Identification of wild soybean miRNAs and their target genes responsive to aluminum stress

Genome-wide identification and expression profile analysis of metal tolerance protein gene family in Eucalyptus grandis under metal stresses

Metal tolerance proteins (MTPs) as Me²⁺/H⁺(K⁺) antiporters participate in the transport of divalent cations, leading to heavy metal stress resistance and mineral utilization in plants. In the present study, to obtain better knowledge of the biological functions of the MTPs family, 20 potential EgMTPs genes were identified in Eucalyptus grandis and classified into seven groups belonging to three cation diffusion facilitator groups (Mn-CDFs, Zn/Fe-CDFs, and Zn-CDFs) and seven groups. EgMTP-encoded amino acids ranged from 315 to 884, and most of them contained 4-6 recognized transmembrane domains and were clearly prognosticated to localize into the cell vacuole. Almost all EgMTP genes experienced gene duplication events, in which some might be uniformly distributed in the genome. The numbers of cation efflux and the zinc transporter dimerization domain were highest in EgMTP proteins. The promoter regions of EgMTP genes have different cis-regulatory elements, indicating that the transcription rate of EgMTP genes can be a controlled response to different stimuli in multiple pathways. Our findings provide accurate perception on the role of the predicted miRNAs and the presence of SSR marker in the Eucalyptus genome and clarify their functions in metal tolerance regulation and marker-assisted selection, respectively. Gene expression profiling based on previous RNA-seq data indicates a probable function for EgMTP genes during development and responses to biotic stress. Additionally, the upregulation of EgMTP6, EgMTP5, and EgMTP11.1 to excess Cd²⁺ and Cu²⁺ exposure might be responsible for metal translocation from roots to leaves.

microRNAomic profiling of maize root reveals multifaceted mechanisms to cope with Cr (VI) stress

Chromium (Cr) contamination of soil and water poses serious threats to agricultural crop production. MicroRNAs (miRNAs) are conserved, non-coding small RNAs that play pivotal roles in plant growth, development and stress responses through fine-tuning of post-transcriptional gene expression. To better understand the molecular circuit of Cr-responsive miRNAs, two sRNA libraries were prepared from control and Cr (VI) [100 ppm] exposed maize roots. Using deep sequencing, we identified 80 known (1 up and 79 down) and 18 downregulated novel miRNAs from Cr (VI) challenged roots. Gene ontology (GO) analysis reveals that predicted target genes of Cr (VI) responsive miRNAs are potentially involved in diverse cellular and biological processes including plant growth and development (miR159c, miR164d, miR319b-3p and zma_25.145), redox homeostasis (miR528-5p, miR396a-5p and zma_9.132), heavy metal uptake and detoxification (miR159f-5p, 164e-5p, miR408a, miR444f and zma_2.127), signal transduction (miR159f, miR160a-5p, miR393a-5p, miR408-5p and zma_43.158), cell signalling (miR156j, 159c-5p, miR166c-5p and miR398b). Higher accumulation of Cr in maize roots might be due to upregulation of ABC transporter G family member 29 targeted by miR444f. Instead of isolated increase in SOD expression, significant decline in GSH:GSSH ratio and histochemical staining strongly suggest Cr (VI) stress mediated disruption of ROS scavenging machinery thus unbalancing normal cellular homeostasis. Moreover, miR159c-mediated enhanced expression of GAMYB might be a reason for impaired root growth under Cr (VI) stress. In a nutshell, the present microRNAomic study sheds light on the miRNA-target gene regulatory network involved in adaptive responses of maize seedlings to Cr (VI) stress.

Comparative Transcriptome Profiling Reveals Key MicroRNAs and Regulatory Mechanisms for Aluminum Tolerance in Olive

Aluminum toxicity (Al) is one of the major constraints to crop production in acidic soils. MicroRNAs (miRNAs) have emerged as key regulatory molecules at post-transcriptional levels, playing crucial roles in modulating various stress responses in plants. However, miRNAs and their target genes conferring Al tolerance are poorly studied in olive (Olea europaea L.). Here, genome-wide expression changes in miRNAs of the roots from two contrasting olive genotypes Zhonglan (ZL, Al-tolerant) and Frantoio selezione (FS, Al-sensitive) were investigated by high-throughput sequencing approaches. A total of 352 miRNAs were discovered in our dataset, consisting of 196 conserved miRNAs and 156 novel miRNAs. Comparative analyses showed 11 miRNAs have significantly different expression patterns in response to Al stress between ZL and FS. In silico prediction identified 10 putative target gene of these miRNAs, including MYB transcription factors, homeobox-leucine zipper (HD-Zip) proteins, auxin response factors (ARF), ATP-binding cassette (ABC) transporters and potassium efflux antiporter. Further functional classification and enrichment analysis revealed these Al-tolerance associated miRNA-mRNA pairs are mainly involved in transcriptional regulation, hormone signaling, transportation and metabolism. These findings provide new information and perspectives into the regulatory roles of miRNAs and their target for enhancing Al tolerance in olives.

GsMYB7 encoding a R2R3-type MYB transcription factor enhances the tolerance to aluminum stress in soybean (Glycine max L.)

Background

MYB transcription factor (TF) is one of the largest families of TFs in plants and play essential roles in plant growth and development, and is involved in responses to biological and abiotic stress. However, there are few reports on GsMYB7 gene in soybean under aluminum acid stress, and its regulatory mechanism remains unclear.

Results

The GsMYB7 protein is localized in the nucleus and has transcriptional activation ability. Quantitative real-time PCR (qRT-PCR) results showed that GsMYB7 held a constitutive expression pattern rich in roots. When AlCl₃ concentration was 25 µM, the total root surface area (SA) of GsMYB7 transgenic lines were 34.97% higher than that of wild-type Huachun 6 (HC6). While the accumulation of Al³⁺ in root tip of transgenic plants after aluminum treatment was 17.39% lower than that of wild-type. RNA-sequencing analysis indicated that over 1181 genes were regulated by GsMYB7 and aluminum stress. Among all the regulated genes, the expression levels of glutathione peroxidase, protein kinase, cytochrome and other genes in the transgenic lines were significantly higher than those in wild type by acidic aluminum stress. The bioinformatics and qRT-PCR results showed that 9 candidate genes were induced under the treatments of acidic aluminum stress which were indirectly and/or directly regulated by GsMYB7. After AlCl₃ treatments, the transcripts of these genes in GsMYB7 transgenic seedlings were significantly higher than those of wide-type HC6.

