC 1.11.1.6), one of the most important antioxidant enzymes, can control excess levels of H₂O₂ produced under oxidative stress in plants. In this study, 16, 8, and 7 CAT genes in the genome of Brassica napus, B. rapa, and B. oleracea were identified, respectively. Phylogenetic studies showed that CATs could be divided into two main groups, each containing specific monocotyledon and dicotyledon subgroups. Motifs, gene structure, and intron phase of CATs in B. napus, Brassica rapa, and Brassica oleracea are highly conserved. Analysis of codon usage bias showed the mutation pressure and natural selection of the codon usage of CATs. Segmental duplication and polyploid were major factors in the expansion of this gene family in B. napus, and genes have experienced  negative selection during evolution. Existence of hormones and stress-responsive cis-elements and identifying miRNA molecules affecting CATs showed that these genes are complexly regulated at the transcriptional and posttranscriptional levels. Based on RNA-seq data, CATs are divided into two groups; the first group has moderate and specific expression in flowers, leaves, stems, and roots, while the second group shows expression in most tissues. qRT-PCR analysis showed that the expression of these genes is dynamic and has a specific expression consistent with other CAT genes in response to salinity and cadmium (Cd) stresses. These results provide information for further investigation of the function of CAT genes in response to stresses and the development of tolerant  plants.

miRNA transcriptome reveals key miRNAs and their targets contributing to the difference in Cd tolerance of two contrasting maize genotypes

Soil cadmium (Cd) contamination is a global environmental and food safety production issue. microRNAs (miRNAs) are proven to be involved in plant growth and development, and abiotic/biotic stress response, but their role in Cd tolerance is largely unknown in maize. To understand the genetic basis of Cd tolerance, two maize genotypes differing in Cd tolerance (L42, a sensitive genotype and L63, a tolerant genotype) were selected, and miRNA sequencing was carried out at nine-day-old seedlings exposed to 24 h Cd stress (5 μM CdCl₂). A total of 151 differentially expressed miRNAs were identified, including 20 known miRNAs and 131 novel miRNAs. The results revealed that 90 and 22 miRNAs were up-regulated and down-regulated by Cd in Cd-tolerant genotype L63, and there were 23 and 43 miRNAs in Cd-sensitive genotype L42, respectively. Twenty-six miRNAs were up-regulated in L42 and unchanged or down-regulated in L63, or unchanged in L42 and down-regulated in L63. There were 108 miRNAs that were up-regulated in L63 and unchanged or down-regulated in L42, or unchanged in L63 and down-regulated in L42. Their target genes were enriched mainly in peroxisomes, glutathione (GSH) metabolism, ABC transporter, and ubiquitin-protease system. Among them, target genes involved in the peroxisome pathway and GSH metabolism might play key roles in Cd tolerance in L63. Besides, several ABC transporters which might involve in Cd uptake and transport were identified. The differentially expressed miRNAs or target genes could be used for breeding low grain Cd accumulation and high Cd tolerance cultivars in maize.

The miR166d/TaCPK7-D Signaling Module Is a Critical Mediator of Wheat (Triticum aestivum L.) Tolerance to K+ Deficiency

It is well established that potassium (K⁺) is an essential nutrient for wheat (Triticum aestivum L.) growth and development. Several microRNAs (miRNAs), including miR166, are reportedly vital roles related to plant growth and stress responses. In this study, a K⁺ starvation-responsive miRNA (miR166d) was identified, which showed increased expression in the roots of wheat seedlings exposed to low-K⁺ stress. The overexpression of miR166d considerably increased the tolerance of transgenic Arabidopsis plants to K⁺ deprivation treatment. Furthermore, disrupting miR166d expression via virus-induced gene silencing (VIGS) adversely affected wheat adaptation to low-K⁺ stress. Additionally, miR166d directly targeted the calcium-dependent protein kinase 7-D gene (TaCPK7-D) in wheat. The TaCPK7-D gene expression was decreased in wheat seedling roots following K⁺ starvation treatment. Silencing TaCPK7-D in wheat increased K⁺ uptake under K⁺ starvation. Moreover, we observed that the miR166d/TaCPK7-D module could affect wheat tolerance to K⁺ starvation stress by regulating TaAKT1 and TaHAK1 expression. Taken together, our results indicate that miR166d is vital for K⁺ uptake and K⁺ starvation tolerance of wheat via regulation of TaCPK7-D.

Comprehensive evolutionary analysis of growth-regulating factor gene family revealing the potential molecular basis under multiple hormonal stress in Gramineae crops

Growth-regulating factors (GRFs) are plant-specific transcription factors that contain two highly conserved QLQ and WRC domains, which control a range of biological functions, including leaf growth, floral organ development, and phytohormone signaling. However, knowledge of the evolutionary patterns and driving forces of GRFs in Gramineae crops is limited and poorly characterized. In this study, a total of 96 GRFs were identified from eight crops of Brachypodium distachyon, Hordeum vulgare, Oryza sativa L. ssp. indica, Oryza rufipogon, Oryza sativa L. ssp. japonica, Setaria italic, Sorghum bicolor and Zea mays. Based on their protein sequences, the GRFs were classified into three groups. Evolutionary analysis indicated that the whole-genome or segmental duplication plays an essential role in the GRFs expansion, and the GRFs were negatively selected during the evolution of Gramineae crops. The GRFs protein function as transcriptional activators with distinctive structural motifs in different groups. In addition, the expression of GRFs was induced under multiple hormonal stress, including IAA, BR, GA3, 6BA, ABA, and MeJ treatments. Specifically, OjGRF11 was significantly induced by IAA at 6 h after phytohormone treatment. Transgenic experiments showed that roots overexpressing OjGRF11 were more sensitive to IAA and affect root elongation. This study will broaden our insights into the origin and evolution of the GRF family in Gramineae crops and will facilitate further research on GRF function.

