Genome-wide identification of Thellungiella salsuginea microRNAs with putative roles in the salt stress response

Profiling of conserved orthologs and miRNAs for understanding their role in salt tolerance mechanism of Sesuvium portulacastrum L

BACKGROUND

Sesuvium portulacastrum is a facultative halophyte capable of thriving in a saline environment. Despite molecular studies conducted to unravel its salt adaptation mechanism, there is a paucity of information on the role of salt-responsive orthologs and microRNAs (miRNAs) in this halophyte. Here, we searched the orthology to identify salt-responsive orthologs and miRNA targets of Sesuvium using the Arabidopsis genome.

METHODS

The relative fold change of orthologs, conserved miRNAs, and miRNA targets of Sesuvium was analyzed under 100 mM (LS) and 250 mM NaCl (HS) treatment at 24 h using qRT-PCR. The comparison between the expression of Sesuvium orthologs and Arabidopsis orthologs (Arabidopsis eFP browser database) was used to identify differentially expressed genes.

RESULTS

Upon salt treatment, we found that SpCIPK3 (1.95-fold in LS and 2.90-fold in HS) in Sesuvium roots, and SpNHX7 (1.61-fold in LS and 6.39-fold in HS) and, SpSTPK2 (2.54-fold in LS and 7.65-fold in HS) in Sesuvium leaves were upregulated in a salt concentration-specific manner. In Arabidopsis, these genes were either downregulated or did not show significant variation, implicating its significance in the halophytic nature of Sesuvium. Furthermore, miRNAs like miR394a, miR396a, and miR397a exhibited a negative correlation with their targets-Frigida interacting protein 1, Cysteine proteinases superfamily protein, and Putative laccase, respectively under different salt treatments.

CONCLUSION

The study revealed that the high salt tolerance in Sesuvium is associated with distinct transcriptional reprogramming, hence, to gain holistic mechanistic insights, global-scale profiling is required.

Rapid sequence and functional diversification of a miRNA superfamily targeting calcium signaling components in seed plants

MicroRNA (miRNA)-directed posttranscriptional gene silencing (miR-PTGS) is an integral component of gene regulatory networks governing plant development and responses to the environment. The sequence homology between Sly-miR4376, a miRNA common to Solanaceae and reported to target autoinhibited Ca²⁺ -ATPase 10 (ACA10) messenger RNA (mRNA) in tomato, and Arabidopsis miR391 (Ath-miR391), previously annotated as a nonconserved member of the deeply conserved miR390 family, has prompted us to revisit the function of Ath-miR391, as well as its regulatory conservation. A combination of genetic, molecular, and bioinformatic analyses revealed a hidden conservation for miR-PTGS of ACA10 homologs in spermatophytes. We found that the Arabidopsis ACA10 mRNA undergoes miR391-directed cleavage in vivo. Furthermore, transgenic overexpression of miR391 recapitulated the compact inflorescence (cif) phenotypes characteristic of ACA10 loss-of-function mutants, due to miR391-directed PTGS of ACA10. Significantly, comprehensive data mining revealed robust evidence for widespread PTGS of ACA10 homologs directed by a superfamily of related miRNAs sharing a conserved sequence core. Intriguingly, the ACA-targeting miRNAs in Poaceae also direct PTGS for calmodulin-like proteins which are putative Ca²⁺ sensors. The PTGS of ACA10 homologs is therefore directed by a miRNA superfamily that is of ancient origin and has undergone rapid sequence diversification associated with functional innovation.

Adaptative Mechanisms of Halophytic Eutrema salsugineum Encountering Saline Environment

Salt cress (Eutrema salsugineum), an Arabidopsis-related halophyte, can naturally adapt to various harsh climates and soil conditions; thus, it is considered a desirable model plant for deciphering mechanisms of salt and other abiotic stresses. Accumulating evidence has revealed that compared with Arabidopsis, salt cress possesses stomata that close more tightly and more succulent leaves during extreme salt stress, a noticeably higher level of proline, inositols, sugars, and organic acids, as well as stress-associated transcripts in unstressed plants, and they are induced rapidly under stress. In this review, we systematically summarize the research on the morphology, physiology, genome, gene expression and regulation, and protein and metabolite profile of salt cress under salt stress. We emphasize the latest advances in research on the genome adaptive evolution encountering saline environments, and epigenetic regulation, and discuss the mechanisms underlying salt tolerance in salt cress. Finally, we discuss the existing questions and opportunities for future research in halophytic Eutrema. Together, the review fosters a better understanding of the mechanism of plant salt tolerance and provides a reference for the research and utilization of Eutrema as a model extremophile in the future. Furthermore, the prospects for salt cress applied to explore the mechanism of salt tolerance provide a theoretical basis to develop new strategies for agricultural biotechnology.

Biopriming of Durum Wheat Seeds with Endophytic Diazotrophic Bacteria Enhances Tolerance to Fusarium Head Blight and Salinity

There is growing interest in the use of bio inoculants based on plant growth-promoting bacteria (PGPB) to promote plant growth under biotic and abiotic stresses. Here, we provided a detailed account of the effectiveness of a number of endophytic PGPB strains, isolated from the roots of the halophyte Salicornia brachiata in promoting durum wheat growth and enhancing its tolerance to salinity and fusarium head blight (FHB) disease. Bacillus spp. strains MA9, MA14, MA17, and MA19 were found to have PGPB characteristics as they produced indole-3-acetic acid, siderophores, and lytic enzymes, fixed free atmospheric nitrogen, and solubilized inorganic phosphate in vitro. Additionally, the in vivo study that involved in planta inoculation assays under control and stress conditions indicated that all PGPB strains significantly (p < 0.05) increased the total plant length, dry weight, root area, seed weight, and nitrogen, protein, and mineral contents. Particularly, the MA17 strain showed a superior performance since it was the most efficient in reducing disease incidence in wheat explants by 64.5%, in addition to having the strongest plant growth promotion activity under salt stress. Both in vitro and in vivo assays showed that MA9, MA14, MA17, and MA19 strains were able to play significant PGPB roles. However, biopriming with Bacillus subtilis MA17 offered the highest plant growth promotion and salinity tolerance, and bioprotection against FHB. Hence, it would be worth testing the MA17 strain under field conditions as a step towards its commercial production. Moreover, the strain could be further assessed for its plausible role in bioprotection and growth promotion in other crop plants. Thus, it was believed that the strain has the potential to significantly contribute to wheat production in arid and semi-arid regions, especially the salt-affected Middle Eastern Region, in addition to its potential role in improving wheat production under biotic and abiotic stresses in other parts of the world.