Conclusions

The results suggested that GsMYB7 may enhance soybean tolerance to acidic aluminum stress by regulating the downstream genes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08744-w.

Roles of non-coding RNAs in the hormonal and nutritional regulation in nodulation and nitrogen fixation

Symbiotic nitrogen fixation is an important component in the nitrogen cycle and is a potential solution for sustainable agriculture. It is the result of the interactions between the plant host, mostly restricted to legume species, and the rhizobial symbiont. From the first encounter between the host and the symbiont to eventual successful nitrogen fixation, there are delicate processes involved, such as nodule organogenesis, rhizobial infection thread progression, differentiation of the bacteroid, deregulation of the host defense systems, and reallocation of resources. All these processes are tightly regulated at different levels. Recent evidence revealed that non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), participate in these processes by controlling the transcription and translation of effector genes. In general, ncRNAs are functional transcripts without translation potential and are important gene regulators. MiRNAs, negative gene regulators, bind to the target mRNAs and repress protein production by causing the cleavage of mRNA and translational silencing. LncRNAs affect the formation of chromosomal loops, DNA methylation, histone modification, and alternative splicing to modulate gene expression. Both lncRNAs and circRNAs could serve as target mimics of miRNA to inhibit miRNA functions. In this review, we summarized and discussed the current understanding of the roles of ncRNAs in legume nodulation and nitrogen fixation in the root nodule, mainly focusing on their regulation of hormone signal transduction, the autoregulation of nodulation (AON) pathway and nutrient homeostasis in nodules. Unraveling the mediation of legume nodulation by ncRNAs will give us new insights into designing higher-performance leguminous crops for sustainable agriculture.

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.

GmWRKY21, a Soybean WRKY Transcription Factor Gene, Enhances the Tolerance to Aluminum Stress in Arabidopsis thaliana

The WRKY transcription factors (TFs) are one of the largest families of TFs in plants and play multiple roles in plant growth and development and stress response. In this study, GmWRKY21 encoding a WRKY transcription factor was functionally characterized in Arabidopsis and soybean. The GmWRKY21 protein containing a highly conserved WRKY domain and a C₂H₂ zinc-finger structure is located in the nucleus and has the characteristics of transcriptional activation ability. The GmWRKY21 gene presented a constitutive expression pattern rich in the roots, leaves, and flowers of soybean with over 6-fold of relative expression levels and could be substantially induced by aluminum stress. As compared to the control, overexpression of GmWRKY21 in Arabidopsis increased the root growth of seedlings in transgenic lines under the AlCl₃ concentrations of 25, 50, and 100 μM with higher proline and lower MDA accumulation. The results of quantitative real-time polymerase chain reaction (qRT-PCR) showed that the marker genes relative to aluminum stress including ALMT, ALS3, MATE, and STOP1 were induced in GmWRKY21 transgenic plants under AlCl₃ treatment. The stress-related genes, such as KIN1, COR15A, COR15B, COR47, GLOS3, and RD29A, were also upregulated in GmWRKY21 transgenic Arabidopsis under aluminum stress. Similarly, stress-related genes, such as GmCOR47, GmDREB2A, GmMYB84, GmKIN1, GmGST1, and GmLEA, were upregulated in hair roots of GmWRKY21 transgenic plants. In summary, these results suggested that the GmWRKY21 transcription factor may promote the tolerance to aluminum stress mediated by the pathways regulating the expression of the acidic aluminum stress-responsive genes and abiotic stress-responsive genes.

GsERF1 enhances Arabidopsis thaliana aluminum tolerance through an ethylene-mediated pathway

Ethylene response factor (ERF) transcription factors constitute a subfamily of the AP2/ERF superfamily in plants and play multiple roles in plant growth and development as well as in stress responses. In this study, the GsERF1 gene from the wild soybean BW69 line (an Al-resistant Glycine soja line) was rapidly induced in response to aluminum stress. Quantitative real-time PCR (qRT-PCR) analysis showed that the GsERF1 gene maintained a constitutive expression pattern and was induced in soybean in response to aluminum stress, with increased amounts of transcripts detected in the roots. The putative GsERF1 protein, which contains an AP2 domain, was located in the nucleus and maintained transactivation activity. In addition, under AlCl3 treatment, GsERF1 overexpression increased the relative growth rate of the roots of Arabidopsis and weakened the hematoxylin staining of hairy roots. Ethylene synthesis-related genes such as ACS4, ACS5 and ACS6 were upregulated in GsERF1 transgenic lines compared with the wild type under AlCl3 treatment. Furthermore, the expression levels of stress/ABA-responsive marker genes, including ABI1, ABI2, ABI4, ABI5 and RD29B, in the GsERF1 transgenic lines were affected by AlCl3 treatment, unlike those in the wild type. Taken together, the results indicated that overexpression of GsERF1 may enhance aluminum tolerance of Arabidopsis through an ethylene-mediated pathway and/or ABA signaling pathway, the findings of which lay a foundation for breeding soybean plants tolerant to aluminum stress.

Small RNA Sequencing Revealed that miR4415, a Legume-Specific miRNA, was Involved in the Cold Acclimation of Ammopiptanthus nanus by Targeting an L-Ascorbate Oxidase Gene and Regulating the Redox State of Apoplast

MicroRNAs (miRNAs) are small endogenous single-stranded RNAs that regulate plant growth, development, and environmental stress response posttranscriptionally. Ammopiptanthus nanus, a rare evergreen broad-leaved shrub in the temperate area of Central Asia, can tolerate freezing stress as low as -30 degrees centigrade in winter, and miRNA might be involved in the cold acclimation which enables A. nanus to obtain tolerance to freezing stress. Systematic identification and functional analysis of the miRNAs involved in the cold acclimation in A. nanus may promote understanding of the miRNA-mediated gene regulation network underlying cold acclimation. Here, based on small RNA and degradome sequencing, 256 miRNAs and 1,808 miRNA-target pairs were identified in A. nanus. A total of 39 cold-responsive miRNAs were identified, of which 29 were upregulated and ten were downregulated. These cold-responsive miRNAs may participate in the cold acclimation by regulating redox homeostasis (miR398, miR4415, and miR408), calcium signaling (miR5225 and miR5211), growth and development (miR159 and miR390), and small RNA-mediated gene silencing (miR168 and miR1515). We found that miR4415, a legume-specific miRNA, is involved in the cold acclimation of A. nanus by targeting an L-ascorbate oxidase gene and then regulating the redox state of the apoplast. Our study provides important data for understanding the regulatory role of miRNA in the cold acclimation of A. nanus.