Transcriptional Regulatory Network of Plant Cadmium Stress Response

Cadmium (Cd) is a non-essential heavy metal with high toxicity to plants. Plants have acquired specialized mechanisms to sense, transport, and detoxify Cd. Recent studies have identified many transporters involved in Cd uptake, transport, and detoxification. However, the complex transcriptional regulatory networks involved in Cd response remain to be elucidated. Here, we provide an overview of current knowledge regarding transcriptional regulatory networks and post-translational regulation of the transcription factors involved in Cd response. An increasing number of reports indicate that epigenetic regulation and long non-coding and small RNAs are important in Cd-induced transcriptional responses. Several kinases play important roles in Cd signaling that activate transcriptional cascades. We also discuss the perspectives to reduce grain Cd content and improve crop tolerance to Cd stress, which provides a theoretical reference for food safety and the future research of plant varieties with low Cd accumulation.

Tweaking the Small Non-Coding RNAs to Improve Desirable Traits in Plant

Plant transcriptome contains an enormous amount of non-coding RNAs (ncRNAs) that do not code for proteins but take part in regulating gene expression. Since their discovery in the early 1990s, much research has been conducted to elucidate their function in the gene regulatory network and their involvement in plants' response to biotic/abiotic stresses. Typically, 20-30 nucleotide-long small ncRNAs are a potential target for plant molecular breeders because of their agricultural importance. This review summarizes the current understanding of three major classes of small ncRNAs: short-interfering RNAs (siRNAs), microRNA (miRNA), and transacting siRNAs (tasiRNAs). Furthermore, their biogenesis, mode of action, and how they have been utilized to improve crop productivity and disease resistance are discussed here.

Molecular mechanisms underlying the toxicity and detoxification of trace metals and metalloids in plants

Plants take up a wide range of trace metals/metalloids (hereinafter referred to as trace metals) from the soil, some of which are essential but become toxic at high concentrations (e.g., Cu, Zn, Ni, Co), while others are non-essential and toxic even at relatively low concentrations (e.g., As, Cd, Cr, Pb, and Hg). Soil contamination of trace metals is an increasing problem worldwide due to intensifying human activities. Trace metal contamination can cause toxicity and growth inhibition in plants, as well as accumulation in the edible parts to levels that threatens food safety and human health. Understanding the mechanisms of trace metal toxicity and how plants respond to trace metal stress is important for improving plant growth and food safety in contaminated soils. The accumulation of excess trace metals in plants can cause oxidative stress, genotoxicity, programmed cell death, and disturbance in multiple physiological processes. Plants have evolved various strategies to detoxify trace metals through cell-wall binding, complexation, vacuolar sequestration, efflux, and translocation. Multiple signal transduction pathways and regulatory responses are involved in plants challenged with trace metal stresses. In this review, we discuss the recent progress in understanding the molecular mechanisms involved in trace metal toxicity, detoxification, and regulation, as well as strategies to enhance plant resistance to trace metal stresses and reduce toxic metal accumulation in food crops.

Genetic Regulation Mechanism of Cadmium Accumulation and Its Utilization in Rice Breeding

Cadmium (Cd) is a heavy metal whose pollution in rice fields leads to varying degrees of Cd accumulation in rice. Furthermore, the long-term consumption of Cd-contaminated rice is harmful to human health. Therefore, it is of great theoretical significance and application value to clarify the genetic regulation mechanism of Cd accumulation in rice and cultivate rice varieties with low Cd accumulation for the safe use of Cd-contaminated soils. This review summarizes the effects of Cd on rice growth, yield, and quality; the physiological and molecular mechanisms of Cd absorption in the roots, loading, and transport of Cd in the xylem, the distribution of Cd in nodes, redistribution of Cd in leaves, and accumulation of Cd in the grains; the regulation mechanism of the Cd stress response; and the breeding of rice with low Cd accumulation. Future directions on the genetic regulation of Cd in rice and application are also discussed. This review provides a theoretical basis for studies exploring the genetic regulation of Cd stress in rice. It also offers a basis for formulating effective strategies to reduce the Cd content in rice.

Genome-wide identification and characterization of the HD-Zip gene family and expression analysis in response to stress in Rehmannia glutinosa Libosch

The HD-Zip family of transcription factors is unique to the plant kingdom, and play roles in modulation of plant growth and response to environmental stresses. R. glutinosa is an important Chinese medicinal material. Its yield and quality are susceptible to various stresses. The HD-Zip transcription factors is unique to the plant, and roles in modulation of plant growth and response to environmental stresses. However, there is no relevant research on the HD-ZIP of R. glutinosa. In this study, 92 HD-Zip transcription factors were identified in R. glutinosa, and denominated as RgHDZ1-RgHDZ92. Members of RgHDZ were classified into four groups (HD-ZipI-IV) based on the phylogenetic relationship of Arabidopsis HD-Zip proteins, and each group contains 38, 18, 17, and 19 members, respectively. Expression analyses of RgHDZ genes based on transcriptome data showed that the expression of these genes could be induced by the endophytic fungus of R. glutinosa. Additionally, we showed that RgHDZ genes were differentially expressed in response to drought, waterlogging, temperature, and salinity treatments. This study provides important information for different expression patterns of stress-responsive HD-Zip and may contribute to the better understanding of the different responses of plants to biotic and abiotic stresses, and provide a molecular basis for the cultivation of resistant varieties of R. glutinosa.

