History and current status of wheat miRNAs using next-generation sequencing and their roles in development and stress

MicroRNAs potentially targeting DDR-related genes are differentially expressed upon exposure to γ-rays during seed germination in wheat

DNA damage response (DDR), a complex network of cellular pathways that cooperate to sense and repair DNA lesions, is regulated by several mechanisms, including microRNAs. As small, single-stranded RNA molecules, miRNAs post-transcriptionally regulate their target genes by mRNA cleavage or translation inhibition. Knowledge regarding miRNAs influence on DDR-associated genes is still scanty in plants. In this work, an in silico analysis was performed to identify putative miRNAs that could target DDR sensors, signal transducers and effector genes in wheat. Selected putative miRNA-gene pairs were tested in an experimental system where seeds from two wheat mutant lines were irradiated with 50 Gy and 300 Gy gamma(γ)-rays. To evaluate the effect of the treatments on wheat germination, phenotypic and molecular (DNA damage, ROS accumulation, gene/miRNA expression profile) analyses have been carried out. The results showed that in dry seeds ROS accumulated immediately after irradiation and decayed soon after while the negative impact on seedling growth was supported by enhanced accumulation of DNA damage. When a qRT-PCR analysis was performed, the selected miRNAs and DDR-related genes were differentially modulated by the γ-rays treatments in a dose-, time- and genotype-dependent manner. A significant negative correlation was observed between the expression of tae-miR5086 and the RAD50 gene, involved in double-strand break sensing and homologous recombination repair, one of the main processes that repairs DNA breaks induced by γ-rays. The results hereby reported can be relevant for wheat breeding programs and screening of the radiation response and tolerance of novel wheat varieties.

SARS-CoV-2-associated organs failure and inflammation: a focus on the role of cellular and viral microRNAs

SARS-CoV-2 has been responsible for the recent pandemic all over the world, which has caused many complications. One of the hallmarks of SARS-CoV-2 infection is an induced immune dysregulation, in some cases resulting in cytokine storm syndrome, acute respiratory distress syndrome and many organs such as lungs, brain, and heart that are affected during the SARS-CoV-2 infection. Several physiological parameters are altered as a result of infection and cytokine storm. Among them, microRNAs (miRNAs) might reflect this poor condition since they play a significant role in immune cellular performance including inflammatory responses. Both host and viral-encoded miRNAs are crucial for the successful infection of SARS-CoV-2. For instance, dysregulation of miRNAs that modulate multiple genes expressed in COVID-19 patients with comorbidities (e.g., type 2 diabetes, and cerebrovascular disorders) could affect the severity of the disease. Therefore, altered expression levels of circulating miRNAs might be helpful to diagnose this illness and forecast whether a COVID-19 patient could develop a severe state of the disease. Moreover, a number of miRNAs could inhibit the expression of proteins, such as ACE2, TMPRSS2, spike, and Nsp12, involved in the life cycle of SARS-CoV-2. Accordingly, miRNAs represent potential biomarkers and therapeutic targets for this devastating viral disease. In the current study, we investigated modifications in miRNA expression and their influence on COVID-19 disease recovery, which may be employed as a therapy strategy to minimize COVID-19-related disorders.

Plant transcriptional memory and associated mechanism of abiotic stress tolerance

Plants face various adverse environmental conditions, particularly with the ongoing changes in global climate, which drastically affect the growth, development and productivity of crops. To cope with these stresses, plants have evolved complex mechanisms, and one of the crucial ways is to develop transcriptional memories from stress exposure. This induced learning enables plants to better and more strongly restart the response and adaptation mechanism to stress when similar or dissimilar stresses reoccur. Understanding the molecular mechanism behind plant transcriptional memory of stress can provide a theoretical basis for breeding stress-tolerant crops with resilience to future climates. Here we review the recent research progress on the transcriptional memory of plants under various stresses and the applications of underlying mechanisms for sustainable agricultural production. We propose that a thorough understanding of plant transcriptional memory is crucial for both agronomic management and resistant breeding, and thus may help to improve agricultural yield and quality under changing climatic conditions.

Identification of drought-tolerant hub genes in Iranian KC-2226 genotype of Aegilops tauschii using transcriptomic analysis

Aegilops tauschii, as a donor of D genome to the bread wheat with a valuable source of resistance to different biotic and abiotic stresses, is used to improve the quality of wheat cultivars. Every genotype has a specific genetic content, the investigation of which can lead to the identification of useful genes such as stress tolerance genes, including drought. Therefore, 23 genotypes of Ae. tauschii were selected to evaluate their morphological and physiological traits under greenhouse conditions. Among them, a superior tolerant genotype (KC-2226) was chosen for transcriptomic analysis. Our result showed that 5007 and 3489 genes were deferentially up- and downregulated, respectively. Upregulated genes were involved in photosynthesis, glycolysis/gluconeogenesis, and amino acid biosynthesis whereas downregulated genes were often engaged in DNA synthesis, replication, repair and topological changes. The result of protein-protein interaction network analysis showed that AT1G76550 (1.46), AT1G20950 (1.42), IAR4 (1.19), and PYD2 (1.16) among upregulated genes and THY-1 (44), PCNA1 (41) and TOPII (22) among down-regulated genes had the highest interactions with other genes. In conclusion, Ae. tauschii employs elevated transcription of specific genes involved in photosynthesis, glycolysis and gluconeogenesis and amino acid biosynthesis pathways rather than genes active in DNA synthesis and repair to provide the energy needed for the plant to survive under stress conditions.