Application of exogenous glutathione decreases chromium translocation and alleviates its toxicity in soybean (Glycine max L.)

Chromium is considered one of the most severe toxic elements affecting agriculture. Soybean seedlings under chromium stress were treated with glutathione and buthionine sulfoximine. The effects of exogenous glutathione on the physiological effects of two different chromium-resistant soybean seedlings and the expression levels of expression levels related genes were studied. This study tested the seedling weight and SPAD values, detected enzymatic antioxidants (i.e., superoxide dismutase, peroxidase, catalase, catalase, ascorbate peroxidase), and non-enzymatic antioxidants (i.e., glutathione, proline, soluble sugars, and soluble phenols) that attenuate chromium-induced reactive oxygen species, and quantified several genes associated with glutathione-mediated chromium stress. The results showed that exogenous glutathione could improve the physiological adaptability of soybean seedlings by regulating photosynthesis, antioxidant, and related enzyme activities, osmotic system, the compartmentalization of ion chelation, and regulating the transcription level of related genes, thereby increasing the chromium accumulation of soybean seedlings, enhancing the tolerance of chromium stress, and reducing the toxicity of chromium. Overall, the application of glutathione alleviates chromium toxicity in soybeans, and this strategy may be a potential farming option for soybean bioremediation in chromium-contaminated soils.

Using the Knowledge of Post-transcriptional Regulations to Guide Gene Selections for Molecular Breeding in Soybean

The omics approaches allow the scientific community to successfully identify genomic regions associated with traits of interest for marker-assisted breeding. Agronomic traits such as seed color, yield, growth habit, and stress tolerance have been the targets for soybean molecular breeding. Genes governing these traits often undergo post-transcriptional modifications, which should be taken into consideration when choosing elite genes for molecular breeding. Post-transcriptional regulations of genes include transcript regulations, protein modifications, and even the regulation of the translational machinery. Transcript regulations involve elements such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) for the maintenance of transcript stability or regulation of translation efficiency. Protein modifications involve molecular modifications of target proteins and the alterations of their interacting partners. Regulations of the translational machinery include those on translation factors and the ribosomal protein complex. Post-transcriptional regulations usually involve a set of genes instead of a single gene. Such a property may facilitate molecular breeding. In this review, we will discuss the post-transcriptional modifications of genes related to favorable agronomic traits such as stress tolerance, growth, and nutrient uptake, using examples from soybean as well as other crops. The examples from other crops may guide the selection of genes for marker-assisted breeding in soybean.

Is Genetic Engineering a Route to Enhance Microalgae-Mediated Bioremediation of Heavy Metal-Containing Effluents?

Contamination of the biosphere by heavy metals has been rising, due to accelerated anthropogenic activities, and is nowadays, a matter of serious global concern. Removal of such inorganic pollutants from aquatic environments via biological processes has earned great popularity, for its cost-effectiveness and high efficiency, compared to conventional physicochemical methods. Among candidate organisms, microalgae offer several competitive advantages; phycoremediation has even been claimed as the next generation of wastewater treatment technologies. Furthermore, integration of microalgae-mediated wastewater treatment and bioenergy production adds favorably to the economic feasibility of the former process—with energy security coming along with environmental sustainability. However, poor biomass productivity under abiotic stress conditions has hindered the large-scale deployment of microalgae. Recent advances encompassing molecular tools for genome editing, together with the advent of multiomics technologies and computational approaches, have permitted the design of tailor-made microalgal cell factories, which encompass multiple beneficial traits, while circumventing those associated with the bioaccumulation of unfavorable chemicals. Previous studies unfolded several routes through which genetic engineering-mediated improvements appear feasible (encompassing sequestration/uptake capacity and specificity for heavy metals); they can be categorized as metal transportation, chelation, or biotransformation, with regulation of metal- and oxidative stress response, as well as cell surface engineering playing a crucial role therein. This review covers the state-of-the-art metal stress mitigation mechanisms prevalent in microalgae, and discusses putative and tested metabolic engineering approaches, aimed at further improvement of those biological processes. Finally, current research gaps and future prospects arising from use of transgenic microalgae for heavy metal phycoremediation are reviewed.

Identification of an ATP-Binding Cassette Transporter Implicated in Aluminum Tolerance in Wild Soybean (Glycine soja)

The toxicity of aluminum (Al) in acidic soil limits global crop yield. The ATP-binding cassette (ABC) transporter-like gene superfamily has functions and structures related to transportation, so it responds to aluminum stress in plants. In this study, one half-size ABC transporter gene was isolated from wild soybeans (Glycine soja) and designated GsABCI1. By real-time qPCR, GsABCI1 was identified as not specifically expressed in tissues. Phenotype identification of the overexpressed transgenic lines showed increased tolerance to aluminum. Furthermore, GsABCI1 transgenic plants exhibited some resistance to aluminum treatment by ion translocation or changing root components. This work on the GsABCI1 identified the molecular function, which provided useful information for understanding the gene function of the ABC family and the development of new aluminum-tolerant soybean germplasm.

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.

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.

Analysis of Cadmium-Stress-Induced microRNAs and Their Targets Reveals bra-miR172b-3p as a Potential Cd2+-Specific Resistance Factor in Brassica juncea

The contamination of soil with high levels of cadmium (Cd) is of increasing concern, as Cd is a heavy metal element that seriously limits crop productivity and quality, thus affecting human health. (1) Background: Some miRNAs play key regulatory roles in response to Cd stress, but few have been explored in the highly Cd-enriched coefficient oilseed crop, Brassica juncea. (2) Methods: The genome-wide identification and characterization of miRNAs and their targets in leaves and roots of Brassica juncea exposed to Cd stress was undertaken using strand specific transcript sequencing and miRNA sequencing. (3) Results: In total, 11 known and novel miRNAs, as well as 56 target transcripts, were identified as Cd-responsive miRNAs and transcripts. Additionally, four corresponding target transcripts of six miRNAs, including FLA9 (Fasciclin-Like Arabinogalactan-protein 9), ATCAT3 (catalase 3), DOX1 (dioxygenases) and ATCCS (copper chaperone for superoxide dismutase), were found to be involved in the plant’s biotic stress pathway. We further validated the expression of three miRNA and six target genes in response to Cd, hydrargyrum (Hg), manganese (Mn), plumbum (Pb) or natrium (Na) stress and Mucor infection by qRT-PCR, and show that ATCCS and FLA9 were significantly and differentially regulated in the Cd-treated leaves. In addition, our results showed that DOX1 was obviously induced by Pb stress. Among the respective target miRNAs, bra-miR172b-3p (target for ATCCS) and ra-miR398-3p (target for FLA9) were down-regulated in Cd-treated leaves. (4) Conclusions: We identified bra-miR172b-3p as a potential Cd-specific resistant inhibitor, which may be negatively regulated in ATCCS in response to Cd stress. These findings could provide further insight into the regulatory networks of Cd-responsive miRNA in Brassica juncea.