Eutrema EsMYB90 Gene Improves Growth and Antioxidant Capacity of Transgenic Wheat Under Salinity Stress

The ectopic expression of the EsMYB90 transcription factor gene from halophytic Eutrema salsugineum has been reported to enhance the level of anthocyanin and other flavonoid metabolites in transgenic tobacco. In this study, the wheat JW1 overexpressing EsMYB90 showed longer roots and higher fresh weight than that in wild type (WT) under salt stress. In addition, the transgenic wheat plants displayed significantly higher peroxidase (POD) and glutathione S-transferase (GST) activity, as well as markedly lower malondialdehyde (MDA) content than that of the WT during salt stress conditions. The analysis of histochemical staining and H₂O₂ level indicated that the accumulation of reactive oxygen species (ROS) was significantly lower in the roots of transgenic wheat plants compared to the WT under salt stress. Transcriptome analysis revealed that the EsMYB90 gene affected the expression of considerable amounts of stress-related genes that were involved in phenylpropanoid biosynthesis and antioxidant activity in transgenic plants subjected to NaCl treatment. Importantly, the significantly upregulated expression genes in transgenic wheat under salt stress were mainly associated with the antioxidative enzymes POD and GST encoding genes compared with the WT. Furthermore, EsMYB90 is suggested to bind with the MYB-binding elements of pTaANS2 and pTaDFR1 by dual luciferase assay, to activate the transcription of TaANS2 and TaDFR1 genes that are encoding key enzymes of anthocyanin biosynthesis in transgenic wheat plants. All the results indicated that, under salt stress, the EsMYB90 gene plays a crucial role in preventing wheat seedlings from oxidative stress damage via enhancing the accumulation of non-enzymatic flavonoids and activities of antioxidative enzymes, which suggested that EsMYB90 is an ideal candidate gene for the genetic engineering of crops.

Impact of Nanomaterials on the Regulation of Gene Expression and Metabolomics of Plants under Salt Stress

Plant salinity resistance results from a combination of responses at the physiological, molecular, cellular, and metabolic levels. This article focuses on plant stress tolerance mechanisms for controlling ion homeostasis, stress signaling, hormone metabolism, anti-oxidative enzymes, and osmotic balance after nanoparticle applications. Nanoparticles are used as an emerging tool to stimulate specific biochemical reactions related to plant ecophysiological output because of their small size, increased surface area and absorption rate, efficient catalysis of reactions, and adequate reactive sites. Regulated ecophysiological control in saline environments could play a crucial role in plant growth promotion and survival of plants under suboptimal conditions. Plant biologists are seeking to develop a broad profile of genes and proteins that contribute to plant salt resistance. These plant metabolic profiles can be developed due to advancements in genomic, proteomic, metabolomic, and transcriptomic techniques. In order to quantify plant stress responses, transmembrane ion transport, sensors and receptors in signaling transduction, and metabolites involved in the energy supply require thorough study. In addition, more research is needed on the plant salinity stress response based on molecular interactions in response to nanoparticle treatment. The application of nanoparticles as an aspect of genetic engineering for the generation of salt-tolerant plants is a promising area of research. This review article addresses the use of nanoparticles in plant breeding and genetic engineering techniques to develop salt-tolerant crops.

MicroRNAs in Woody Plants

MicroRNAs (miRNAs) are small (∼21-nucleotides) non-coding RNAs found in plant and animals. MiRNAs function as critical post-transcriptional regulators of gene expression by binding to complementary sequences in their target mRNAs, leading to mRNA destabilization and translational inhibition. Plant miRNAs have some distinct characteristics compared to their animal counterparts, including greater evolutionary conservation and unique miRNA processing methods. The lifecycle of a plant begins with embryogenesis and progresses through seed germination, vegetative growth, reproductive growth, flowering and fruiting, and finally senescence and death. MiRNAs participate in the transformation of plant growth and development and directly monitor progression of these processes and the expression of certain morphological characteristics by regulating transcription factor genes involved in cell growth and differentiation. In woody plants, a large and rapidly increasing number of miRNAs have been identified, but their biological functions are largely unknown. In this review, we summarize the progress of miRNA research in woody plants to date. In particular, we discuss the potential roles of these miRNAs in growth, development, and biotic and abiotic stresses responses in woody plants.

Identification and Functional Characterization of Plant MiRNA Under Salt Stress Shed Light on Salinity Resistance Improvement Through MiRNA Manipulation in Crops

Salinity, as a major environmental stressor, limits plant growth, development, and crop yield remarkably. However, plants evolve their own defense systems in response to salt stress. Recently, microRNA (miRNA) has been broadly studied and considered to be an important regulator of the plant salt-stress response at the post-transcription level. In this review, we have summarized the recent research progress on the identification, functional characterization, and regulatory mechanism of miRNA involved in salt stress, have discussed the emerging manipulation of miRNA to improve crop salt resistance, and have provided future direction for plant miRNA study under salt stress, suggesting that the salinity resistance of crops could be improved by the manipulation of microRNA.

Effect of red light on photosynthetic acclimation and the gene expression of certain light signalling components involved in the microRNA biogenesis in the extremophile Eutrema salsugineum

The photosynthetic acclimation of extremophile Eutrema salsugineum plants to red light (RL) (14 days, 150 μmol photons m^-2 s^-1, 660 nm) and the expression of the key photoreceptor apoprotein genes, transcription factors (TFs) and associated with phytochrome system MIR (microRNA) genes were studied. RL exposure induced an increase in the content of anthocyanin and total phenolic compounds and the level of Chls was decreased. The photosystem 2 electron transport rate and the number of open reaction centres (q_L) were not changed in RL plants, however, the levels of non-photochemical quenching (NPQ) and the regulated quantum yield of non-photochemical quenching Y(NPQ) were significantly higher in the RL plants. The rate of CO₂ uptake was decreased by almost 1.4-fold but the respiration and transpiration rates, as well as the stomatal conductance were not changed in the RL plants. An increase in the expression of the photoreceptor apoprotein genes PHYA, PHYB and PHYC, the TF genes PIF4, PIF5 and miR395, miR408, miR165 and decreases in the levels of the transcripts of the TF gene HY5 and miR171, miR157, and miR827 were detected. The acclimation effect of photosynthetic apparatus to RL was accompanied by an increase of pigment content such as total phenolic compounds and carotenoids and it is due to the changes in the expression of the apoprotein phytochrome genes PHYA, PHYB, PHYC and phytochrome signalling TFs (PIF4, PIF5 and HY5) as well as MIR genes associated with phytochrome system.

Gene duplication and stress genomics in Brassicas: Current understanding and future prospects

Polyploidy or whole genome duplication (WGD) is an evolutionary phenomenon that happened in all angiosperms multiple times over millions of years. Extensive studies on the model plant Arabidopsis thaliana genome have revealed that it has undergone five rounds of WGDs followed, in the Brassicaceae tribe, by a characteristic whole genome triplication (WGT). In addition, small-scale events such as tandem or segmental duplications and retrotransposition also enable plants to reshape their genomes. Over the decades, extensive research efforts have been undertaken to understand the evolutionary significance of polyploidy. On the other hand, much less attention has been paid to understanding the impact of gene duplication on the diversification of important stress response genes. The main objective of this review is to discuss key aspects of gene and genome duplications with a focus on genes primarily regulated by osmotic stresses. The focal family is the Brassicaceae, since it (i) underwent multiple rounds of WGDs plus WGTs, (ii) hosts many economically important crops and wild relatives that are tolerant to a range of stresses, and (iii) comprises many species that have already been sequenced. Diverse molecular mechanisms that lead to structural and regulatory alterations of duplicated genes are discussed. Examples are drawn from recent literature to elucidate expanded, stress responsive gene families identified from different Brassica crops. A combined bioinformatic and transcriptomic method has been proposed and tested on a known stress-responsive gene pair to prove that stress-responsive duplicated allelic variants can be identified by this method. Finally, future prospects for engineering these genes into crops to enhance stress tolerance are discussed, and important resources for Brassica genome research are provided.