Genome-Wide Identification and Expression Profile of the HD-Zip Transcription Factor Family Associated with Seed Germination and Abiotic Stress Response in Miscanthus sinensis

Miscanthus sinensis is an ornamental grass, non-food bioenergy crop, and forage with high feeding value. It can adapt to many kinds of soil conditions due to its high level of resistance to various abiotic stresses. However, a low level of seed germination restricts the utilization and application of M. sinensis. It is reported that the Homeodomain-leucine zipper (HD-Zip) gene family participates in plant growth and development and ability to cope with outside environment stresses, which may potentially regulate seed germination and stress resistance in M. sinensis. In this study, a complete overview of M. sinensis HD-Zip genes was conducted, including gene structure, conserved motifs, chromosomal distribution, and gene duplication patterns. A total of 169 members were identified, and the HD-Zip proteins were divided into four subgroups. Inter-chromosomal evolutionary analysis revealed that four pairs of tandem duplicate genes and 72 segmental duplications were detected, suggesting the possible role of gene replication events in the amplification of the M. sinensis HD-Zip gene family. There was an uneven distribution of HD-Zip genes on 19 chromosomes of M. sinensis. Also, evolutionary analysis showed that M. sinensis HD-Zip gene family members had more collinearity with monocotyledons and less with dicotyledons. The gene structure analysis showed that there were 93.5% of proteins with motif 1 and motif 4, while motif 10 was only found in group IV. Based on the cis-elements analysis, it appeared that most of the genes were related to plant growth and development, various hormones, and abiotic stress. Furthermore, qRT-PCR analysis showed that Misin06G303300.1 was significantly expressed in seed germination and Misin05G030000.1 and Misin06G303300.1 were highly expressed under chromium, salt, and drought stress. Results in this study will provide a basis for further exploring the potential role of HD-Zip genes in stress responses and genetic improvement of M. sinensis seed germination.

The roles of HD-ZIP proteins in plant abiotic stress tolerance

Homeodomain leucine zipper (HD-ZIP) proteins are plant-specific transcription factors that contain a homeodomain (HD) and a leucine zipper (LZ) domain. The highly conserved HD binds specifically to DNA and the LZ mediates homodimer or heterodimer formation. HD-ZIP transcription factors control plant growth, development, and responses to abiotic stress by regulating downstream target genes and hormone regulatory pathways. HD-ZIP proteins are divided into four subclasses (I-IV) according to their sequence conservation and function. The genome-wide identification and expression profile analysis of HD-ZIP proteins in model plants such as Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) have improved our understanding of the functions of the different subclasses. In this review, we mainly summarize and discuss the roles of HD-ZIP proteins in plant response to abiotic stresses such as drought, salinity, low temperature, and harmful metals. HD-ZIP proteins mainly mediate plant stress tolerance by regulating the expression of downstream stress-related genes through abscisic acid (ABA) mediated signaling pathways, and also by regulating plant growth and development. This review provides a basis for understanding the roles of HD-ZIP proteins and potential targets for breeding abiotic stress tolerance in plants.

OsNAC15 Regulates Tolerance to Zinc Deficiency and Cadmium by Binding to OsZIP7 and OsZIP10 in Rice

Zinc (Zn) deficiency and cadmium (Cd) stress are severe threats to the growth and development of plants. Increasing Zn content and/or decreasing Cd content in grain are also important objectives of rice breeding. However, the molecular mechanisms of Zn deficiency tolerance (ZDT) and Cd stress tolerance (CDT) are largely unknown in rice. Here, we report that a NAM/CUC2-like transcription factor, OsNAC15, contributes to ZDT and CDT in rice. Knockout of OsNAC15 reduced ZDT and CDT at the vegetative stage. OsNAC15 expresses in all tissues of different developmental stages, and is repressed by Zn deficiency and induced by Cd stress. OsNAC15 is a functional transcription factor with transactivation and DNA binding activities. Expression analysis of rice ZIP family genes suggested that the knockout of OsNAC15 activates or inhibits their transcriptions under Zn deficiency or Cd stress conditions. The yeast one-hybrid assay, transient transcriptional activity assay using the dual-luciferase reporter system and electrophoretic mobility shift assay demonstrated that OsNAC15 directly binds to the zinc deficiency-responsive element motifs in the promoters of OsZIP7 and OsZIP10 to repress their transcriptions. The OsNAC15–OsZIP7/10 module is an essential foundation for further study on the regulatory mechanisms of ZDT and CDT in rice.

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.

Advances in molecular mechanisms underlying cadmium uptake and translocation in rice

The increasing cadmium (Cd) pollution in paddy fields has severely threatened China's ecological and food safety. Cultivation of low Cd accumulation varieties to reduce Cd content in rice or cultivation of Cd-tolerant varieties for phytoremediation are considered effective methods to control Cd pollution in paddy fields. However, the underlying molecular mechanism of Cd absorption and transport by rice plants needs to be deciphered to cultivate these varieties. Here, we summarized the molecular mechanisms underlying Cd absorption and transport in rice, as well as the variation of Cd accumulation among rice varieties, the QTLs related to Cd accumulation in rice, and discusses the direction of future research.