Integrated Multi-Omics Reveals Significant Roles of Non-Additively Expressed Small RNAs in Heterosis for Maize Plant Height

Heterosis is a complex biological phenomenon regulated by genetic variations and epigenetic changes. However, the roles of small RNAs (sRNAs), an important epigenetic regulatory element, on plant heterosis are still poorly understood. Here, an integrative analysis was performed with sequencing data from multi-omics layers of maize hybrids and their two homologous parental lines to explore the potential underlying mechanisms of sRNAs in plant height (PH) heterosis. sRNAome analysis revealed that 59 (18.61%) microRNAs (miRNAs) and 64,534 (54.00%) 24-nt small interfering RNAs (siRNAs) clusters were non-additively expressed in hybrids. Transcriptome profiles showed that these non-additively expressed miRNAs regulated PH heterosis through activating genes involved in vegetative growth-related pathways while suppressing those related to reproductive and stress response pathways. DNA methylome profiles showed that non-additive methylation events were more likely to be induced by non-additively expressed siRNA clusters. Genes associated with low-parental expression (LPE) siRNAs and trans-chromosomal demethylation (TCdM) events were enriched in developmental processes as well as nutrients and energy metabolism, whereas genes associated with high-parental expression (HPE) siRNAs and trans-chromosomal methylation (TCM) events were gathered in stress response and organelle organization pathways. Our results provide insights into the expression and regulation patterns of sRNAs in hybrids and help to elucidate their potential targeting pathways contributing to PH heterosis.

Regulation of miR319b-Targeted SlTCP10 during the Tomato Response to Low-Potassium Stress

Potassium deficiency confines root growth and decreases root-to-shoot ratio, thereby limiting root K⁺ acquisition. This study aimed to identify the regulation network of microRNA319 involved in low-K⁺ stress tolerance in tomato (Solanum lycopersicum). SlmiR319b-OE roots demonstrated a smaller root system, a lower number of root hairs and lower K⁺ content under low-K⁺ stress. We identified SlTCP10 as the target of miR319b using a modified RLM-RACE procedure from some SlTCPs' predictive complementarity to miR319b. Then, SlTCP10-regulated SlJA2 (an NAC transcription factor) influenced the response to low-K⁺ stress. CR-SlJA2 (CRISPR-Cas9-SlJA2) lines showed the same root phenotype to SlmiR319-OE compared with WT lines. OE-SlJA2(Overexpression-SlJA2) lines showed higher root biomass, root hair number and K⁺ concentration in the roots under low-K⁺ conditions. Furthermore, SlJA2 has been reported to promote abscisic acid (ABA) biosynthesis. Therefore, SlJA2 increases low-K⁺ tolerance via ABA. In conclusion, enlarging root growth and K⁺ absorption by the expression of SlmiR319b-regulated SlTCP10, mediating SlJA2 in roots, could provide a new regulation mechanism for increasing K⁺ acquisition efficiency under low-K⁺ stress.

An Integrated Bioinformatics and Functional Approach for miRNA Validation

MicroRNAs (miRNAs) are small (20-24 nucleotides) non-coding ribo-regulatory molecules with significant roles in regulating target mRNA and long non-coding RNAs at transcriptional and post-transcriptional levels. Rapid advancement in the small RNA sequencing methods with integration of degradome sequencing has accelerated the understanding of miRNA-mediated regulatory hubs in plants and yielded extensive annotation of miRNAs and corresponding targets. However, it is becoming clear that large numbers of such annotations are questionable. Therefore, it is imperative to adopt reliable and strict bioinformatics pipelines for miRNA identification. Furthermore, sensitive methods are needed for validation and functional characterization of miRNA and its target(s). In this chapter, we have provided a comprehensive and streamlined methodology for miRNA identification and its functional validation in plants. This includes a combination of various in silico and experimental methodologies. To identify miRNA compendium from large-scale Next-Generation Sequencing (NGS) small RNA datasets, the miR-PREFeR (miRNA PREdiction From small RNA-Seq data) bioinformatics tool has been described. Also, a homology-based search protocol for finding members of a specific miRNA family has been discussed. The chapter also includes techniques to ascertain miRNA:target pair specificity using in silico target prediction from degradome NGS libraries using CleaveLand pipeline, miRNA:target validation by in planta transient assays, 5' RLM-RACE and expression analysis as well as functional techniques like miRNA overexpression, short tandem target mimic and resistant target approaches. The proposed strategy offers a reliable and sensitive way for miRNA:target identification and validation. Additionally, we strongly promulgate the use of multiple methodologies to validate a miRNA as well as its target.