Abiotic stress signalling in extremophile land plants

Plant life relies on complex arrays of environmental stress sensing and signalling mechanisms. Extremophile plants develop and grow in harsh environments with extremes of cold, heat, drought, desiccation, or salinity, which have resulted in original adaptations. In accordance with their polyphyletic origins, extremophile plants likely possess core mechanisms of plant abiotic stress signalling. However, novel properties or regulations may have emerged in the context of extremophile adaptations. Comparative omics of extremophile genetic models, such as Arabidopsis lyrata, Craterostigma plantagineum, Eutrema salsugineum, and Physcomitrella patens, reveal diverse strategies of sensing and signalling that lead to a general improvement in abiotic stress responses. Current research points to putative differences of sensing and emphasizes significant modifications of regulatory mechanisms, at the level of secondary messengers (Ca2+, phospholipids, reactive oxygen species), signal transduction (intracellular sensors, protein kinases, transcription factors, ubiquitin-mediated proteolysis) or signalling crosstalk. Involvement of hormone signalling, especially ABA signalling, cell homeostasis surveillance, and epigenetic mechanisms, also shows that large-scale gene regulation, whole-plant integration, and probably stress memory are important features of adaptation to extreme conditions. This evolutionary and functional plasticity of signalling systems in extremophile plants may have important implications for plant biotechnology, crop improvement, and ecological risk assessment under conditions of climate change.

Integrated small RNA and Degradome sequencing provide insights into salt tolerance in sesame (Sesamum indicum L.)

BACKGROUND

MicroRNAs (miRNAs) exhibit important regulatory roles in the response to abiotic stresses by post-transcriptionally regulating the target gene expression in plants. However, their functions in sesame response to salt stress are poorly known. To dissect the complex mechanisms underlying salt stress response in sesame, miRNAs and their targets were identified from two contrasting sesame genotypes by a combined analysis of small RNAs and degradome sequencing.

RESULTS

A total of 351 previously known and 91 novel miRNAs were identified from 18 sesame libraries. Comparison of miRNA expressions between salt-treated and control groups revealed that 116 miRNAs were involved in salt stress response. Using degradome sequencing, potential target genes for some miRNAs were also identified. The combined analysis of all the differentially expressed miRNAs and their targets identified miRNA-mRNA regulatory networks and 21 miRNA-mRNA interaction pairs that exhibited contrasting expressions in sesame under salt stress.

CONCLUSIONS

This comprehensive integrated analysis may provide new insights into the genetic regulation mechanism of miRNAs underlying the adaptation of sesame to salt stress.

Plant science's next top models

BACKGROUND

Model organisms are at the core of life science research. Notable examples include the mouse as a model for humans, baker's yeast for eukaryotic unicellular life and simple genetics, or the enterobacteria phage λ in virology. Plant research was an exception to this rule, with researchers relying on a variety of non-model plants until the eventual adoption of Arabidopsis thaliana as primary plant model in the 1980s. This proved to be an unprecedented success, and several secondary plant models have since been established. Currently, we are experiencing another wave of expansion in the set of plant models.

SCOPE

Since the 2000s, new model plants have been established to study numerous aspects of plant biology, such as the evolution of land plants, grasses, invasive and parasitic plant life, adaptation to environmental challenges, and the development of morphological diversity. Concurrent with the establishment of new plant models, the advent of the 'omics' era in biology has led to a resurgence of the more complex non-model plants. With this review, we introduce some of the new and fascinating plant models, outline why they are interesting subjects to study, the questions they will help to answer, and the molecular tools that have been established and are available to researchers.

CONCLUSIONS

Understanding the molecular mechanisms underlying all aspects of plant biology can only be achieved with the adoption of a comprehensive set of models, each of which allows the assessment of at least one aspect of plant life. The model plants described here represent a step forward towards our goal to explore and comprehend the diversity of plant form and function. Still, several questions remain unanswered, but the constant development of novel technologies in molecular biology and bioinformatics is already paving the way for the next generation of plant models.

Integrated small RNA and mRNA expression profiles reveal miRNAs and their target genes in response to Aspergillus flavus growth in peanut seeds

BACKGROUND

MicroRNAs are important gene expression regulators in plants immune system. Aspergillus flavus is the most common causal agents of aflatoxin contamination in peanuts, but information on the function of miRNA in peanut-A. flavus interaction is lacking. In this study, the resistant cultivar (GT-C20) and susceptible cultivar (Tifrunner) were used to investigate regulatory roles of miRNAs in response to A. flavus growth.

RESULTS

A total of 30 miRNAs, 447 genes and 21 potential miRNA/mRNA pairs were differentially expressed significantly when treated with A. flavus. A total of 62 miRNAs, 451 genes and 44 potential miRNA/mRNA pairs exhibited differential expression profiles between two peanut varieties. Gene Ontology (GO) analysis showed that metabolic-process related GO terms were enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses further supported the GO results, in which many enriched pathways were related with biosynthesis and metabolism, such as biosynthesis of secondary metabolites and metabolic pathways. Correlation analysis of small RNA, transcriptome and degradome indicated that miR156/SPL pairs might regulate the accumulation of flavonoids in resistant and susceptible genotypes. The miR482/2118 family might regulate NBS-LRR gene which had the higher expression level in resistant genotype. These results provided useful information for further understanding the roles of miR156/157/SPL and miR482/2118/NBS-LRR pairs.

CONCLUSIONS

Integration analysis of the transcriptome, miRNAome and degradome of resistant and susceptible peanut varieties were performed in this study. The knowledge gained will help to understand the roles of miRNAs of peanut in response to A. flavus.

Identification of the Eutrema salsugineum EsMYB90 gene important for anthocyanin biosynthesis

BACKGROUND

Anthocyanins contribute to coloration and antioxidation effects in different plant tissues. MYB transcription factors have been demonstrated to be a key regulator for anthocyanin synthesis in many plants. However, little information was available about the MYB genes in the halophyte species Eutrema salsugineum.

RESULT

Here we report the identification of an important anthocyanin biosynthesis regulator EsMYB90 from Eutrema salsugineum, which is a halophyte tolerant to multiple abiotic stresses. Our phylogenetic and localization analyses supported that EsMYB90 is an R2R3 type of MYB transcription factor. Ectopic expression of EsMYB90 in tobacco and Arabidopsis enhanced pigmentation and anthocyanin accumulation in various organs. The transcriptome analysis revealed that 42 genes upregulated by EsMYB90 in 35S:EsMYB90 tobacco transgenic plants are required for anthocyanin biosynthesis. Moreover, our qRT-PCR results showed that EsMYB90 promoted expression of early (PAL, CHS, and CHI) and late (DFR, ANS, and UFGT) anthocyanin biosynthesis genes in stems, leaves, and flowers of 35S:EsMYB90 tobacco transgenic plants.