Transcriptome analysis reveals significant difference in gene expression and pathways between two peanut cultivars under Al stress

Aluminum (Al) toxicity is an important factor in limiting peanut growth on acidic soil. The molecular mechanisms underlying peanut responses to Al stress are largely unknown. In this study, we performed transcriptome analysis of the root tips (0-1 cm) of peanut cultivar ZH2 (Al-sensitive) and 99-1507 (Al-tolerant) respectively. Root tips of peanuts that treated with 100 μM Al for 8 h and 24 h were analyzed by RNA-Seq, and a total of 8,587 differentially expressed genes (DEGs) were identified. GO and KEGG pathway analysis excavated a group of important Al-responsive genes related to organic acid transport, metal cation transport, transcription regulation and programmed cell death (PCD). These homologs were promising targets to modulate Al tolerance in peanuts. It was found that the rapid transcriptomic response to Al stress in 99-1507 helped to activate effective Al tolerance mechanisms. Protein and protein interaction analysis indicated that MAPK signal transduction played important roles in the early response to Al stress in peanuts. Moreover, weighted correlation network analysis (WGCNA) identified a predicted EIL (EIN3-like) gene with greatly increased expression as an Al-associated gene, and revealed a link between ethylene signaling transduction and Al resistance related genes in peanut, which suggested the enhanced signal transduction mediated the rapid transcriptomic responses. Our results revealed key pathways and genes associated with Al stress, and improved the understanding of Al response in peanut.

Genome-Wide Identification of Copper Stress-Regulated and Novel MicroRNAs in Mulberry Leaf

Copper (Cu) is an essential trace element for plant growth and development. It is widely involved in respiration, photosynthesis, pollen formation, and other biological processes. Therefore, low or excessive copper causes damage to plants. Mulberry is an essential perennial economic tree. At present, research on the abiotic stress responses in mulberry is mainly focused on the identification of resistant germplasm resources and cloning of resistant genes. In contrast, studies on the resistance function of microRNAs and the regulatory gene responses to stress are rare. In this study, small RNA libraries (control and copper stressed) were constructed from mulberry leaf RNA. High-throughput sequencing and screening were employed, a total of 65 known miRNAs and 78 predicted novel mature miRNAs were identified, among which 40 miRNAs were differentially expressed under copper stress. Subsequently, expression patterns were verified for 14 miRNAs by real-time fluorescence quantitative PCR (qPCR). The target genes of miRNAs were validated by 5' RLM-RACE. Our results provide the bases for further study on the molecular mechanism of copper stress regulation in mulberry.

Origin and Evolutionary Dynamics of the miR2119 and ADH1 Regulatory Module in Legumes

MicroRNAs are important regulators of gene expression in eukaryotes. Previously, we reported that in Phaseolus vulgaris, the precursor for miR2119 is located in the same gene as miR398a, conceiving a dicistronic MIR gene. Both miRNA precursors are transcribed and processed from a single transcript resulting in two mature microRNAs that regulate the mRNAs encoding ALCOHOL DEHYDROGENASE 1 (ADH1) and COPPER-ZINC SUPEROXIDE DISMUTASE 1 (CSD1). Genes for miR398 are distributed throughout the spermatophytes; however, miR2119 is only found in Leguminosae species, indicating its recent emergence. Here, we used public databases to explore the presence of the miR2119 sequence in several plant species. We found that miR2119 is present only in specific clades within the Papilionoideae subfamily, including important crops used for human consumption and forage. Within this subfamily, MIR2119 and MIR398a are found together as a single gene in the genomes of the Millettioids and Hologalegina. In contrast, in the Dalbergioids MIR2119 is located in a different locus from MIR398a, suggesting this as the ancestral genomic organization. To our knowledge, this is a unique example where two separate MIRNA genes have merged to generate a single polycistronic gene. Phylogenetic analysis of ADH1 gene sequences in the Papilionoideae subfamily revealed duplication events resulting in up to four ADH1 genes in certain species. Notably, the presence of MIR2119 correlates with the conservation of target sites in particular ADH1 genes in each clade. Our results suggest that post-transcriptional regulation of ADH1 genes by miR2119 has contributed to shaping the expansion and divergence of this gene family in the Papilionoideae. Future experimental work on ADH1 regulation by miR2119 in more legume species will help to further understand the evolutionary history of the ADH1 gene family and the relevance of miRNA regulation in this process.

Heterologous Expression of a Glycine soja C2H2 Zinc Finger Gene Improves Aluminum Tolerance in Arabidopsis

Aluminum (Al) toxicity limits plant growth and has a major impact on the agricultural productivity in acidic soils. The zinc-finger protein (ZFP) family plays multiple roles in plant development and abiotic stresses. Although previous reports have confirmed the function of these genes, their transcriptional mechanisms in wild soybean (Glycine soja) are unclear. In this study, GsGIS3 was isolated from Al-tolerant wild soybean gene expression profiles to be functionally characterized in Arabidopsis. Laser confocal microscopic observations demonstrated that GsGIS3 is a nuclear protein, containing one C2H2 zinc-finger structure. Our results show that the expression of GsGIS3 was of a much higher level in the stem than in the leaf and root and was upregulated under AlCl3, NaCl or GA3 treatment. Compared to the control, overexpression of GsGIS3 in Arabidopsis improved Al tolerance in transgenic lines with more root growth, higher proline and lower Malondialdehyde (MDA) accumulation under concentrations of AlCl3. Analysis of hematoxylin staining indicated that GsGIS3 enhanced the resistance of transgenic plants to Al toxicity by reducing Al accumulation in Arabidopsis roots. Moreover, GsGIS3 expression in Arabidopsis enhanced the expression of Al-tolerance-related genes. Taken together, our findings indicate that GsGIS3, as a C2H2 ZFP, may enhance tolerance to Al toxicity through positive regulation of Al-tolerance-related genes.