Small RNA, Transcriptome and Degradome Analysis of the Transgenerational Heat Stress Response Network in Durum Wheat

Heat stress is a major limiting factor of grain yield and quality in crops. Abiotic stresses have a transgenerational impact and the mechanistic basis is associated with epigenetic regulation. The current study presents the first systematic analysis of the transgenerational effects of post-anthesis heat stress in tetraploid wheat. Leaf physiological traits, harvest components and grain quality traits were characterized under the impact of parental and progeny heat stress. The parental heat stress treatment had a positive influence on the offspring for traits including chlorophyll content, grain weight, grain number and grain total starch content. Integrated sequencing analysis of the small RNAome, mRNA transcriptome and degradome provided the first description of the molecular networks mediating heat stress adaptation under transgenerational influence. The expression profile of 1771 microRNAs (733 being novel) and 66,559 genes was provided, with differentially expressed microRNAs and genes characterized subject to the progeny treatment, parental treatment and tissue-type factors. Gene Ontology and KEGG pathway analysis of stress responsive microRNAs-mRNA modules provided further information on their functional roles in biological processes such as hormone homeostasis, signal transduction and protein stabilization. Our results provide new insights on the molecular basis of transgenerational heat stress adaptation, which can be used for improving thermo-tolerance in breeding.

MicroRNA and regulation of auxin and cytokinin signalling during post-mowing regeneration of winter wheat (Triticum aestivum L.)

Winter wheat not only provides adequate fresh forage grass in winter, but also ensures ample grain production in summer. The mechanisms underlying the regeneration of winter wheat after mowing or grazing are not well understood. In this study, the miRNA expression profile of winter wheat was determined using RNA sequencing and the endogenous auxin and cis-zeatin concentrations, as well as the expression of related miRNA-targeted genes, were measured. During the post-mowing regeneration of winter wheat, the concentrations of endogenous indole-3-acetic acid (IAA), methyl indole-3-acetate (ME-IAA), and indole-3-carboxaldehyde (ICA) decreased, while those of cis-zeatin (cZ) increased. Moreover, 15 novel miRNAs and three known miRNAs were found to be involved in the synthesis and signalling transduction of auxins and cytokinins (CKs). Among these miRNAs, miR1153-y, miR5059-x, miR2916-x, novel-miR1532-3p, novel-miR1060-3p, and novel-miR0890-3p, were found to be negatively correlated with the expression of their target genes including auxin response GH3.7, auxin response factor (ARF), type-A two-component response regulator (A-ARR), aldehyde dehydrogenase (ALDH), and O-glucosyltransferase (CISZOG). Furthermore, miR1153-y was identified as mediating the cleavage of GH3.7 by RACE assay. In turn, these genes inhibited the biosynthesis and signalling of IAA and activated CK signal transduction, resulting in the rapid regeneration of mowed winter wheat. This study revealed that some miRNAs exert a positive regulatory effect on the post-mowing regeneration of winter wheat by controlling the synthesis and signal transduction of IAA and CK, and our founding will aid developments in biotechnology aimed at improving the post-mowing regeneration ability of winter wheat.

Integrated Analysis of Small RNA, Transcriptome, and Degradome Sequencing Reveals the Water-Deficit and Heat Stress Response Network in Durum Wheat

Water-deficit and heat stress negatively impact crop production. Mechanisms underlying the response of durum wheat to such stresses are not well understood. With the new durum wheat genome assembly, we conducted the first multi-omics analysis with next-generation sequencing, providing a comprehensive description of the durum wheat small RNAome (sRNAome), mRNA transcriptome, and degradome. Single and combined water-deficit and heat stress were applied to stress-tolerant and -sensitive Australian genotypes to study their response at multiple time-points during reproduction. Analysis of 120 sRNA libraries identified 523 microRNAs (miRNAs), of which 55 were novel. Differentially expressed miRNAs (DEMs) were identified that had significantly altered expression subject to stress type, genotype, and time-point. Transcriptome sequencing identified 49,436 genes, with differentially expressed genes (DEGs) linked to processes associated with hormone homeostasis, photosynthesis, and signaling. With the first durum wheat degradome report, over 100,000 transcript target sites were characterized, and new miRNA-mRNA regulatory pairs were discovered. Integrated omics analysis identified key miRNA-mRNA modules (particularly, novel pairs of miRNAs and transcription factors) with antagonistic regulatory patterns subject to different stresses. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis revealed significant roles in plant growth and stress adaptation. Our research provides novel and fundamental knowledge, at the whole-genome level, for transcriptional and post-transcriptional stress regulation in durum wheat.

TIAs pathway genes and associated miRNA identification in Vinca minor: supporting aspidosperma and eburnamine alkaloids linkage via transcriptomic analysis

V. minor contains monomeric eburnamine-type of indole alkaloids having utilization as a neuro-medicinal plant. The biosynthetic pathway studies using miRNAs has been the focal point for plant genomic research in recent years and this technique is utilized to get an insight into a possible pathway level study in V. minor as understanding of genes in this prized medicinal plant is meagrely understood. The de novo transcriptomic analysis using Illumina Next gen sequencing has been performed in glasshouse shifted plant and transformed roots to elucidate the possible non confirmed steps of terpenoid indole alkaloids (TIAs) pathway in V. minor. A putative TIA pathway is elucidated in the study including twelve possible TIAs biosynthetic genes. The specific miRNA associated with TIAs pathway were identified and their roles were discussed for the first time in V. minor. The comparative analysis of transcriptomic data of glasshouse shifted plant and transformed roots showed that the raw reads of transformed roots were higher (83,740,316) compared to glasshouse shifted plant (67,733,538). The EST-SSR prediction showed the maximum common repeats among glasshouse shifted plant and transformed roots, although small variation was found in trinucleotide repeats restricted to glasshouse shifted plant. The study reveals overall 37 miRNAs which were observed to be true and can have a role in pathway as they can regulate the growth and alkaloid production. The identification of putative pathway genes plays an important role in establishing linkage between Aspidosperma and Eburnamine alkaloids.