CONCLUSIONS

Our results indicated that EsMYB90 is a MYB transcription factor, which regulates anthocyanin biosynthesis genes to control anthocyanin biosynthesis. Our work provides a new tool to enhance anthocyanin production in various plants.

Identification of the Eutrema salsugineum EsMYB90 gene important for anthocyanin biosynthesis

BACKGROUND

Anthocyanins contribute to coloration and antioxidation effects in different plant tissues. MYB transcription factors have been demonstrated to be a key regulator for anthocyanin synthesis in many plants. However, little information was available about the MYB genes in the halophyte species Eutrema salsugineum.

RESULT

Here we report the identification of an important anthocyanin biosynthesis regulator EsMYB90 from Eutrema salsugineum, which is a halophyte tolerant to multiple abiotic stresses. Our phylogenetic and localization analyses supported that EsMYB90 is an R2R3 type of MYB transcription factor. Ectopic expression of EsMYB90 in tobacco and Arabidopsis enhanced pigmentation and anthocyanin accumulation in various organs. The transcriptome analysis revealed that 42 genes upregulated by EsMYB90 in 35S:EsMYB90 tobacco transgenic plants are required for anthocyanin biosynthesis. Moreover, our qRT-PCR results showed that EsMYB90 promoted expression of early (PAL, CHS, and CHI) and late (DFR, ANS, and UFGT) anthocyanin biosynthesis genes in stems, leaves, and flowers of 35S:EsMYB90 tobacco transgenic plants.

CONCLUSIONS

Our results indicated that EsMYB90 is a MYB transcription factor, which regulates anthocyanin biosynthesis genes to control anthocyanin biosynthesis. Our work provides a new tool to enhance anthocyanin production in various plants.

Comparative Transcriptome Analysis Reveals New lncRNAs Responding to Salt Stress in Sweet Sorghum

Long non-coding RNAs (lncRNAs) can enhance plant stress resistance by regulating the expression of functional genes. Sweet sorghum is a salt-tolerant energy crop. However, little is known about how lncRNAs in sweet sorghum respond to salt stress. In this study, we identified 126 and 133 differentially expressed lncRNAs in the salt-tolerant M-81E and the salt-sensitive Roma strains, respectively. Salt stress induced three new lncRNAs in M-81E and inhibited two new lncRNAs in Roma. These lncRNAs included lncRNA13472, lncRNA11310, lncRNA2846, lncRNA26929, and lncRNA14798, which potentially function as competitive endogenous RNAs (ceRNAs) that influence plant responses to salt stress by regulating the expression of target genes related to ion transport, protein modification, transcriptional regulation, and material synthesis and transport. Additionally, M-81E had a more complex ceRNA network than Roma. This study provides new information regarding lncRNAs and the complex regulatory network underlying salt-stress responses in sweet sorghum.

Advances in salt tolerance molecular mechanism in tobacco plants

Tobacco, an economic crop and important model plant, has received more progress in salt tolerance with the aid of transgenic technique. Salt stress has become a key research field in abiotic stress. The study of tobacco promotes the understanding about the important adjustment for survival in high salinity environments, including cellular ion transport, osmotic regulation, antioxidation, signal transduction and expression regulation, and protection of cells from stress damage. Genes, which response to salt, have been studied using targeted transgenic technologies in tobacco plants to investigate the molecular mechanisms. The transgenic tobacco plants exhibited higher seed germination and survival rates, better root and shoot growth under salt stress treatments. Transgenic approach could be the promising option for enhancing tobacco production under saline condition. This review highlighted the salt tolerance molecular mechanisms of tobacco.

Cell Cycle Regulation in the Plant Response to Stress

As sessile organisms, plants face a variety of environmental challenges. Their reproduction and survival depend on their ability to adapt to these stressors, which include water, heat stress, high salinity, and pathogen infection. Failure to adapt to these stressors results in programmed cell death and decreased viability, as well as reduced productivity in the case of crop plants. The growth and development of plants are maintained by meiosis and mitosis as well as endoreduplication, during which DNA replicates without cytokinesis, leading to polyploidy. As in other eukaryotes, the cell cycle in plants consists of four stages (G1, S, G2, and M) with two major check points, namely, the G1/S check point and G2/M check point, that ensure normal cell division. Progression through these checkpoints involves the activity of cyclin-dependent kinases and their regulatory subunits known as cyclins. In order for plants to survive, cell cycle control must be balanced with adaption to dynamic environmental conditions. In this review, we summarize recent advances in our understanding of cell cycle regulation in plants, with a focus on the molecular interactions of cell cycle machinery in the context of stress tolerance.

Genetic mechanisms of salt stress responses in halophytes

Abiotic stress is a major threat to plant growth and development, resulting in extensive crop loss worldwide. Plants react to abiotic stresses through physiological, biochemical, molecular, and genetic adaptations that promote survival. Exploring the molecular mechanisms involved in abiotic stress responses across various plant species is essential for improving crop yields in unfavorable environments. Halophytes are characterized as plants that survive to reproduce in soils containing high salt concentrations, and thus act as an ideal model to comprehend complicated genetic and physiological mechanisms of salinity stress tolerance. Plant ecologists classify halophytes into three main groups: euhalophytes, recretohalophytes, and pseudo-halophytes. Recent genetic and molecular research has showed complicated regulatory networks by which halophytes coordinate stress adaptation and tolerance. Furthermore, investigation of natural variations in these stress responses has supplied new perspectives on the evolution of mechanisms that regulate tolerance and adaptation. This review discusses the current understanding of the genetic mechanisms that contribute to salt-stress tolerance among different classes of halophytes.

Aquaporins and their function in root water transport under salt stress conditions in Eutrema salsugineum

Eutrema salsugineum is considered as extremophile model species. To gain insights into the root hydraulic conductivity and the role played by aquaporins in E. salsugineum, we investigated the aquaporin family profiles, plant water status and root hydraulic conductivity under standard (salt-free) and salt stress conditions. We found that there was no variation in the relative electric conductivity of the leaves when the salt concentration was less than 200 mM NaCl, and the transpiration rate dropped to 60.6% at 100 mM NaCl for 14 days compared to that at standard conditions. The pressure chamber techniques indicated that the root hydraulic conductivity of E. salsugineum was repressed by salt stress. However, propionic acid, usually used as an aquaporin inhibitor, unexpectedly enhanced the root hydraulic conductivity of E. salsugineum. The aquaporin family in E. salsugineum was profiled and the PIP aquaporin expression was investigated at the transcriptional and translational levels. Finally, two EsPIPs were identified to play a role in salt stress. The overall study provides evidence on how halophytes maintain their water status and aquaporin regulation pattern under salt stress conditions.