Application of RNAi technology: a novel approach to navigate abiotic stresses

BACKGROUND

Due to the rising population globally, and the demand for food, it is critical to significantly increase crop production by 2050. However, climate change estimates show that droughts and heatwaves will become more prevalent in many parts of the world, posing a severe danger to food output.

METHODS

Selective breeding based on genetic diversity is falling short of meeting the expanding need for food and feed. However, the advent of modern plant genetic engineering, genome editing, and synthetic biology provides precise techniques for producing crops capable of sustaining yield under stress situations.

RESULTS

As a result, crop varieties with built-in genetic tolerance to environmental challenges are desperately needed. In the recent years, small RNA (sRNA) data has progressed to become one of the most effective approaches for the improvement of crops. So many sRNAs (18-30nt) have been found with the use of hi-tech bioinformatics and sequencing techniques which are involved in the regulation of sequence specific gene noncoding RNAs (short ncRNAs) i.e., microRNA (miRNA) and small interfering RNA (siRNA). Such research outcomes may advance our understanding of the genetic basis of adaptability of plants to various environmental challenges and the genetic variation of plant's tolerance to a number of abiotic stresses.

CONCLUSION

The review article highlights current trends and advances in sRNAs' critical role in responses of plants to drought, heat, cold, and salinity, and also the potential technology that identifies the abiotic stress-regulated sRNAs, and techniques for analyzing and validating the target genes.

Arsenic perception and signaling: The yet unexplored world

Arsenic is one of the most potent carcinogens in the biosphere, jeopardizing the health of millions of people due to its entrance into the human food chain through arsenic-contaminated waters and staple crops, particularly rice. Although the mechanisms of arsenic sensing are widely known in yeast and bacteria, scientific evidence concerning arsenic sensors or components of early arsenic signaling in plants is still in its infancy. However, in recent years, we have gained understanding of the mechanisms involved in arsenic uptake and detoxification in different plant species and started to get insights into arsenic perception and signaling, which allows us to glimpse the possibility to design effective strategies to prevent arsenic accumulation in edible crops or to increase plant arsenic extraction for phytoremediation purposes. In this context, it has been recently described a mechanism according to which arsenite, the reduced form of arsenic, regulates the arsenate/phosphate transporter, consistent with the idea that arsenite functions as a selective signal that coordinates arsenate uptake with detoxification mechanisms. Additionally, several transcriptional and post-translational regulators, miRNAs and phytohormones involved in arsenic signaling and tolerance have been identified. On the other hand, studies concerning the developmental programs triggered to adapt root architecture in order to cope with arsenic toxicity are just starting to be disclosed. In this review, we compile and analyze the latest advances toward understanding how plants perceive arsenic and coordinate its acquisition with detoxification mechanisms and root developmental programs.

Roles of microRNAs in abiotic stress response and characteristics regulation of plant

MicroRNAs (miRNAs) are a class of non-coding endogenous small RNAs (long 20-24 nucleotides) that negatively regulate eukaryotes gene expression at post-transcriptional level via cleavage or/and translational inhibition of targeting mRNA. Based on the diverse roles of miRNA in regulating eukaryotes gene expression, research on the identification of miRNA target genes has been carried out, and a growing body of research has demonstrated that miRNAs act on target genes and are involved in various biological functions of plants. It has an important influence on plant growth and development, morphogenesis, and stress response. Recent case studies indicate that miRNA-mediated regulation pattern may improve agronomic properties and confer abiotic stress resistance of plants, so as to ensure sustainable agricultural production. In this regard, we focus on the recent updates on miRNAs and their targets involved in responding to abiotic stress including low temperature, high temperature, drought, soil salinity, and heavy metals, as well as plant-growing development. In particular, this review highlights the diverse functions of miRNAs on achieving the desirable agronomic traits in important crops. Herein, the main research strategies of miRNAs involved in abiotic stress resistance and crop traits improvement were summarized. Furthermore, the miRNA-related challenges and future perspectives of plants have been discussed. miRNA-based research lays the foundation for exploring miRNA regulatory mechanism, which aims to provide insights into a potential form of crop improvement and stress resistance breeding.

Genome-wide identification and comprehensive analyses of NAC transcription factor gene family and expression analysis under Fusarium kyushuense and drought stress conditions in Passiflora edulis