LncRNA improves cold resistance of winter wheat by interacting with miR398

One of the important functions of long non-coding RNA (lncRNA) is to be competing endogenous RNAs (ceRNAs). As miR398 is reported to respond to different stressors, it is necessary to explore its relationship with lncRNA in the cold resistance mechanism of winter wheat. Tae-miR398-precursor sequence was isolated from the winter wheat (Triticum aestivum). RLM-RACE verified that tae-miR398 cleaved its target CSD1. Quantitative detection at 5°C, -10°C and -25°C showed that the expression of tae-miR398 decreased in response to low temperatures, whereas CSD1 showed an opposite expression pattern. LncR9A, lncR117 and lncR616 were predicted and verified to interact with miR398. tae-miR398 and three lncRNAs were transferred into Arabidopsis thaliana respectively. The lncR9A were transferred into Brachypodium distachyom. Transgenic plants were cultivated at -8°C and assessed for the expression of malondialdehyde, chlorophyll, superoxide dismutase and miR398-lncRNA-target mRNA. The results demonstrate that tae-miR398 regulates low temperature tolerance by downregulating its target, CSD1. lncRNA regulates the expression of CSD1 indirectly by competitively binding miR398, which, in turn, affects the resistance of Dn1 to cold. miR398-regulation triggers a regulatory loop that is critical to cold stress tolerance in wheat. Our findings offer an improved strategy to crop plants with enhanced stress tolerance.

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.

Comparative profiling of roots small RNA expression and corresponding gene ontology and pathway analyses for low- and high-cadmium-accumulating genotypes of wheat in response to cadmium stress

MicroRNAs (miRNAs) participate in multiple biological processes in plant. Cd accumulation ability differs among varieties in wheat, but little is known about miRNAs and their function in Cd accumulation of wheat under Cd stress. Therefore, the present study detected small RNAs responsible for differential Cd accumulation between two contrasting wheat genotypes (low-Cd accumulation one L17 and high-Cd accumulation one H17) to identify novel targets to further study Cd stress in wheat. Under normal conditions, 139 miRNAs were differentially expressed between L17 and H17, while this value reached 142 after Cd exposure. For Cd-induced DEMs, total 25 miRNAs were differentially expressed in L17 after Cd treatment, while, 70 Cd-induced DEMs were found in H17. Moreover, GO analysis revealed that target genes of DEMs related to lipid biosynthetic process and chlorophyll binding are uniquely enriched in L17, target genes of DEMs related to ribosome biogenesis and sucrose alpha-glucosidase activity are uniquely enriched in H17. By pathway analysis, target genes of DEMs related to PI3K-Akt signaling pathway was specifically enriched in L17, target genes of DEMs related to carbohydrate digestion and absorption pathway was uniquely enriched in H17. In addition, miRNA-gene co-expression showed that tae-miR9774 was uniquely expressed between L17Cd and L17CK, while tae-miR398 was specially expressed between H17Cd and H17CK. Our results suggested that Cd-accumulating ability of L17 and H17 varied from the expression of induced unique miRNA, such as expression of tae-miR-9774 and tae-miR-398. Our study not only provide the foundation for further exploring the miRNAs-induced molecular mechanisms of Cd accumulation in wheat but also supply novel strategies for improving phytoremediation ability of food plants through genetic engineering.

Identification of Fusarium graminearum-responsive miRNAs and their targets in wheat by sRNA sequencing and degradome analysis

Fusarium head blight (FHB), a prevalent disease of bread wheat (Triticum aestivum L.) caused by Fusarium graminearum, leads to considerable losses of yield and quality in wheat production. MicroRNAs (miRNAs) are important regulators of plant defense responses. Here, to better understand the F. graminearum-responsive miRNAs, we constructed sRNA libraries for wheat cultivar Sumai 3 challenged with F. graminearum and sterile water, respectively. As a result, a total of 203 known miRNAs from 46 families and 68 novel miRNAs were identified. Among them, 18 known and six novel miRNAs were found to be differentially expressed between the F. graminearum-infected samples and the controls and thus were considered to be responsive to F. graminearum. The expression patterns of eight miRNAs were further validated by stem-loop qRT-PCR. Meanwhile, target genes were validated by degradome sequencing. Integrative analysis of the differentially expressed miRNAs and their targets revealed complex miRNA-mediated regulatory networks involved in the response of wheat to F. graminearum infection. Our findings are expected to facilitate a better understanding of the miRNA regulation in wheat-F. graminearum interaction.

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.

Salinity-associated microRNAs and their potential roles in mediating salt tolerance in rice colonized by the endophytic root fungus Piriformospora indica

Piriformospora indica (P. indica), an endophytic root fungus, supports the growth and enhanced tolerance of plants to biotic and abiotic stresses. Several recent studies showed the significant role of small RNA (sRNA) molecules including microRNAs (miRNAs) in plant adaption to environmental stress, but little is known concerning the symbiosis-mediated salt stress tolerance regulated at miRNAs level. The overarching goal of this research is to elucidate the impact of miRNAs in regulating the P. indica-mediated salt tolerance in rice. Applying sRNA-seq analysis led to identify a set of 547 differentially abundant miRNAs in response to P. indica inoculation and salt stress. These included 206 rice-specific and 341 previously known miRNAs from other plant species. In silico analysis of miRNAs predictions of the differentially abundant miRNAs led to identifying of 193 putatively target genes, most of which were encoded either genes or transcription factors involved in nutrient uptake, sodium ion transporters, growth regulators, and auxin- responsive proteins. The rice-specific miRNAs targeted the transcription factors involved in the import of potassium ions into the root cells, the export of sodium ions, and plant growth and development. Interestingly, P. indica affected the differential abundance of miRNAs regulated genes and transcription factors linked to salt stress tolerance. Our data helps to understand the molecular basis of salt stress tolerance mediated by symbionts in plant and the potential impact of miRNAs for genetic improvement of rice varieties for tolerance to salt stress.