Global transcriptome analysis provides new insights in Thellungiella salsuginea stress response

Thellungiella salsuginea is highly tolerant to abiotic stress, while its a close relative Arabidopsis thaliana is sensitive to stress. This characteristic makes T. salsuginea an excellent model for uncovering the mechanisms of abiotic stress tolerance. Abscisic acid (ABA) plays essential roles in plant abiotic and biotic stress tolerance. To test the changes in gene expression of T. salsuginea under ABA treatment, in this study, the transcriptomes of T. salsuginea roots and leaves were compared in response to exogenously application of ABA. The results showed that ABA treatment caused different expression of 2,200 and 3,305 genes in leaves and roots, respectively, compared with the untreated control. In particular, genes encoding transcription factors such as WRKY, MYB, NAC, GATA, ethylene-responsive factors (ERFs), heat stress transcription factors, basic helix-loop-helix, PLATZ and B3 domain-containing family members were enriched. In addition, 49 and 114 differentially expressed genes were identified as ABA-regulated genes, separately in leaves and roots, respectively, which were related to biotic and abiotic stresses. The expression levels of some genes were validated by qRT-PCR. Different responses of genes to ABA treatment were discovered in T. salsuginea and A. thaliana. This transcriptome analysis expands our understanding of the role of ABA in stress tolerance in T. salsuginea. Our study provides a wealth of information for improving stress tolerance in crop plants.

Roles of malic enzymes in plant development and stress responses

Malic enzyme (ME) comprises a family of proteins with multiple isoforms located in different compartments of eukaryotic cells. It is a key enzyme regulating malic acid metabolism and can catalyze the reversible reaction of oxidative decarboxylation of malic acid. And it is also one of the important enzymes in plant metabolism and is involved in multiple metabolic processes. ME is widely present in plants and mainly discovered in cytoplasmic stroma, mitochondria, chloroplasts. It is involved in plant growth, development, and stress response. Plants are stressed by various environmental factors such as drought, high salt, and high temperature during plant growth, and the mechanisms of plant response to various environmental stresses are synergistic. Numerous studies have shown that ME participates in the process of coping with the above environmental factors by increasing water use efficiency, improving photosynthesis of plants, providing reducing power, and so on. In this review, we discuss the important role of ME in plant development and plant stress response, and prospects for its application. It provides a theoretical basis for the future use of ME gene for molecular resistance breeding.

The microtubule cytoskeleton acts as a sensor for stress response signaling in plants

Stress tolerance pathways are protective mechanisms that have evolved to protect plant growth and increase production under various environmental stress conditions. Enhancing stress tolerance in crop plants has become an area of intense study with aims of increasing crop production and enhancing economic benefits. A growing number of studies suggest that in addition to playing vital roles in mechanical architecture and cell division, microtubules are also involved the adaptation to severe environmental conditions in plants. However, the mechanisms that integrate microtubule regulation, cellular metabolism and cell signaling in plant stress responses remain unclear. Recent studies suggest that microtubules act as sensors for different abiotic stresses and maintain mechanical stability by forming bundles. Characterizing the diverse roles of plant microtubules is vital to furthering our understanding of stress 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.

Abiotic Stresses: General Defenses of Land Plants and Chances for Engineering Multistress Tolerance

Abiotic stresses, such as low or high temperature, deficient or excessive water, high salinity, heavy metals, and ultraviolet radiation, are hostile to plant growth and development, leading to great crop yield penalty worldwide. It is getting imperative to equip crops with multistress tolerance to relieve the pressure of environmental changes and to meet the demand of population growth, as different abiotic stresses usually arise together in the field. The feasibility is raised as land plants actually have established more generalized defenses against abiotic stresses, including the cuticle outside plants, together with unsaturated fatty acids, reactive species scavengers, molecular chaperones, and compatible solutes inside cells. In stress response, they are orchestrated by a complex regulatory network involving upstream signaling molecules including stress hormones, reactive oxygen species, gasotransmitters, polyamines, phytochromes, and calcium, as well as downstream gene regulation factors, particularly transcription factors. In this review, we aimed at presenting an overview of these defensive systems and the regulatory network, with an eye to their practical potential via genetic engineering and/or exogenous application.

Halophytism: What Have We Learnt From Arabidopsis thaliana Relative Model Systems?

Halophytes are able to thrive in salt concentrations that would kill 99% of other plant species, and identifying their salt-adaptive mechanisms has great potential for improving the tolerance of crop plants to salinized soils. Much research has focused on the physiological basis of halophyte salt tolerance, whereas the elucidation of molecular mechanisms has traditionally lagged behind due to the absence of a model halophyte system. However, over the last decade and a half, two Arabidopsis (Arabidopsis thaliana) relatives, Eutrema salsugineum and Schrenkiella parvula, have been established as transformation-competent models with various genetic resources including high-quality genome assemblies. These models have facilitated powerful comparative analyses with salt-sensitive Arabidopsis to unravel the genetic adaptations that enable a halophytic lifestyle. The aim of this review is to explore what has been learned about halophytism using E. salsugineum and S. parvula We consider evidence from physiological and molecular studies suggesting that differences in salt tolerance between related halophytes and salt-sensitive plants are associated with alterations in the regulation of basic physiological, biochemical, and molecular processes. Furthermore, we discuss how salt tolerance mechanisms of the halophytic models are reflected at the level of their genomes, where evolutionary processes such as subfunctionalization and/or neofunctionalization have altered the expression and/or functions of genes to facilitate adaptation to saline conditions. Lastly, we summarize the many areas of research still to be addressed with E. salsugineum and S. parvula as well as obstacles hindering further progress in understanding halophytism.

Survival Mechanisms to Selective Pressures and Implications

Organisms have evolved a spectrum of strategies that facilitate survival in the face of adverse environmental conditions. In order to make full use of the unfavorable resources of nature, human beings usually impose selective pressures to breed phenotypic traits that can survive in adverse environments. Animals are frequently under attack by biotic stress, such as bacterial and viral infections, while plants are more often subjected to abiotic stress, including high salinity, drought, and cold. In response to these diverse stresses, animals and plants initiate wide-ranging changes in gene expression by altering regulation of transcriptional and post-transcriptional activities. Recent studies have identified a number of key responsive components that promote survival of animals and plants in response to biotic and abiotic stresses. Importantly, with recent developments in genome-editing technology based on the CRISPR/Cas9 system, manipulation of genetic elements to generate stress-resistant animals and plants has become both feasible and cost-effective. Herein, we review important mechanisms that govern the response of organisms to biotic and abiotic stresses with the aim of applying our understanding to the agriculture and animal husbandry industries.

Identification of Salt Stress Responding Genes Using Transcriptome Analysis in Green Alga Chlamydomonas reinhardtii

Salinity is one of the most important abiotic stresses threatening plant growth and agricultural productivity worldwide. In green alga Chlamydomonas reinhardtii, physiological evidence indicates that saline stress increases intracellular peroxide levels and inhibits photosynthetic-electron flow. However, understanding the genetic underpinnings of salt-responding traits in plantae remains a daunting challenge. In this study, the transcriptome analysis of short-term acclimation to salt stress (200 mM NaCl for 24 h) was performed in C. reinhardtii. A total of 10,635 unigenes were identified as being differently expressed by RNA-seq, including 5920 up- and 4715 down-regulated unigenes. A series of molecular cues were screened for salt stress response, including maintaining the lipid homeostasis by regulating phosphatidic acid, acetate being used as an alternative source of energy for solving impairment of photosynthesis, and enhancement of glycolysis metabolism to decrease the carbohydrate accumulation in cells. Our results may help understand the molecular and genetic underpinnings of salt stress responses in green alga C. reinhardtii.