The NAC gene family is one of the largest plant transcription factors (TFs) families and plays important roles in plant growth, development, metabolism, and biotic and abiotic stresses. However, NAC gene family has not been reported in passion fruit (Passiflora edulis). In this study, a total of 105 NAC genes were identified in the passion fruit genome and were unevenly distributed across all nine-passion fruit chromomere, with a maximum of 48 PeNAC genes on chromosome one. The physicochemical features of all 105 PeNAC genes varied including 120 to 3,052 amino acids, 3 to 8 conserved motifs, and 1 to 3 introns. The PeNAC genes were named (PeNAC001-PeNAC105) according to their chromosomal locations and phylogenetically grouped into 15 clades (NAC-a to NAC-o). Most PeNAC proteins were predicted to be localized in the nucleus. The cis-element analysis indicated the possible roles of PeNAC genes in plant growth, development, light, hormones, and stress responsiveness. Moreover, the PeNAC gene duplications including tandem (11 gene pairs) and segmental (12 gene pairs) were identified and subjected to purifying selection. All PeNAC proteins exhibited similar 3D structures, and a protein-protein interaction network analysis with known Arabidopsis proteins was predicted. Furthermore, 17 putative ped-miRNAs were identified to target 25 PeNAC genes. Potential TFs including ERF, BBR-BPC, Dof, and bZIP were identified in promoter region of all 105 PeNAC genes and visualized in a TF regulatory network. GO and KEGG annotation analysis exposed that PeNAC genes were related to different biological, molecular, and cellular terms. The qRT-PCR expression analysis discovered that most of the PeNAC genes including PeNAC001, PeNAC003, PeNAC008, PeNAC028, PeNAC033, PeNAC058, PeNAC063, and PeNAC077 were significantly upregulated under Fusarium kyushuense and drought stress conditions compared to controls. In conclusion, these findings lay the foundation for further functional studies of PeNAC genes to facilitate the genetic improvement of plants to stress resistance.

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.

MicroRNA-mediated host defense mechanisms against pathogens and herbivores in rice: balancing gains from genetic resistance with trade-offs to productivity potential

BACKGROUND

Rice (Oryza sativa L.) is the major source of daily caloric intake for more than 30% of the human population. However, the sustained productivity of this staple food crop is continuously threatened by various pathogens and herbivores. Breeding has been successful in utilizing various mechanisms of defense by gene pyramiding in elite cultivars, but the continuous resurgence of highly resistant races of pathogens and herbivores often overcomes the inherent capacity of host plant immunity. MicroRNAs (miRNAs) are endogenous, short, single-stranded, non-coding RNA molecules that regulate gene expression by sequence-specific cleavage of target mRNA or suppressing target mRNA translation. While miRNAs function as upstream regulators of plant growth, development, and host immunity, their direct effects on growth and development in the context of balancing defenses with agronomic potential have not been extensively discussed and explored as a more viable strategy in breeding for disease and pest resistant cultivars of rice with optimal agronomic potentials.

RESULTS

Using the available knowledge in rice and other model plants, this review examines the important roles of miRNAs in regulating host responses to various fungal, bacterial, and viral pathogens, and insect pests, in the context of gains and trade-offs to crop yield. Gains from R-gene-mediated resistance deployed in modern rice cultivars are often undermined by the rapid breakdown of resistance, negative pleiotropic effects, and linkage drags with undesirable traits. In stark contrast, several classes of miRNAs are known to efficiently balance the positive gains from host immunity without significant costs in terms of losses in agronomic potentials (i.e., yield penalty) in rice. Defense-related miRNAs such as Osa-miR156, Osa-miR159, Osa-miR162, Osa-miR396, Osa-530, Osa-miR1432, Osa-miR1871, and Osa-miR1873 are critical in fine-tuning and integrating immune responses with physiological processes that are necessary to the maintenance of grain yield. Recent research has shown that many defense-related miRNAs regulate complex and agronomically important traits.

CONCLUSIONS

Identification of novel immune-responsive miRNAs that orchestrate physiological processes critical to the full expression of agronomic potential will facilitate the stacking of optimal combinations of miRNA-encoding genes to develop high-yielding cultivars with durable resistance to disease and insect pests with minimal penalties to yield.

Cadmium in Cereal Crops: Uptake and Transport Mechanisms and Minimizing Strategies

Cadmium (Cd) contamination in soils and accumulation in cereal grains have posed food security risks and serious health concerns worldwide. Understanding the Cd transport process and its management for minimizing Cd accumulation in cereals may help to improve crop growth and grain quality. In this review, we summarize Cd uptake, translocation, and accumulation mechanisms in cereal crops and discuss efficient measures to reduce Cd uptake as well as potential remediation strategies, including the applications of plant growth regulators, microbes, nanoparticles, and cropping systems and developing low-Cd grain cultivars by CRISPR/Cas9. In addition, miRNAs modulate Cd translocation, and accumulation in crops through the regulation of their target genes was revealed. Combined use of multiple remediation methods may successfully decrease Cd concentrations in cereals. The findings in this review provide some insights into innovative and applicable approaches for reducing Cd accumulation in cereal grains and sustainable management of Cd-contaminated paddy fields.

Regulatory role of microRNAs (miRNAs) in the recent development of abiotic stress tolerance of plants

MicroRNAs (miRNAs) are a distinct groups of single-stranded non-coding, tiny regulatory RNAs approximately 20-24 nucleotides in length. miRNAs negatively influence gene expression at the post-transcriptional level and have evolved considerably in the development of abiotic stress tolerance in a number of model plants and economically important crop species. The present review aims to deliver the information on miRNA-mediated regulation of the expression of major genes or Transcription Factors (TFs), as well as genetic and regulatory pathways. Also, the information on adaptive mechanisms involved in plant abiotic stress responses, prediction, and validation of targets, computational tools, and databases available for plant miRNAs, specifically focus on their exploration for engineering abiotic stress tolerance in plants. The regulatory function of miRNAs in plant growth, development, and abiotic stresses consider in this review, which uses high-throughput sequencing (HTS) technologies to generate large-scale libraries of small RNAs (sRNAs) for conventional screening of known and novel abiotic stress-responsive miRNAs adds complexity to regulatory networks in plants. The discoveries of miRNA-mediated tolerance to multiple abiotic stresses, including salinity, drought, cold, heat stress, nutritional deficiency, UV-radiation, oxidative stress, hypoxia, and heavy metal toxicity, are highlighted and discussed in this review.