Development of species specific putative miRNA and its target prediction tool in wheat (Triticum aestivum L.)

MicroRNA are 20-24 nt, non-coding, single stranded molecule regulating traits and stress response. Tissue and time specific expression limits its detection, thus is major challenge in their discovery. Wheat has limited 119 miRNAs in MiRBase due to limitation of conservation based methodology where old and new miRNA genes gets excluded. This is due to origin of hexaploid wheat by three successive hybridization, older AA, BB and younger DD subgenome. Species specific miRNA prediction (SMIRP concept) based on 152 thermodynamic features of training dataset using support vector machine learning approach has improved prediction accuracy to 97.7%. This has been implemented in TamiRPred ( http://webtom.cabgrid.res.in/tamirpred ). We also report highest number of putative miRNA genes (4464) of wheat from whole genome sequence populated in database developed in PHP and MySQL. TamiRPred has predicted 2092 (>45.10%) additional miRNA which was not predicted by miRLocator. Predicted miRNAs have been validated by miRBase, small RNA libraries, secondary structure, degradome dataset, star miRNA and binding sites in wheat coding region. This tool can accelerate miRNA polymorphism discovery to be used in wheat trait improvement. Since it predicts chromosome-wise miRNA genes with their respective physical location thus can be transferred using linked SSR markers. This prediction approach can be used as model even in other polyploid crops.

High-throughput sequencing of small RNAs revealed the diversified cold-responsive pathways during cold stress in the wild banana (Musa itinerans)

BACKGROUND

Cold stress is one of the most severe abiotic stresses affecting the banana production. Although some miRNAs have been identified, little is known about the role of miRNAs in response to cold stress in banana, and up to date, there is no report about the role of miRNAs in the response to cold stress in the plants of the cultivated or wild bananas.

RESULT

Here, a cold-resistant line wild banana (Musa itinerans) from China was used to profile the cold-responsive miRNAs by RNA-seq during cold stress. Totally, 265 known mature miRNAs and 41 novel miRNAs were obtained. Cluster analysis of differentially expressed (DE) miRNAs indicated that some miRNAs were specific for chilling or 0 °C treated responses, and most of them were reported to be cold-responsive; however, some were seldom reported to be cold-responsive in response to cold stress, e.g., miR395, miR408, miR172, suggesting that they maybe play key roles in response to cold stress. The GO and KEGG pathway enrichment analysis of DE miRNAs targets indicated that there existed diversified cold-responsive pathways, and miR172 was found likely to play a central coordinating role in response to cold stress, especially in the regulation of CK2 and the circadian rhythm. Finally, qPCR assays indicated the related targets were negatively regulated by the tested DE miRNAs during cold stress in the wild banana.

CONCLUSIONS

In this study, the profiling of miRNAs by RNA-seq in response to cold stress in the plants of the wild banana (Musa itinerans) was reported for the first time. The results showed that there existed diversified cold-responsive pathways, which provided insight into the roles of miRNAs during cold stress, and would be helpful for alleviating cold stress and cold-resistant breeding in bananas.

Comparative profiling of microRNAs and their effects on abiotic stress in wild-type and dark green leaf color mutant plants of Anthurium andraeanum 'Sonate'

MicroRNAs (miRNAs) are a class of non-coding small RNAs that play important roles in the regulation of gene expression. Although plant miRNAs have been extensively studied in model systems, less is known in other plants with limited genome sequence data, including Anthurium andraeanum. To identify miRNAs and their target genes in A. andraeanum and study their responses to abiotic stresses, we conducted deep-sequencing of two small RNA (sRNA) libraries prepared from young leaves of wild-type (WT) and dark green (dg) leaf color mutant plants of A. andraeanum 'Sonate'. A total of 53 novel miRNAs were identified, 32 of which have been annotated to 18 miRNA families. 10 putative miRNAs were found to be differentially expressed in WT and dg, among which two miRNAs were significantly up-regulated and eight down-regulated in dg relative to WT. One differentially expressed miRNA, Aa-miR408, was dramatically up-regulated in dg. qRT-PCR analysis and heterologous expression of Aa-miR408 in Arabidopsis under different stress treatments suggest that Aa-miR408 is involved in abiotic stress responses in A. andraeanum. Our results provide a foundation for further dissecting the roles of miRNAs and their targets in regulating abiotic stress tolerance in A. andraeanum.