Combined small RNA and gene expression analysis revealed roles of miRNAs in maize response to rice black-streaked dwarf virus infection

Maize rough dwarf disease, caused by rice black-streaked dwarf virus (RBSDV), is a devastating disease in maize (Zea mays L.). MicroRNAs (miRNAs) are known to play critical roles in regulation of plant growth, development, and adaptation to abiotic and biotic stresses. To elucidate the roles of miRNAs in the regulation of maize in response to RBSDV, we employed high-throughput sequencing technology to analyze the miRNAome and transcriptome following RBSDV infection. A total of 76 known miRNAs, 226 potential novel miRNAs and 351 target genes were identified. Our dataset showed that the expression patterns of 81 miRNAs changed dramatically in response to RBSDV infection. Transcriptome analysis showed that 453 genes were differentially expressed after RBSDV infection. GO, COG and KEGG analysis results demonstrated that genes involved with photosynthesis and metabolism were significantly enriched. In addition, twelve miRNA-mRNA interaction pairs were identified, and six of them were likely to play significant roles in maize response to RBSDV. This study provided valuable information for understanding the molecular mechanism of maize disease resistance, and could be useful in method development to protect maize against RBSDV.

Regulation mechanism of long non-coding RNA in plant response to stress

Long non-coding RNA (lncRNA) is a non-coding RNA greater than 200 nucleotides in length. LncRNAs can regulate gene expression at transcription and post-transcription, epigenetic level, and plays an important role in a wide range of biological processes such as genomic imprinting, chromatin remodeling, transcriptional activation, transcriptional interference and cell cycle. It becomes the current hot topics in the study of molecular biology and genetics. Emerging evidence proposed that lncRNAs play important roles in response to both abiotic and biotic stress. In this review, we discuss the role of lncRNAs in drought resistance, salt resistance, disease resistance, and immunity of plants, providing strong evidence for exploring the important role of lncRNAs in plant resistance, in order to explore new ideas and new targets for prevention and control.

Mechanisms of Salt Tolerance in Halophytes: Current Understanding and Recent Advances

Halophytes are plants that exhibit high salt tolerance, allowing them to survive and thrive under extremely saline conditions. The study of halophytes advances our understanding about the important adaptations that are required for survival in high salinity conditions, including secretion of salt through the salt glands, regulation of cellular ion homeostasis and osmotic pressure, detoxification of reactive oxygen species, and alterations in membrane composition. To explore the mechanisms that contribute to tolerance to salt stress, salt-responsive genes have been isolated from halophytes and expressed in non-salt tolerant plants using targeted transgenic technologies. In this review, we discuss the mechanisms that underpin salt tolerance in different halophytes.

Molecular mechanisms underlying stress response and adaptation

Environmental stresses are ubiquitous and unavoidable to all living things. Organisms respond and adapt to stresses through defined regulatory mechanisms that drive changes in gene expression, organismal morphology, or physiology. Immune responses illustrate adaptation to bacterial and viral biotic stresses in animals. Dysregulation of the genotoxic stress response system is frequently associated with various types of human cancer. With respect to plants, especially halophytes, complicated systems have been developed to allow for plant growth in high salt environments. In addition, drought, waterlogging, and low temperatures represent other common plant stresses. In this review, we summarize representative examples of organismal response and adaptation to various stresses. We also discuss the molecular mechanisms underlying the above phenomena with a focus on the improvement of organismal tolerance to unfavorable environments.

Transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene/miRNA alterations between the dimorphic seeds during germination

BACKGROUND

Dimorphic seeds from Suaeda aralocaspica exhibit different germination behaviors that are thought to be a bet-hedging strategy advantageous in harsh and unpredictable environments. To understand the molecular mechanisms of Suaeda aralocaspica dimorphic seed germination, we applied RNA sequencing and small RNA sequencing for samples collected at three germination stages.

RESULTS

A total of 79,414 transcripts were assembled using Trinity, of which 57.67% were functionally annotated. KEGG enrichment unveiled that photosynthesis and flavonol biosynthesis pathways were activated earlier in brown seed compared with black seed. Gene expression analysis revealed that nine candidate unigenes in gibberellic acid and abscisic acid signal transduction and 23 unigenes in circadian rhythm-plant pathway showed distinct expression profiles to promote dimorphic seed germination. 194 conserved miRNAs comprising 40 families and 21 novel miRNAs belonging to 20 families in Suaeda aralocaspica were identified using miRDeep-P and Mfold. The expression of miRNAs in black seed was suppressed at imbibition stage. Among the identified miRNAs, 59 conserved and 13 novel miRNAs differentially expressed during seed germination. Of which, 43 conserved and nine novel miRNAs showed distinct expression patterns between black and brown seed. Using TAPIR, 208 unigenes were predicted as putative targets of 35 conserved miRNA families and 17 novel miRNA families. Among functionally annotated targets, genes participated in transcription regulation constituted the dominant category, followed by genes involved in signaling and stress response. Seven of the predicted targets were validated using 5' rapid amplification of cDNA ends or real-time quantitative reverse transcription-PCR.

CONCLUSIONS

Our results indicate that specific genes and miRNAs are regulated differently between black and brown seed during germination, which may contribute to the different germination behaviors of Suaeda aralocaspica dimorphic seeds in unpredictable variable environments. Our results lay a solid foundation for further studying the roles of candidate genes and miRNAs in Suaeda aralocaspica dimorphic seed germination.

Identification of Ice Plant (Mesembryanthemum crystallinum L.) MicroRNAs Using RNA-Seq and Their Putative Roles in High Salinity Responses in Seedlings

The halophyte Mesembryanthemum crystallinum (common or crystalline ice plant) is a useful model for studying molecular mechanisms of salt tolerance. The morphology, physiology, metabolism, and gene expression of ice plant have been studied and large-scale analyses of gene expression profiling have drawn an outline of salt tolerance in ice plant. A rapid root growth to a sudden increase in salinity was observed in ice plant seedlings. Using a fluorescent dye to detect Na(+), we found that ice plant roots respond to an increased flux of Na(+) by either secreting or storing Na(+) in specialized cells. High-throughput sequencing was used to identify small RNA profiles in 3-day-old seedlings treated with or without 200 mM NaCl. In total, 135 conserved miRNAs belonging to 21 families were found. The hairpin precursor of 19 conserved mcr-miRNAs and 12 novel mcr-miRNAs were identified. After 6 h of salt stress, the expression of most mcr-miRNAs showed decreased relative abundance, whereas the expression of their corresponding target genes showed increased mRNA relative abundance. The cognate target genes are involved in a broad range of biological processes: transcription factors that regulate growth and development, enzymes that catalyze miRNA biogenesis for the most conserved mcr-miRNA, and proteins that are involved in ion homeostasis and drought-stress responses for some novel mcr-miRNAs. Analyses of the functions of target genes revealed that cellular processes, including growth and development, metabolism, and ion transport activity are likely to be enhanced in roots under salt stress. The expression of eleven conserved miRNAs and two novel miRNAs were correlated reciprocally with predicted targets within hours after salt stress exposure. Several conserved miRNAs have been known to regulate root elongation, root apical meristem activity, and lateral root formation. Based upon the expression pattern of miRNA and target genes in combination with the observation of Na(+) distribution, ice plant likely responds to increased salinity by using Na(+) as an osmoticum for cell expansion and guard cell opening. Excessive Na(+) could either be secreted through the root epidermis or stored in specialized leaf epidermal cells. These responses are regulated in part at the miRNA-mediated post-transcriptional level.