The miR166 mediated regulatory module controls plant height by regulating gibberellic acid biosynthesis and catabolism in soybean

MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play critical roles in regulating plant growth and development. Here, we used Short Tandem Target Mimic (STTM) technology to generate soybean (Glycine max (L.) Merr.) miRNA knockdown lines and identify miRNAs that regulate plant height, a key agronomic trait that affects yield. STTM166 successfully silenced miR166 in soybean and upregulated the expression of miR166 target genes, such as ATHB14-LIKE. The miR166 knockdown lines (GmSTTM166) displayed a reduced plant height phenotype. Moreover, GmSTTM166 plants contained lower levels of bioactive gibberellic acid (GA3) than wild-type plants, and application of exogenous GA partially rescued the dwarf phenotype of GmSTTM166. Knockdown of miR166 altered the expression of genes involved in GA biosynthesis and catabolism. Further analysis revealed that ATHB14-LIKE directly represses transcription of the GA biosynthesis genes GmGA1 and GmGA2, while activating transcription of the GA catabolic gene GIBBERLLIN 2 OXIDASE 2 (GmGA2ox2). Collectively, these results reveal a pivotal role for miR166 in the genetic control of plant height in soybean, thereby providing invaluable insights for molecular breeding to improve soybean yield.

GABA-mediated inhibition of cadmium uptake and accumulation in apples

GABA, a four-carbon non-protein amino acid, plays an important role in animals and plants. We previously found GABA could alleviate alkali stress in apple seedlings. However, its physiological mechanism under heavy metal cadmium (Cd) stress need to be further studied. Thus, we explored its biological role in response to Cd stress. It was verified that 0.5 mM GABA could effectively alleviate Cd toxicity. Using NMT technique, we found that exogenous GABA could significantly reduce the net Cd²⁺ fluxes in apple roots, and Cd content was significantly lower than that in roots under Cd stress. Further analysis indicated exogenous GABA could significantly reduce the expression of genes related to the uptake and transport of Cd in apples under Cd stress. In addition, exogenous GABA could significantly increase the content of amino acids in apple roots under Cd stress. GAD is a key enzyme in GABA synthesis, we obtained transgenic apple roots of overexpression MdGAD1. Compared with the control, transgenic roots accumulated less Cd, maintained lower Cd uptake by roots, and lower expression of related transport genes. These results showed that GABA could effectively alleviate Cd toxicity in apple seedlings and provide a new perspective of GABA to alleviate Cd stress.

A Glucuronic Acid-Producing Endophyte Pseudomonas sp. MCS15 Reduces Cadmium Uptake in Rice by Inhibition of Ethylene Biosynthesis

Dynamic regulation of phytohormone levels is pivotal for plant adaptation to harmful conditions. It is increasingly evidenced that endophytic bacteria can regulate plant hormone levels to help their hosts counteract adverse effects imposed by abiotic and biotic stresses, but the mechanisms underlying the endophyte-induced stress resistance of plants remain largely elusive. In this study, a glucuronic acid-producing endophyte Pseudomonas sp. MCS15 alleviated cadmium (Cd) toxicity in rice plants. Inoculation with MCS15 significantly inhibited the expression of ethylene biosynthetic genes including OsACO3, OsACO4, OsACO5, OsACS2, and OsACS5 and thus reduced the content of ethylene in rice roots. In addition, the expression of iron uptake-related genes including OsIRT1, OsIRT2, OsNAS1, OsNAS2 and OsYSL15 was significantly downregulated in the MCS15-inoculated roots under Cd stress. Similarly, glucuronic acid treatment also remarkably inhibited root uptake of Cd and reduced the production of ethylene. However, treatment with 1-aminocyclopropyl carboxylic acid (ACC), a precursor of ethylene, almost abolished the MCS15 or glucuronic acid-induced inhibition of Cd accumulation in rice plants. Conversely, treatment with aminoethoxyvinyl glycine (AVG), an inhibitor of ethylene biosynthesis, markedly reduced the Cd accumulation in plants. Taken together, our results revealed that the endophytic bacteria MCS15-secreted glucuronic acid inhibited the biosynthesis of ethylene and thus weakened iron uptake-related systems in rice roots, which contributed to preventing the Cd accumulation.

An Integration of MicroRNA and Transcriptome Sequencing Analysis Reveal Regulatory Roles of miRNAs in Response to Chilling Stress in Wild Rice