GsMAS1 Encoding a MADS-box Transcription Factor Enhances the Tolerance to Aluminum Stress in Arabidopsis thaliana

The MADS-box transcription factors (TFs) are essential in regulating plant growth and development, and conferring abiotic and metal stress resistance. This study aims to investigate GsMAS1 function in conferring tolerance to aluminum stress in Arabidopsis. The GsMAS1 from the wild soybean BW69 line encodes a MADS-box transcription factor in Glycine soja by bioinformatics analysis. The putative GsMAS1 protein was localized in the nucleus. The GsMAS1 gene was rich in soybean roots presenting a constitutive expression pattern and induced by aluminum stress with a concentration-time specific pattern. The analysis of phenotypic observation demonstrated that overexpression of GsMAS1 enhanced the tolerance of Arabidopsis plants to aluminum (Al) stress with larger values of relative root length and higher proline accumulation compared to those of wild type at the AlCl3 treatments. The genes and/or pathways regulated by GsMAS1 were further investigated under Al stress by qRT-PCR. The results indicated that six genes resistant to Al stress were upregulated, whereas AtALMT1 and STOP2 were significantly activated by Al stress and GsMAS1 overexpression. After treatment of 50 μM AlCl3, the RNA abundance of AtALMT1 and STOP2 went up to 17-fold and 37-fold than those in wild type, respectively. Whereas the RNA transcripts of AtALMT1 and STOP2 were much higher than those in wild type with over 82% and 67% of relative expression in GsMAS1 transgenic plants, respectively. In short, the results suggest that GsMAS1 may increase resistance to Al toxicity through certain pathways related to Al stress in Arabidopsis.

Comparative Analysis of miRNA Expression Profiles Between Heat-Tolerant and Heat-Sensitive Genotypes of Flowering Chinese Cabbage Under Heat Stress Using High-Throughput Sequencing

Heat stress disturbs cellular homeostasis, thus usually impairs yield of flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee). MicroRNAs (miRNAs) play a significant role in plant responses to different stresses by modulating gene expression at the post-transcriptional level. However, the roles that miRNAs and their target genes may play in heat tolerance of flowering Chinese cabbage remain poorly characterized. The current study sequenced six small RNA libraries generated from leaf tissues of flowering Chinese cabbage collected at 0, 6, and 12 h after 38 °C heat treatment, and identified 49 putative novel miRNAs and 43 known miRNAs that differentially expressed between heat-tolerant and heat-sensitive flowering Chinese cabbage. Among them, 14 novel and nine known miRNAs differentially expressed only in the heat-tolerant genotype under heat-stress, therefore, their target genes including disease resistance protein TAO1-like, RPS6, reticuline oxidase-like protein, etc. might play important roles in enhancing heat-tolerance. Gene Ontology (GO) analysis revealed that targets of these differentially expressed miRNAs may play key roles in responses to temperature stimulus, cell part, cellular process, cell, membrane, biological regulation, binding, and catalytic activities. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis identified their important functions in signal transduction, environmental adaptation, global and overview maps, as well as in stress adaptation and in MAPK signaling pathways such as cell death. These findings provide insight into the functions of the miRNAs in heat stress tolerance of flowering Chinese cabbage.

Plant microRNAs: biogenesis, gene silencing, web-based analysis tools and their use as molecular markers

MicroRNAs (miRNAs) are tiny (20-24 nt bp) regulatory non-protein-coding RNA molecules that have been extensively characterized and found important for many physiological and developmental processes. The miss-expression of miRNAs leads to various defects in plants. MicroRNAs repress gene expression by directing mRNA degradation or translational arrest. Several proteins such as PP43A, HYL1, DCL, HST are indispensable role players in promoting miRNA biogenesis in plants. During miRNA biogenesis, lariat RNAs are produced as by-products of pre-mRNA splicing which have a negative role in regulation of miRNA homeostasis. By acting as a decoy and by sequestering to the dicing complex, lariat RNA can prevent the processing of miRNAs. A number of bioinformatic tools with different methodologies are available to identify and validate miRNAs and their targets. Many miRNAs have been reported in different crops for different traits; however, no reports are available on their use in plant breeding. Recently, researchers have developed trait specific miRNA-based molecular markers (miRNA-SSRs/SNP) for many quantitative traits in different plant species. In the future, these molecular markers can be used for plant breeding programs. In this review, a comprehensive up-to-date information is provided on the bioinformatic tools used for analysis of plant miRNAs and their targets, the number of miRNAs, their biogenesis, gene silencing mechanism and miRNA-based molecular markers.

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.

Identification of miRNAs and Their Response to Cold Stress in Astragalus Membranaceus

Astragalus membranaceus is an important medicinal plant widely cultivated in East Asia. MicroRNAs (miRNAs) are endogenous regulatory molecules that play essential roles in plant growth, development, and the response to environmental stresses. Cold is one of the key environmental factors affecting the yield and quality of A. membranaceus, and miRNAs may mediate the gene regulation network under cold stress in A. membranaceus. To identify miRNAs and reveal their functions in cold stress response in A. membranaceus, small RNA sequencing was conducted followed by bioinformatics analysis, and quantitative real time PCR (qRT-PCR) analysis was performed to profile the expression of miRNAs under cold stress. A total of 168 conserved miRNAs belonging to 34 families and 14 putative non-conserved miRNAs were identified. Many miRNA targets were predicted and these targets were involved in diversified regulatory and metabolic pathways. By using qRT-PCR, 27 miRNAs were found to be responsive to cold stress, including 4 cold stress-induced and 17 cold-repressed conserved miRNAs, and 6 cold-induced non-conserved miRNAs. These cold-responsive miRNAs probably mediate the response to cold stress by regulating development, hormone signaling, defense, redox homeostasis, and secondary metabolism in A. membranaceus. These cold-corresponsive miRNAs may be used as the candidate genes in further molecular breeding for improving cold tolerance of A. membranaceus.

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.

Genome-wide identification and characterization of the metal tolerance protein (MTP) family in grape (Vitis vinifera L.)