New insights into tomato microRNAs

Cultivated tomato, Solanum lycopersicum, is one of the most common fruits in the global food industry. Together with the wild tomato Solanum pennellii, it is widely used for developing better cultivars. MicroRNAs affect mRNA regulation, inhibiting its translation and/or promoting its degradation. Important proteins involved in these processes are ARGONAUTE and DICER. This study aimed to identify and characterize the genes involved in the miRNA processing pathway, miRNA molecules and target genes in both species. We validated the presence of pathway genes and miRNA in different NGS libraries and 6 miRNA families using quantitative RT-PCR. We identified 71 putative proteins in S. lycopersicum and 108 in S. pennellii likely involved in small RNAs processing. Of these, 29 and 32 participate in miRNA processing pathways, respectively. We identified 343 mature miRNAs, 226 pre-miRNAs in 87 families, including 192 miRNAs, which were not previously identified, belonging to 38 new families in S. lycopersicum. In S. pennellii, we found 388 mature miRNAs and 234 pre-miRNAs contained in 85 families. All miRNAs found in S. pennellii were unpublished, being identified for the first time in our study. Furthermore, we identified 2471 and 3462 different miRNA target in S. lycopersicum and S. pennellii, respectively.

Elevated carbon dioxide and drought modulate physiology and storage-root development in sweet potato by regulating microRNAs

Elevated CO₂ along with drought is a serious global threat to crop productivity. Therefore, understanding the molecular mechanisms plants use to protect these stresses is the key for plant growth and development. In this study, we mimicked natural stress conditions under a controlled Soil-Plant-Atmosphere-Research (SPAR) system and provided the evidence for how miRNAs regulate target genes under elevated CO₂ and drought conditions. Significant physiological and biomass data supported the effective utilization of source-sink (leaf to root) under elevated CO₂. Additionally, elevated CO₂ partially rescued the effect of drought on total biomass. We identified both known and novel miRNAs differentially expressed during drought, CO₂, and combined stress, along with putative targets. A total of 32 conserved miRNAs belonged to 23 miRNA families, and 25 novel miRNAs were identified by deep sequencing. Using the existing sweet potato genome database and stringent analyses, a total of 42 and 22 potential target genes were predicted for the conserved and novel miRNAs, respectively. These target genes are involved in drought response, hormone signaling, photosynthesis, carbon fixation, sucrose and starch metabolism, etc. Gene ontology and KEGG ontology functional enrichment revealed that these miRNAs might target transcription factors (MYB, TCP, NAC), hormone signaling regulators (ARF, AP2/ERF), cold and drought factors (corA), carbon metabolism (ATP synthase, fructose-1,6-bisphosphate), and photosynthesis (photosystem I and II complex units). Our study is the first report identifying targets of miRNAs under elevated CO₂ levels and could support the molecular mechanisms under elevated CO₂ in sweet potato and other crops in the future.

TaMIR1139: a wheat miRNA responsive to Pi-starvation, acts a critical mediator in modulating plant tolerance to Pi deprivation

Wheat miRNA member TaMIR1139 targets genes functional in various families and plays crucial roles in regulating plant Pi starvation tolerance. Through regulating target genes at posttranscriptional or translational level, plant miRNAs are involved in mediating diverse biological processes associated with growth, development, and responses to adverse stresses. In this study, we characterized the expression pattern and function of TaMIR1139, a miRNA member of wheat (T. aestivum) under Pi deprivation. TaMIR1139 precursor is also present in N. tabucum, suggesting the conserved nature of miR1139 across monocots and eudicots. TaMIR1139 targets seven genes within different families. The transcripts abundance of TaMIR1139 was induced upon Pi deprivation and the upregulated expression under Pi starvation was downregulated by the Pi recovery treatment, In contrast, the genes targeted by TaMIR1139 exhibited reduced transcripts upon Pi starvation and their downregulated expression was recovered by Pi-recovery condition, suggesting the regulation of them under TaMIR1139 through a cleavage mechanism. TaMIR1139 overexpression conferred the Pi-deprived plants improved phenotype, biomass, photosynthesis, and Pi acquisition. Transcriptome analysis identified numerous genes involving biological process, cellular components, and molecular function were differentially expressed in the TaMIR1139 overexpression lines, which suggests the TaMIR1139-mediated plant Pi starvation tolerance to be associated with the role of miRNA in extensively modulating the transcript profiling. A phosphate transporter (PT) gene NtPT showed significantly upregulated expression in TaMIR1139 overexpression lines; overexpression of it conferred plants improved Pi acquisition upon Pi starvation, suggesting its contribution to the TaMIR1139-mediated plant low-Pi stress resistance. Our investigation indicates that TaMIR1139 is critical in plant Pi starvation tolerance through transcriptionally regulating the target genes and modulating the Pi stress-defensiveness processes.

MicroRNAs in durum wheat seedlings under chronic and short-term nitrogen stress

Nitrogen is an essential macronutrient for plant growth and reproduction. In durum wheat, an appropriate nitrogen soil availability is essential for an optimal seed development. miRNAs contribute to the environmental change adaptation of plants through the regulation of important genes involved in stress processes. In this work, nitrogen stress response was evaluated in durum wheat seedlings of Ciccio and Svevo cultivars. Eight small RNA libraries from leaves and roots of chronically stressed plants were sequenced to detect conserved and novel miRNAs. A total of 294 miRNAs were identified, 7 of which were described here for the first time. The expression level of selected miRNAs and target genes was analyzed by qPCR in seedlings subjected to chronic (Ciccio and Svevo, leaves and roots) or short-term (Svevo roots) stress conditions. Some miRNAs showed an immediate stress response, and their level of expression was either maintained or returned to a basal level during a long-term stress. Other miRNAs showed a gradual up- or downregulation during the short-term stress. The newly identified miRNA ttu-novel-106 showed an immediate strongly downregulation after nitrogen stress, which was negatively correlated with the expression of MYB-A, its putative target gene. PHO2 gene was significantly upregulated after 24-48-h stress, corresponding to a downregulation of miR399b. Ttu-miR399b putative binding sites in the 5' UTR region of the Svevo PHO2 gene were identified in the A and B genomes. Both MYB-A and PHO2 genes were validated for their cleavage site using 5' RACE assay.