A chromosome single segment substitution line (CSSL) DC90, which was generated by introgressing CTS-12, a locus derived from common wild rice (Oryza rufipogon Griff.), into the 9311 (Oryza sativa L. ssp. indica) background, exhibits a chilling tolerance phenotype under chilling stress. Here, an integration of microRNA (miRNA) deep sequencing and transcriptomic sequencing analysis was performed to explore the expression profiles of miRNAs and their target genes mediated by CTS-12 under chilling stress, and to reveal the possible regulatory mechanisms of miRNAs that are involved in chilling tolerance. Integration analysis revealed that a number of differentially expressed miRNAs (DEMs) and putative target genes with different expression patterns and levels were identified in 9311 and DC90 under chilling stress. KEGG enrichment analysis revealed that the target genes that are regulated by chilling-induced miRNAs are involved in the regulation of various biological processes/pathways, including protein biosynthesis, redox process, photosynthetic process, and chloroplast development in two genotypes. CRISPR/Cas9 editing of the target genes of the key DEMs in a chilling tolerant rice variety Zhonghua 11 (ZH11) found that LOC_Os11g48020 (OsGL1-11), one of the putative target genes of osa-miR1846a/b-5p and encoding a wax synthesis protein, is correlated with a chilling stress tolerance phenotype, implying osa-miR1846a/b-5p/OsGL1-11 plays an important role in CTS-12-mediated chilling stress tolerance regulatory pathway(s). Therefore, we speculate that the CTS-12 may regulate the key miRNA target genes in response to chilling stress by differential regulation of miRNAs in wild rice, thereby resulting in the variation of chilling tolerance phenotype between 9311 and DC90.

Ectopic Expression of JcCPL1, 2, and 4 Affects Epidermal Cell Differentiation, Anthocyanin Biosynthesis and Leaf Senescence in Arabidopsis thaliana

The CAPRICE (CPC)-like (CPL) genes belong to a single-repeat R3 MYB family, whose roles in physic nut (Jatropha curcas L.), an important energy plant, remain unclear. In this study, we identified a total of six CPL genes (JcCPL1–6) in physic nut. The JcCPL3, 4, and 6 proteins were localized mainly in the nucleus, while proteins JcCPL1, 2, and 5 were localized in both the nucleus and the cytoplasm. Ectopic overexpression of JcCPL1, 2, and 4 in Arabidopsis thaliana resulted in an increase in root hair number and decrease in trichome number. Consistent with the phenotype of reduced anthocyanin in shoots, the expression levels of anthocyanin biosynthesis genes were down-regulated in the shoots of these three transgenic A. thaliana lines. Moreover, we observed that OeJcCPL1, 2, 4 plants attained earlier leaf senescence, especially at the late developmental stage. Consistent with this, the expression levels of several senescence-associated and photosynthesis-related genes were, respectively, up-regulated and down-regulated in leaves. Taken together, our results indicate functional divergence of the six CPL proteins in physic nut. These findings also provide insight into the underlying roles of CPL transcription factors in leaf senescence.

Catalase (CAT) Gene Family in Wheat (Triticum aestivum L.): Evolution, Expression Pattern and Function Analysis

Catalases (CATs) are present in almost all living organisms and play important roles in plant development and response to various stresses. However, there is relatively little information on CAT genes in wheat and related Triticeae species. A few studies on CAT family genes in wheat have been reported. In this study, ten CAT proteins (TaCATs) were identified in wheat and classified into three groups based on their phylogenetic features and sequence analysis. The analysis of the structure and motif composition of the TaCAT proteins suggested that a segmental duplication event occurred in the TaCAT gene family. Collinearity relationship analysis among different species showed that there were three orthologous CAT genes in rice and in maize. By analyzing the cis-elements in the promoter regions, we speculated that TaCAT genes expression might be regulated by light, oxygen deficit, methyl jasmonate and abscisic acid, and by transcription factors such as MYB. A Gene Ontology (GO)-based analysis showed that TaCAT proteins may be related to the response to various stresses, are cytoplasm localized, and may function as antioxidant enzymes. RT-qPCR and transcriptome data analyses exhibited distinct expression patterns of TaCAT genes in different tissues and in response to various treatments. In this study, a comprehensive analysis of wheat CAT genes was performed, enriching our knowledge of CAT genes and providing a foundation for further functional analyses of this gene family in wheat.

Toxic metals and metalloids: Uptake, transport, detoxification, phytoremediation, and crop improvement for safer food

Agricultural soils are under threat of toxic metal/metalloid contamination from anthropogenic activities, leading to excessive accumulation of arsenic (As), cadmium (Cd), lead (Pb), and mercury (Hg) in food crops that poses significant risks to human health. Understanding how these toxic metals and their methylated species are taken up, translocated, and detoxified is prerequisite to developing strategies to limit their accumulation for safer food. Toxic metals are taken up and transported across different cellular compartments and plant tissues via various transporters for essential or beneficial nutrients, e.g. As by phosphate and silicon transporters, and Cd by manganese (Mn), zinc (Zn), and iron (Fe) transporters. These transport processes are subjected to interactions with nutrients and the regulation at the transcriptional and post-translational levels. Complexation with thiol-rich compounds, such as phytochelatins, and sequestration in the vacuoles are the common mechanisms for detoxification and for limiting their translocation. A number of genes involved in toxic metal uptake, transport, and detoxification have been identified, offering targets for genetic manipulation via gene editing or transgenic technologies. Natural variations in toxic metal accumulation exist within crop germplasm, and some of the quantitative trait loci underlying these variations have been cloned, paving the way for marker-assisted breeding of low metal accumulation crops. Using plants to extract and remove toxic metals from soil is also possible, but this phytoremediation approach requires metal hyperaccumulation for efficiency. Knowledge gaps and future research needs are also discussed.