Metal tolerance proteins (MTPs) play an important role in the transport of metals at the cellular, tissue and whole plant levels. In the present study, 11 MTP genes were identified and these clustered in three major sub-families Fe/Zn-MTP, Zn-MTP, and Mn-MTP, and seven groups, which are similar to the grouping of MTP genes in both Arabidopsis and rice. Vitis vinifera metal tolerance proteins (VvMTP) ranged from 366 to 1092 amino acids, were predicted to be located in the cell vacuole, and had four to six putative TMDs, except for VvtMTP12 and VvMTP1. The VvMTPs had putative cation diffusion facilitator (CDF) domains and the putative Mn-MTPs also had zinc transporter dimerization domains (ZD-domains). V. vinifera Mn-MTPs had gene structures and motif distributions similar to those of the Fe/Zn-MTP and Zn-MTP sub-families. The upstream regions of VvMTP genes had variable frequencies of cis-regulatory elements that could indicate regulation at different developmental stages and/or differential regulation in response to stress. Comparison of the VvMTP coding sequences with known miRNAs found in various plant species indicated the presence of 13 putative miRNAs, with 7 of these associated with VvMTPs. Temporal and spatial expression profiling indicates a potential role for VvMTP genes during growth and development in grape plants, as well as the involvement of these genes in plant responses to environmental stress, especially osmotic stress. The data generated from this study provides a basis for further investigation of the roles of MTP genes in grapes.

Molecular Mechanisms for Coping with Al Toxicity in Plants

Aluminum (Al) toxicity is one of the major constraints to agricultural production in acid soils. Molecular mechanisms of coping with Al toxicity have now been investigated in a range of plant species. Two main mechanisms of Al tolerance in plants are Al exclusion from the roots and the ability to tolerate Al in the roots. This review focuses on the recent discovery of novel genes and mechanisms that confer Al tolerance in plants and summarizes our understanding of the physiological, genetic, and molecular basis for plant Al tolerance. We hope this review will provide a theoretical basis for the genetic improvement of Al tolerance in plants.

Bioinformatic Exploration of the Targets of Xylem Sap miRNAs in Maize under Cadmium Stress

Cadmium (Cd) has the potential to be chronically toxic to humans through contaminated crop products. MicroRNAs (miRNAs) can move systemically in plants. To investigate the roles of long-distance moving xylem miRNAs in regulating maize response to Cd stress, three xylem sap small RNA (sRNA) libraries were constructed for high-throughput sequencing to identify potential mobile miRNAs in Cd-stressed maize seedlings and their putative targets in maize transcriptomes. In total, about 199 miRNAs (20–22 nucleotides) were identified in xylem sap from maize seedlings, including 97 newly discovered miRNAs and 102 known miRNAs. Among them, 10 miRNAs showed differential expression in xylem sap after 1 h of Cd treatment. Two miRNAs target prediction tools, psRNAtarget (reporting the inhibition pattern of cleavage) and DPMIND (discovering Plant MiRNA-Target Interaction with degradome evidence), were used in combination to identify, via bioinformatics, the targets of 199 significantly expressed miRNAs in maize xylem sap. The integrative results of these two bioinformatic tools suggested that 27 xylem sap miRNAs inhibit 34 genes through cleavage with degradome evidence. Moreover, nearly 300 other genes were also the potential miRNAs cleavable targets without available degradome data support, and the majority of them were enriched in abiotic stress response, cell signaling, transcription regulation, as well as metal handling. These approaches and results not only enhanced our understanding of the Cd-responsive long-distance transported miRNAs from the view of xylem sap, but also provided novel insights for predicting the molecular genetic mechanisms mediated by miRNAs.

GmWRKY16 Enhances Drought and Salt Tolerance Through an ABA-Mediated Pathway in Arabidopsis thaliana

The WRKY transcription factors (TFs) are one of the largest families of TFs in plants and play multiple roles in plant development and stress response. In the present study, GmWRKY16 encoding a WRKY transcription factor in soybean was functionally characterized in Arabidopsis. GmWRKY16 is a nuclear protein that contains a highly conserved WRKY domain and a C2H2 zinc-finger structure, and has the characteristics of transcriptional activation ability, presenting a constitutive expression pattern with relative expression levels of over fourfold in the old leaves, flowers, seeds and roots of soybean. The results of quantitative real time polymerase chain reaction (qRT-PCR) showed that GmWRKY16 could be induced by salt, alkali, ABA, drought and PEG-6000. As compared with the control, overexpression of GmWRKY16 in Arabidopsis increased the seed germination rate and root growth of seedlings in transgenic lines under higher concentrations of mannitol, NaCl and ABA. In the meantime, GmWRKY16 transgenic lines showed over 75% survival rate after rehydration and enhanced Arabidopsis tolerance to salt and drought with higher proline and lower MDA accumulation, less water loss of the detached leaves, and accumulated more endogenous ABA than the control under stress conditions. Further studies showed that AtWRKY8, KIN1, and RD29A were induced in GmWRKY16 transgenic plants under NaCl treatment. The expressions of the ABA biosynthesis gene (NCED3), signaling genes (ABI1, ABI2, ABI4, and ABI5), responsive genes (RD29A, COR15A, COR15B, and RD22) and stress-related marker genes (KIN1, LEA14, LEA76, and CER3) were regulated in transgenic lines under drought stress. In summary, these results suggest that GmWRKY16 as a WRKY TF may promote tolerance to drought and salt stresses through an ABA-mediated pathway.

Identification of copper (Cu) stress-responsive grapevine microRNAs and their target genes by high-throughput sequencing

MicroRNAs (miRNAs) are a class of single-stranded non-coding small RNAs (sRNAs) that are 20-24 nucleotides (nt) in length. Extensive studies have indicated that miRNAs play important roles in plant growth, development and stress responses. With more copper (Cu) and copper containing compounds used as bactericides and fungicides in plants, Cu stress has become one of the serious environmental problems that affect plant growth and development. In order to uncover the hidden response mechanisms of Cu stress, two small RNA libraries were constructed from Cu-treated and water-treated (Control) leaves of 'Summer Black' grapevine. Following high-throughput sequencing and filtering, a total of 158 known and 98 putative novel miRNAs were identified in the two libraries. Among these, 100 known and 47 novel miRNAs were identified as differentially expressed under Cu stress. Subsequently, the expression patterns of nine Cu-responsive miRNAs were validated by quantitative real-time PCR (qRT-PCR). There existed some consistency in expression levels of Cu-responsive miRNAs between high throughput sequencing and qRT-PCR assays. The targets prediction of miRNAs indicates that miRNA may regulate some transcription factors, including AP2, SBP, NAC, MYB and ARF during Cu stress. The target genes for two known and two novel miRNAs showed specific cleavage sites at the 10th and/or 11th nucleotide from the 5'-end of the miRNA corresponding to their miRNA complementary sequences. The findings will lay the foundation for exploring the role of the regulation of miRNAs in response to Cu stress and provide valuable gene information for breeding some Cu-tolerant grapevine cultivars.