Plant small RNAs: the essential epigenetic regulators of gene expression for salt-stress responses and tolerance

Saline environment cues distort the plant growth, development and crop yield. Epigenetics has emerged as one of the prime themes in plant functional genomics for molecular-stress-physiology research, as copious studies have provided new visions into the epigenetic control of stress adaptations. The epigenetic control is associated with the regulation of the expression of stress-related genes which also comprises many steady alterations inherited in next cellular generation as stress memory. These epigenetic amendments also implicate induction of small RNA (sRNA)-mediated fine-tuning of transcriptional and post-transcriptional regulations of gene expression. These tiny (19-24 nt) RNA species, particularly microRNAs (miRNAs) besides endogenous small interfering RNA (siRNA) have emerged as important responsive entities for epigenetic modulation of salt-stress effects on plants. There is a recent upsurge in development of tools and databases useful for prediction, identification and validation of small RNAs (sRNAs) and their target messenger RNAs (mRNAs). Therefore, these small but key regulatory molecules have received a wide attention in post-genomic era as potential targets for engineering stress tolerance in major glycophytic crops, though it is yet to be explored optimally. This review aims to provide critical updates on plant sRNAs as key epigenetic regulators of plant salt-stress responses, their target prediction and validation, computational tools and databases available for plant small RNAs, besides discussing their roles in salt-stress regulatory networks and adaptive mechanisms in plants, with special emphasis on their exploration for engineering salinity tolerance in plants.

Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences

BACKGROUND

MicroRNAs (miRNAs) are important for plant growth and responses to environmental stresses via post-transcriptional regulation of gene expression. Tea, which is primarily produced from one bud and two tender leaves of the tea plant (Camellia sinensis), is one of the most popular non-alcoholic beverages worldwide owing to its abundance of secondary metabolites. A large number of miRNAs have been identified in various plants, including non-model species. However, due to the lack of reference genome sequences and/or information of tea plant genome survey scaffold sequences, discovery of miRNAs has been limited in C. sinensis.

RESULTS

Using small RNA sequencing, combined with our recently obtained genome survey data, we have identified and analyzed 175 conserved and 83 novel miRNAs mainly in one bud and two tender leaves of the tea plant. Among these, 93 conserved and 18 novel miRNAs were validated using miRNA microarray hybridization. In addition, the expression pattern of 11 conserved and 8 novel miRNAs were validated by stem-loop-qRT-PCR. A total of 716 potential target genes of identified miRNAs were predicted. Further, Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that most of the target genes were primarily involved in stress response and enzymes related to phenylpropanoid biosynthesis. The predicted targets of 4 conserved miRNAs were further validated by 5'RLM-RACE. A negative correlation between expression profiles of 3 out of 4 conserved miRNAs (csn-miR160a-5p, csn-miR164a, csn-miR828 and csn-miR858a) and their targets (ARF17, NAC100, WER and MYB12 transcription factor) were observed.

CONCLUSION

In summary, the present study is one of few such studies on miRNA detection and identification in the tea plant. The predicted target genes of majority of miRNAs encoded enzymes, transcription factors, and functional proteins. The miRNA-target transcription factor gene interactions may provide important clues about the regulatory mechanism of these miRNAs in the tea plant. The data reported in this study will make a huge contribution to knowledge on the potential miRNA regulators of the secondary metabolism pathway and other important biological processes in C. sinensis.

RNA Sequencing and Co-expressed Long Non-coding RNA in Modern and Wild Wheats

There is an urgent need for the improvement of drought-tolerant bread and durum wheat. The huge and complex genome of bread wheat (BBAADD genome) stands as a vital obstruction for understanding the molecular mechanism underlying drought tolerance. However, tetraploid wheat (Triticum turgidum ssp., BBAA genome) is an ancestor of modern bread wheat and offers an important model for studying the drought response due to its less complex genome. Additionally, several wild relatives of tetraploid wheat have already shown a significant drought tolerance. We sequenced root transcriptome of three tetraploid wheat varieties with varying stress tolerance profiles, and built differential expression library of their transcripts under control and drought conditions. More than 5,000 differentially expressed transcripts were identified from each genotype. Functional characterization of transcripts specific to drought-tolerant genotype, revealed their association with osmolytes production and secondary metabolite pathways. Comparative analysis of differentially expressed genes and their non-coding RNA partners, long noncoding RNAs and microRNAs, provided valuable insight to gene expression regulation in response to drought stress. LncRNAs as well as coding transcripts share similar structural features in different tetraploid species; yet, lncRNAs slightly differ from coding transcripts. Several miRNA-lncRNA target pairs were detected as differentially expressed in drought stress. Overall, this study suggested an important pool of transcripts where their manipulations confer a better performance of wheat varieties under drought stress.