Genome-wide identification and characterization of Eutrema salsugineum microRNAs for salt tolerance

Eutrema salsugineum, a close relative of Arabidopsis thaliana, is a valuable halophytic model plant that has extreme tolerance to salinity. As posttranscriptional gene regulators, microRNAs (miRNAs) control gene expression and a variety of biological processes, including plant-stress responses. To identify salt-stress responsive miRNAs in E. salsugineum and reveal their possible roles in the adaptive response to salt stress, we chose the Solexa sequencing platform to screen the miRNAs in 4-week-old E. salsugineum seedlings under salt treatment. A total of 82 conserved miRNAs belonging to 27 miRNA families and 17 novel miRNAs were identified and 11 conserved miRNA families and 4 novel miRNAs showed a significant response to salt stress. To investigate the possible biological roles of miRNAs, 1060 potential targets were predicted. Moreover, 35 gene ontology (GO) categories and 1 pathway, including a few terms that were directly and indirectly related to salt stress, were significantly enriched in the salt-stress-responsive miRNAs targets. The relative expression analysis of six target genes was analyzed using quantitative real-time polymerase chain reaction (PCR) and showed a negative correlation with their corresponding miRNAs. Many stress regulatory and phytohormone regulatory cis-regulatory elements were widely present in the promoter region of the salt-responsive miRNA precursors. This study describes the large-scale characterization of E. salsugineum miRNAs and provides a useful resource for further understanding of miRNA functions in the regulation of the E. salsugineum salt-stress response.

Small RNA transcriptomes of mangroves evolve adaptively in extreme environments

MicroRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs) are key players in plant stress responses. Here, we present the sRNA transcriptomes of mangroves Bruguiera gymnorrhiza and Kandelia candel. Comparative computational analyses and target predictions revealed that mangroves exhibit distinct sRNA regulatory networks that differ from those of glycophytes. A total of 32 known and three novel miRNA families were identified. Conserved and mangrove-specific miRNA targets were predicted; the latter were widely involved in stress responses. The known miRNAs showed differential expression between the mangroves and glycophytes, reminiscent of the adaptive stress-responsive changes in Arabidopsis. B. gymnorrhiza possessed highly abundant but less conserved TAS3 trans-acting siRNAs (tasiRNAs) in addition to tasiR-ARFs, with expanded potential targets. Our results indicate that the evolutionary alteration of sRNA expression levels and the rewiring of sRNA-regulatory networks are important mechanisms underlying stress adaptation. We also identified sRNAs that are involved in salt and/or drought tolerance and nutrient homeostasis as possible contributors to mangrove success in stressful environments.

Identification of Novel and Conserved miRNAs from Extreme Halophyte, Oryza coarctata, a Wild Relative of Rice

Oryza coarctata, a halophyte and wild relative of rice, is grown normally in saline water. MicroRNAs (miRNAs) are non-coding RNAs that play pivotal roles in every domain of life including stress response. There are very few reports on the discovery of salt-responsive miRNAs from halophytes. In this study, two small RNA libraries, one each from the control and salt-treated (450 mM NaCl for 24 h) leaves of O. coarctata were sequenced, which yielded 338 known and 95 novel miRNAs. Additionally, we used publicly available transcriptomics data of O. coarctata which led to the discovery of additional 48 conserved miRNAs along with their pre-miRNA sequences through in silico analysis. In total, 36 known and 7 novel miRNAs were up-regulated whereas, 12 known and 7 novel miRNAs were down-regulated under salinity stress. Further, 233 and 154 target genes were predicted for 48 known and 14 novel differentially regulated miRNAs respectively. These targets with the help of gene ontology analysis were found to be involved in several important biological processes that could be involved in salinity tolerance. Relative expression trends of majority of the miRNAs as detected by real time-PCR as well as predicted by Illumina sequencing were found to be coherent. Additionally, expression of most of the target genes was negatively correlated with their corresponding miRNAs. Thus, the present study provides an account of miRNA-target networking that is involved in salinity adaption of O. coarctata.

Genome-wide identification of abiotic stress-regulated and novel microRNAs in mulberry leaf

As the most important food plant for sericultural industry, mulberry trees have to suffer from a wide range of abiotic and biotic stresses, such as drought and high salinity. MicroRNAs (miRNAs) have been proved to play important roles in abiotic stresses regulation in many plants. However, there are seldom reports on the miRNAs expression profiles upon abiotic challenges in mulberry. In this study, three small RNA libraries from mulberry leaf tissue with or without drought or salt treatment were constructed and deep sequenced. Total of 48 conserved miRNAs (including miRNA*) and 162 novel miRNAs were identified (processing precision value>0.1). A total of 270 and 1963 target genes were predicted for conserved miRNAs and novel miRNAs, respectively. 13 differentially expressed miRNAs were detected under drought or salt stresses by deep sequencing and qRT-PCR. 5' RLM-RACE validated Morus 013341 to be the target gene of miR-395a. Our results provided initial clue to further study molecular mechanism on abiotic stresses regulation in mulberry.

High-throughput deep sequencing reveals that microRNAs play important roles in salt tolerance of euhalophyte Salicornia europaea

BACKGROUND

microRNAs (miRNAs) are implicated in plant development processes and play pivotal roles in plant adaptation to environmental stresses. Salicornia europaea, a salt mash euhalophyte, is a suitable model plant to study salt adaptation mechanisms. S. europaea is also a vegetable, forage, and oilseed that can be used for saline land reclamation and biofuel precursor production on marginal lands. Despite its importance, no miRNA has been identified from S. europaea thus far.

RESULTS

Deep sequencing was performed to investigate small RNA transcriptome of S. europaea. Two hundred and ten conserved miRNAs comprising 51 families and 31 novel miRNAs (including seven miRNA star sequences) belonging to 30 families were identified. About half (13 out of 31) of the novel miRNAs were only detected in salt-treated samples. The expression of 43 conserved and 13 novel miRNAs significantly changed in response to salinity. In addition, 53 conserved and 13 novel miRNAs were differentially expressed between the shoots and roots. Furthermore, 306 and 195 S. europaea unigenes were predicted to be targets of 41 conserved and 29 novel miRNA families, respectively. These targets encoded a wide range of proteins, and genes involved in transcription regulation constituted the largest category. Four of these genes encoding laccase, F-box family protein, SAC3/GANP family protein, and NADPH cytochrome P-450 reductase were validated using 5'-RACE.