Deep sequencing identified potential miRNAs involved in defence response, stress and plant growth characteristics of wild genotypes of cardamom

Cardamom has long been used as a food flavouring agent and in ayurvedic medicines for mouth ulcers, digestive problems and even depression. Extensive occurrence of pests and diseases adversely affect its cultivation and result in substantial reductions in total production and productivity. Numerous studies revealed the significant role of miRNAs in plant biotic stress responses. In the current study, miRNA profiling of cultivar and wild cardamom genotypes was performed using an Ion Proton sequencer. We identified 161 potential miRNAs representing 42 families, including monocot/tissue-specific and 14 novel miRNAs in both genotypes. Significant differences in miRNA family abundance between the libraries were observed in read frequencies. A total of 19 miRNAs (from known miRNAs) displayed a twofold difference in expression between wild and cultivar genotypes. We found 1168 unique potential targets for 40 known miRNA families in wild and 1025 potential targets for 42 known miRNA families in cultivar genotypes. The differential expression analysis revealed that most miRNAs identified were highly expressed in cultivars and, furthermore, lower expression of miR169 and higher expression of miR529 in wild cardamom proved evidence that wild genotypes have stronger drought stress tolerance and floral development than cultivars. Potential targets predicted for the newly identified miRNAs from the miRNA libraries of wild and cultivar cardamom genotypes involved in metabolic and developmental processes and in response to various stimuli. qRT-PCR confirmed miRNAs were differentially expressed between wild and cultivar genotypes. Furthermore, four target genes were validated experimentally to confirm miRNA-mRNA target pairing using RNA ligase-mediated 5' Rapid Amplification of cDNA Ends (5'RLM-RACE) PCR.

GsMATE encoding a multidrug and toxic compound extrusion transporter enhances aluminum tolerance in Arabidopsis thaliana

BACKGROUND

Multidrug and toxic compound extrusion (MATE) transporters, which exist widely in plants, function as crucial regulators in plant resistance to aluminum (Al) toxicity by inducing citrate efflux. However, the functions of most MATE family members in soybean (Glycine soja) remain to be elucidated.

RESULTS

Expression pattern analysis showed that GsMATE was constitutively expressed in different soybean organs, with the highest level in root compared with those in stem, leaf and cotyledon. In addition, Al stress induced expression of GsMATE in soybean. Temporal analysis indicated that GsMATE expression was greatly enhanced by increasing concentrations of aluminum [Al3+] after short exposure, reaching the high levels detected in the BW69 (Al-resistant) and the JW81 (Al-sensitive) lines of Glycine soja of wild soybean at 6 h and 8 h, respectively. Furthermore, transient GsMATE expression in Arabidopsis protoplasts showed that GsMATE protein localized to the plasma membrane. Overexpression of GsMATE on an Arabidopsis columbia-0 (Col-0) background resulted in increased Al tolerance in transgenic plants. Analysis of hematoxylin staining showed that the roots of GsMATE transgenic lines were stained less intensely than those of the wild-type exposured to the same AlCl3 concentrations. Therefore, GsMATE enhanced the resistance of transgenic plants to Al toxicity by reducing Al accumulation in Arabidopsis roots.

CONCLUSIONS

In summary, our results indicate that GsMATE is responsive to aluminum stress and may participate in the regulation of sensitivity to Al toxicity in Arabidopsis. In addition, the GsMATE protein is an Al-induced citrate transporter of the MATE family and exerts an essential role in Al tolerance in Glycine soja.

Genome-Wide Analysis of Glycine soja Response Regulator GsRR Genes Under Alkali and Salt Stresses

Soil salt-alkalization is a dramatic challenging factor for plant growth. Wild soybean (Glycine soja) exhibits a favorable trait of superior tolerance to salt-alkali stress, and recent discoveries show that response regulator family genes are involved in diverse abiotic stresses. Genomic and transcriptomic analyses of all response regulator genes in wild soybean will provide insight into their function in plant stress response. In this study, we identified and characterized a total of 56 Glycine soja response regulator (GsRR) genes. Phylogenetic analysis suggested that GsRR genes could be classified into five subclasses (A1, A2, B1, B2, and C). We further investigated the chromosome locations, gene duplications and conserved domains of the GsRRs. Furthermore, the clustering analysis of GsRR transcript profiles revealed five different expression patterns under alkali stress. The A1 and A2 subclasses display significantly higher transcriptional levels than the B subclass. In addition, quantitative real-time PCR results verified that the GsRR genes were also significantly influenced by salt stress. Notably, GsRR2a in the A1 subclass showed opposite expression patterns under salt stress comparing with alkali stress. Moreover, overexpression of GsRR2a in Arabidopsis significantly improved the tolerance to alkali stress, but not salt stress. These results suggest the important roles of GsRR genes in response to salt and alkaline stresses, and also provide valuable clues for further functional characterization of GsRR family genes.

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.

Genome-wide analysis and expression profiling of PP2C clade D under saline and alkali stresses in wild soybean and Arabidopsis

Protein phosphatase 2Cs (PP2Cs) belong to the largest protein phosphatase family in plants. Some members have been described as being negative modulators of plant growth and development, as well as responses to hormones and environmental stimuli. However, little is known about the members of PP2C clade D, which may be involved in the regulation of signaling pathways, especially in response to saline and alkali stresses. Here, we identified 13 PP2C orthologs from the wild soybean (Glycine soja) genome. We examined the sequence characteristics, chromosome locations and duplications, gene structures, and promoter cis-elements of the PP2C clade D genes in Arabidopsis and wild soybean. Our results showed that GsPP2C clade D (GsAPD) genes exhibit more gene duplications than AtPP2C clade D genes. Plant hormone and abiotic stress-responsive elements were identified in the promoter regions of most PP2C genes. Moreover, we investigated their expression patterns in roots, stems, and leaves. Quantitative real-time PCR analyses revealed that the expression levels of representative GsPP2C and AtPP2C clade D genes were significantly influenced by alkali and salt stresses, suggesting that these genes might be associated with or directly involved in the relevant stress signaling pathways. Our results established a foundation for further functional characterization of PP2C clade D genes in the future.