Identification of microRNAs Responding to Aluminium, Cadmium and Salt Stresses in Barley Roots

Plants are frequently exposed to various abiotic stresses, including aluminum, cadmium and salinity stress. Barley (Hordeum vulgare) displays wide genetic diversity in its tolerance to various abiotic stresses. In this study, small RNA and degradome libraries from the roots of a barley cultivar, Golden Promise, treated with aluminum, cadmium and salt or controls were constructed to understand the molecular mechanisms of microRNAs in regulating tolerance to these stresses. A total of 525 microRNAs including 198 known and 327 novel members were identified through high-throughput sequencing. Among these, 31 microRNAs in 17 families were responsive to these stresses, and Gene Ontology (GO) analysis revealed that their targeting genes were mostly highlighted as transcription factors. Furthermore, five (miR166a, miR166a-3p, miR167b-5p, miR172b-3p and miR390), four (MIR159a, miR160a, miR172b-5p and miR393) and three (miR156a, miR156d and miR171a-3p) microRNAs were specifically responsive to aluminum, cadmium and salt stress, respectively. Six miRNAs, i.e., miR156b, miR166a-5p, miR169a, miR171a-5p, miR394 and miR396e, were involved in the responses to the three stresses, with different expression patterns. A model of microRNAs responding to aluminum, cadmium and salt stresses was proposed, which may be helpful in comprehensively understanding the mechanisms of microRNAs in regulating stress tolerance in barley.

RNA-Seq Identification of Cd Responsive Transporters Provides Insights into the Association of Oxidation Resistance and Cd Accumulation in Cucumis sativus L

Greenhouse vegetable production (GVP) has grown rapidly and has become a major force for cucumber production in China. In highly intensive GVP systems, excessive fertilization results in soil acidification, increasing Cd accumulation and oxidative stress damage in vegetables as well as increasing health risk of vegetable consumers. Therefore, enhancing antioxidant capacity and activating the expression level of Cd transporter genes seem to be feasible solutions to promote plant resistance to Cd stress and to reduce accumulated Cd concentration. Here, we used transcriptomics to identify five cucumber transporter genes (CsNRAMP1, CsNRAMP4, CsHMA1, CsZIP1, and CsZIP8) in response to cadmium stress, which were involved in Cd transport activity in yeast. Ionomics, gene expression, and REDOX reaction level association analyses have shown that the transcript of CsNRAMP4 was positively correlated with Cd accumulation and antioxidant capacity of cucumber roots. The expression level of CsHMA1 was negatively correlated with Cd-induced antioxidant capacity. The overexpression of CsHMA1 significantly relieved Cd stress-induced antioxidant activities. In addition, shoots with high CsHMA2 expression remarkably presented Cd bioaccumulation. Grafting experiments confirmed that CsHMA1 contributed to the high antioxidant capacity of cucumber, while CsHMA2 was responsible for the transport of Cd from the roots to the shoots. Our study elucidated a novel regulatory mechanism for Cd transport and oxidative damage removal in horticultural melons and provided a perspective to regulate Cd transport artificially by modulating Cd accumulation and resistance in plants.

MicroRNA-mediated bioengineering for climate-resilience in crops

Global projections on the climate change and the dynamic environmental perturbations indicate severe impacts on food security in general, and crop yield, vigor and the quality of produce in particular. Sessile plants respond to environmental challenges such as salt, drought, temperature, heavy metals at transcriptional and/or post-transcriptional levels through the stress-regulated network of pathways including transcription factors, proteins and the small non-coding endogenous RNAs. Amongs these, the miRNAs have gained unprecedented attention in recent years as key regulators for modulating gene expression in plants under stress. Hence, tailoring of miRNAs and their target pathways presents a promising strategy for developing multiple stress-tolerant crops. Plant stress tolerance has been successfully achieved through the over expression of microRNAs such as Os-miR408, Hv-miR82 for drought tolerance; OsmiR535A and artificial DST miRNA for salinity tolerance; and OsmiR535 and miR156 for combined drought and salt stress. Examples of miR408 overexpression also showed improved efficiency of irradiation utilization and carbon dioxide fixation in crop plants. Through this review, we present the current understanding about plant miRNAs, their roles in plant growth and stress-responses, the modern toolbox for identification, characterization and validation of miRNAs and their target genes including in silico tools, machine learning and artificial intelligence. Various approaches for up-regulation or knock-out of miRNAs have been discussed. The main emphasis has been given to the exploration of miRNAs for development of bioengineered climate-smart crops that can withstand changing climates and stressful environments, including combination of stresses, with very less or no yield penalties.

Combined Stress Conditions in Melon Induce Non-additive Effects in the Core miRNA Regulatory Network

Climate change has been associated with a higher incidence of combined adverse environmental conditions that can promote a significant decrease in crop productivity. However, knowledge on how a combination of stresses might affect plant development is still scarce. MicroRNAs (miRNAs) have been proposed as potential targets for improving crop productivity. Here, we have combined deep-sequencing, computational characterization of responsive miRNAs and validation of their regulatory role in a comprehensive analysis of response of melon to several combinations of four stresses (cold, salinity, short day, and infection with a fungus). Twenty-two miRNA families responding to double and/or triple stresses were identified. The regulatory role of the differentially expressed miRNAs was validated by quantitative measurements of the expression of the corresponding target genes. A high proportion (ca. 60%) of these families (mainly highly conserved miRNAs targeting transcription factors) showed a non-additive response to multiple stresses in comparison with that observed under each one of the stresses individually. Among those miRNAs showing non-additive response to stress combinations, most interactions were negative, suggesting the existence of functional convergence in the miRNA-mediated response to combined stresses. Taken together, our results provide compelling pieces of evidence that the response to combined stresses cannot be easily predicted from the study individual stresses.