CONCLUSIONS

Our results indicate that specific miRNAs are tightly regulated by salinity in the shoots and/or roots of S. europaea, which may play important roles in salt tolerance of this euhalophyte. The S. europaea salt-responsive miRNAs and miRNAs that target transcription factors, nucleotide binding site-leucine-rich repeat proteins and enzymes involved in lignin biosynthesis as well as carbon and nitrogen metabolism may be applied in genetic engineering of crops with high stress tolerance, and genetic modification of biofuel crops with high biomass and regulatable lignin biosynthesis.

Identification of cold-inducible microRNAs in grapevine

Low temperature is one of the most important environmental factors that limits the geographical distribution and productivity of grapevine. However, the molecular mechanisms on how grapevine responds to cold stress remains to be elucidated. MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs that play an essential role during plant development and stress responses. Although miRNAs and their targets have been identified in several Vitis species, their participation during cold accumulation in grapevine remains unknown. In this study, two small RNA libraries were generated from micropropagated 'Muscat Hamburg' (V. vinifera) plantlets under normal and low temperatures (4°C). A total of 163 known miRNAs and 67 putative novel miRNAs were detected from two small RNA libraries by Solexa sequencing. Forty-four cold-inducible miRNAs were identified through differentially expressed miRNAs (DEMs) analysis; among which, 13 belonged to upregulated DEMs while 31 belonged downregulated DEMs. The expression patterns of the 13 DEMs were verified by real-time RT-PCR analysis. The prediction of the target genes for DEMs indicated that miRNA may regulate transcription factors, including AP2, SBP, MYB, bHLH, GRAS, and bZIP under cold stress. The 5'-RLM RACE were conducted to verify the cleavage site of predicted targets. Seven predicted target genes for four known and three novel vvi-miRNAs showed specific cleavage sites corresponding to their miRNA complementary sequences. The expression pattern of these seven target genes revealed negative correlation with the expression level of the corresponding vvi-miRNAs. Our results indicated that a diverse set of miRNAs in V. vinifera are cold-inducible and may play an important role in cold stress response.

A genome-wide identification of the miRNAome in response to salinity stress in date palm (Phoenix dactylifera L.)

Although date palm is relatively salt-tolerant, little is known about the underlying molecular mechanisms that contribute to its salt tolerance. Only recently, investigators have uncovered microRNA-mediated post-transcriptional gene regulation, which is critical for typical plant development and adaptation to stress conditions such as salinity. To identify conserved and novel miRNAs in date palm and to characterize miRNAs that could play a role in salt tolerance, we have generated sRNA libraries from the leaves and roots of NaCl-treated and untreated seedlings of date palm. Deep sequencing of these four sRNA libraries yielded approximately 251 million reads. The bioinformatics analysis has identified 153 homologs of conserved miRNAs, 89 miRNA variants, and 180 putative novel miRNAs in date palm. Expression profiles under salinity revealed differential regulation of some miRNAs in date palm. In leaves, 54 of the identified miRNAs were significantly affected and the majority (70%) of them were upregulated, whereas in roots, 25 of the identified miRNAs were significantly affected and 76% of them were upregulated by the salinity stress. The salt-responsiveness of some of these miRNAs was further validated using semi-quantitative PCR (qPCR). Some of the predicted targets for the identified miRNA include genes with known functions in plant salt tolerance, such as potassium channel AKT2-like proteins, vacuolar protein sorting-associated protein, calcium-dependent and mitogen-activated proteins. As one of the first cultivated trees in the world that can tolerate a wide range of abiotic stresses, date palm contains a large population of conserved and non-conserved miRNAs that function at the post-transcriptional level. This study provided insights into miRNA-mediated gene expression that are important for adaptation to salinity in date palms.

NPK macronutrients and microRNA homeostasis

Macronutrients are essential elements for plant growth and development. In natural, non-cultivated systems, the availability of macronutrients is not a limiting factor of growth, due to fast recycling mechanisms. However, their availability might be an issue in modern agricultural practices, since soil has been frequently over exploited. From a crop management perspective, the nitrogen (N), phosphorus (P), and potassium (K) are three important limiting factors and therefore frequently added as fertilizers. NPK are among the nutrients that have been reported to alter post-embryonic root developmental processes and consequently, impairs crop yield. To cope with nutrients scarcity, plants have evolved several mechanisms involved in metabolic, physiological, and developmental adaptations. In this scenario, microRNAs (miRNAs) have emerged as additional key regulators of nutrients uptake and assimilation. Some studies have demonstrated the intrinsic relation between miRNAs and their targets, and how they can modulate plants to deal with the NPK availability. In this review, we focus on miRNAs and their regulation of targets involved in NPK metabolism. In general, NPK starvation is related with miRNAs that are involved in root-architectural changes and uptake activity modulation. We further show that several miRNAs were discovered to be involved in plant-microbe symbiosis during N and P uptake, and in this way we present a global view of some studies that were conducted in the last years. The integration of current knowledge about miRNA-NPK signaling may help future studies to focus in good candidates genes for the development of important tools for plant nutritional breeding.

Comprehensive analysis of differentially expressed genes and transcriptional regulation induced by salt stress in two contrasting cotton genotypes

Background

Cotton (Gossypium spp.) is one of the major fibre crops of the world. Although it is classified as salt tolerant crop, cotton growth and productivity are adversely affected by high salinity, especially at germination and seedling stages. Identification of genes and miRNAs responsible for salt tolerance in upland cotton (Gossypium hirsutum L.) would help reveal the molecular mechanisms of salt tolerance. We performed physiological experiments and transcriptome sequencing (mRNA-seq and small RNA-seq) of cotton leaves under salt stress using Illumina sequencing technology.

Results

We investigated two distinct salt stress phases—dehydration (4 h) and ionic stress (osmotic restoration; 24 h)—that were identified by physiological changes of 14-day-old seedlings of two cotton genotypes, one salt tolerant and the other salt sensitive, during a 72-h NaCl exposure. A comparative transcriptomics was used to monitor gene and miRNA differential expression at two time points (4 and 24 h) in leaves of the two cotton genotypes under salinity conditions. The expression patterns of differentially co-expressed unigenes were divided into six groups using short time-servies expression miner software. During a 24-h salt exposure, 819 transcription factor unigenes were differentially expressed in both genotypes, with 129 unigenes specifically expressed in the salt-tolerant genotype. Under salt stress, 108 conserved miRNAs from known families were differentially expressed at two time points in the salt-tolerant genotype. We further analyzed the predicted target genes of these miRNAs along with the transcriptome for each time point. Important expressed genes encoding membrane receptors, transporters, and pathways involved in biosynthesis and signal transduction of calcium-dependent protein kinase, mitogen-activated protein kinase, and hormones (abscisic acid and ethylene) were up-regulated. We also analyzed the salt stress response of some key miRNAs and their target genes and found that the expressions of five of nine target genes exhibited significant inverse correlations with their corresponding miRNAs. On the basis of these results, we constructed molecular regulatory pathways and a potential regulatory network for these salt-responsive miRNAs.

Conclusions

Our comprehensive transcriptome analysis has provided new insights into salt-stress response of upland cotton. The results should contribute to the development of genetically modified cotton with salt tolerance.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-760) contains supplementary material, which is available to authorized users.