Molecular regulation of aluminum resistance and sulfur nutrition during root growth

Aluminum toxicity and sulfate deprivation both regulate microRNA395 expression, repressing its low-affinity sulfate transporter ( SULTR2;1 ) target. Sulfate deprivation also induces the high-affinity sulfate transporter gene ( SULTR12 ), allowing enhanced sulfate uptake. Few studies about the relationships between sulfate, a plant nutrient, and aluminum, a toxic ion, are available; hence, the molecular and physiological processes underpinning this interaction are poorly understood. The Al-sulfate interaction occurs in acidic soils, whereby relatively high concentrations of trivalent toxic aluminum (Al³⁺) may hamper root growth, limiting uptake of nutrients, including sulfur (S). On the other side, Al³⁺ may be detoxified by complexation with sulfate in the acid soil solution as well as in the root-cell vacuoles. In this review, we focus on recent insights into the mechanisms governing plant responses to Al toxicity and its relationship with sulfur nutrition, emphasizing the role of phytohormones, microRNAs, and ion transporters in higher plants. It is known that Al³⁺ disturbs gene expression and enzymes involved in biosynthesis of S-containing cysteine in root cells. On the other hand, Al³⁺ may induce ethylene biosynthesis, enhance reactive oxygen species production, alter phytohormone transport, trigger root growth inhibition and promote sulfate uptake under S deficiency. MicroRNA395, regulated by both Al toxicity and sulfate deprivation, represses its low-affinity Sulfate Transporter 2;1 (SULTR2;1) target. In addition, sulfate deprivation induces High Affinity Sulfate Transporters (HAST; SULTR1;2), improving sulfate uptake from low-sulfate soil solutions. Identification of new microRNAs and cloning of their target genes are necessary for a better understanding of the role of molecular regulation of plant resistance to Al stress and sulfate deprivation.

The miR172c-NNC1 module modulates root plastic development in response to salt in soybean

BACKGROUND

Plant roots are highly plastic to high salinity. However, the molecular mechanism by which root developmental plasticity is regulated remains largely unknown. Previously we reported that miR172c-NNC1 module plays a key role in soybean-rhizobial symbiosis. The fact that the miR172c promoter contains several stress-related cis elements indicates that miR172c may have a role in root response to abiotic stress.

RESULTS

Here we showed that miR172c is greatly induced by salt stress in soybean. Overexpression of miR172c and knockdown of miR172c activity resulted in substantially increased and reduced root sensitivity to salt stress, respectively. Furthermore, we show that the target gene NNC1 (Nodule Number Control 1) of miR172c was downregulated by salt stress. The transgenic roots overexpressing or knocking down NNC1 expression also exhibited the altered root sensitivity to salt stress.

CONCLUSION

The study reveals the crucial role of miR172c-NNC1 module in root stress tolerance to salt stress in soybean.

MAPK-mediated auxin signal transduction pathways regulate the malic acid secretion under aluminum stress in wheat (Triticum aestivum L.)

An isobaric tags for relative and absolute quantitative (iTRAQ)-based quantitative proteomic approach was used to screen the differentially expressed proteins during control treatment (CK), aluminum (Al) and Al⁺ indole-3-acetic acid (IAA) treatment of wheat lines ET8 (Al-tolerant). Further, the the expression levels of auxin response factor (ARF), Aux/IAA, Mitogen activated protein kinase (MAPK) 2c, and MAPK1a were analyzed. Results showed that 16 proteins were determined to be differentially expressed in response to Al and IAA co-treatment compared with Al alone. Among them, MAPK2c and MAPK1a proteins displayed markedly differential expression during the processes. The expression of ARF2 was upregulated and Aux/IAA was downregulated by Al, while both in concentration- and time-dependent manners. Western-blot detection of MAPK2c and MAPK1a indicated that Al upregulated MAPK2c and downregulated MAPK1a in both concentration- and time-dependent manners. Exogenous IAA could promote the expression of MAPK2c, but inhibit the expression of MAPK1a in the presence/absence of Al. These findings indicated that IAA acted as one of the key signaling molecule controls the response mechanism of wheat malic acid efflux to Al stress through the suppression/activation of Aux/IAA and ARFs, and the activity of MAPK2c and MAPK1a were positively or negatively regulated.

Abiotic stress miRNomes in the Triticeae

The continued growth in world population necessitates increases in both the quantity and quality of agricultural production. Triticeae members, particularly wheat and barley, make an important contribution to world food reserves by providing rich sources of carbohydrate and protein. These crops are grown over diverse production environments that are characterized by a range of environmental or abiotic stresses. Abiotic stresses such as drought, heat, salinity, or nutrient deficiencies and toxicities cause large yield losses resulting in economic and environmental damage. The negative effects of abiotic stresses have increased at an alarming rate in recent years and are predicted to further deteriorate due to climate change, land degradation, and declining water supply. New technologies have provided an important tool with great potential for improving crop tolerance to the abiotic stresses: microRNAs (miRNAs). miRNAs are small regulators of gene expression that act on many different molecular and biochemical processes such as development, environmental adaptation, and stress tolerance. miRNAs can act at both the transcriptional and post-transcriptional levels, although post-transcriptional regulation is the most common in plants where miRNAs can inhibit the translation of their mRNA targets via complementary binding and cleavage. To date, expression of several miRNA families such as miR156, miR159, and miR398 has been detected as responsive to environmental conditions to regulate stress-associated molecular mechanisms individually and/or together with their various miRNA partners. Manipulation of these miRNAs and their targets may pave the way to improve crop performance under several abiotic stresses. Here, we summarize the current status of our knowledge on abiotic stress-associated miRNAs in members of the Triticeae tribe, specifically in wheat and barley, and the miRNA-based regulatory mechanisms triggered by stress conditions. Exploration of further miRNA families together with their functions under stress will improve our knowledge and provide opportunities to enhance plant performance to help us meet global food demand.

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.

Using genomic information to improve soybean adaptability to climate change

Climate change has brought severe challenges to agriculture. It is anticipated that there will be a drop in crop yield - including that of soybean - due to climatic stress factors that include drastic fluctuations in temperature, drought, flooding and high salinity. Genomic information on soybean has been accumulating rapidly since initial publication of its reference genome, providing a valuable tool for the improvement of cultivated soybean. Not only are many molecular markers that are associated with important quantitative trait loci now identified, but we also have a more detailed picture of the genomic variations among soybean germplasms, enabling us to utilize these as tools to assist crop breeding. In this review, we will summarize and discuss the currently available soybean genomic approaches, including whole-genome sequencing, sequencing-based genotyping, functional genomics, proteomics, and epigenomics. The information uncovered through these techniques will help further pinpoint important gene candidates and genomic loci associated with adaptive traits, as well as achieving a better understanding of how soybeans cope with the changing climate.