Durum wheat miRNAs in response to nitrogen starvation at the grain filling stage

Durum wheat highly depends on nitrogen for seed development and yield, and the obtainment of varieties with a better nitrogen use efficiency is crucial to reduce production costs and environmental pollution. In this study, sequencing of two small RNA libraries obtained from tissues of Ciccio and Svevo cultivars grown under nitrogen starvation conditions produced 84 novel, and 161 conserved miRNAs. Of these, 7 novel and 13 known miRNAs were newly identified in this work. Quantitative PCR analysis of selected miRNAs highlighted that the expression levels of some of them depends on the tissue and on the cultivar, Svevo being the most responsive to nitrogen starvation. A number of target genes were predicted to be involved in nitrogen metabolism. An inverse correlation for the qPCR expression data of miRNA/target pairs miR399b/PHO2, miR393c/AFB2, ttu-novel-61/CCAAT-TF was observed in specific tissues or cultivar. Especially, ttu-novel-61 was down-regulated and its target CCAAT-TF up-regulated in almost all tissues both in Svevo and in Ciccio. Moreover, CCAAT-TF was confirmed to be cleaved by ttu-novel-61 at the expected site. The discovery of miRNAs involved in the response to nitrogen stress represents an important step towards functional analyses, with the final aim to design strategies for improving nitrogen use efficiency in durum wheat.

Genome-Wide Identification and Characterization of Salinity Stress-Responsive miRNAs in Wild Emmer Wheat (Triticum turgidum ssp. dicoccoides)

MicroRNAs (miRNAs) are a class of endogenous small noncoding RNAs which regulate diverse molecular and biochemical processes at a post-transcriptional level in plants. As the ancestor of domesticated wheat, wild emmer wheat (Triticum turgidum ssp. dicoccoides) has great genetic potential for wheat improvement. However, little is known about miRNAs and their functions on salinity stress in wild emmer. To obtain more information on miRNAs in wild emmer, we systematically investigated and characterized the salinity-responsive miRNAs using deep sequencing technology. A total of 88 conserved and 124 novel miRNAs were identified, of which 50 were proven to be salinity-responsive miRNAs, with 32 significantly up-regulated and 18 down-regulated. miR172b and miR1120a, as well as mi393a, were the most significantly differently expressed. Targets of these miRNAs were computationally predicted, then Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis found that the targets of salinity-responsive miRNAs were enriched in transcription factors and stress-related proteins. Finally, we investigated the expression profiles of seven miRNAs ranging between salt-tolerant and sensitive genotypes, and found that they played critical roles in salinity tolerance in wild emmer. Our results systematically identified the salinity-responsive miRNAs in wild emmer, not only enriching the miRNA resource but also laying the foundation for further study on the biological functions and evolution of miRNAs in wild wheat and beyond.

MicroRNAs in model and complex organisms

Non-coding RNAs such as microRNAs (miRNAs) are very tiny ribonucleotides having an essential role in gene regulation at both post-transcriptional and translational levels. They are very conserved and expressed in worms, flies, plants, and mammals in a sequence-specific manner. Furthermore, it is now possible to clone miRNAs using the new genome editing tool CRISPR/cas9, which shows benefit in control of untargeted effect. In this special issue, we tried to cover researches associated with functional roles of miRNAs accross model and complex organisms.

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.

MicroRNA156 improves drought stress tolerance in alfalfa (Medicago sativa) by silencing SPL13

Alfalfa (Medicago sativa) is an important forage crop that is often grown in areas that frequently experience drought and water shortage. MicroRNA156 (miR156) is an emerging tool for improving various traits in plants. We tested the role of miR156d in drought response of alfalfa, and observed a significant improvement in drought tolerance of miR156 overexpression (miR156OE) alfalfa genotypes compared to the wild type control (WT). In addition to higher survival and reduced water loss, miR156OE genotypes also maintained higher stomatal conductance compared to WT during drought stress. Furthermore, we observed an enhanced accumulation of compatible solute (proline) and increased levels of abscisic acid (ABA) and antioxidants in miR156OE genotypes. Similarly, alfalfa plants with reduced expression of miR156-targeted SPL13 showed reduced water loss and enhanced stomatal conductance, chlorophyll content and photosynthetic assimilation. Several genes known to be involved in drought tolerance were differentially expressed in leaf and root of miR156 overexpression plants. Taken together, our findings reveal that miR156 improves drought tolerance in alfalfa at least partially by silencing SPL13.

Long noncoding miRNA gene represses wheat β-diketone waxes

The cuticle of terrestrial plants functions as a protective barrier against many biotic and abiotic stresses. In wheat and other Triticeae, β-diketone waxes are major components of the epicuticular layer leading to the bluish-white glaucous trait in reproductive-age plants. Glaucousness in durum wheat is controlled by a metabolic gene cluster at the WAX1 (W1) locus and a dominant suppressor INHIBITOR of WAX1 (Iw1) on chromosome 2B. The wheat D subgenome from progenitor Aegilops tauschii contains W2 and Iw2 paralogs on chromosome 2D. Here we identify the Iw1 gene from durum wheat and demonstrate the unique regulatory mechanism by which Iw1 acts to suppress a carboxylesterase-like protein gene, W1-COE, within the W1 multigene locus. Iw1 is a long noncoding RNA (lncRNA) containing an inverted repeat (IR) with >80% identity to W1-COE The Iw1 transcript forms a miRNA precursor-like long hairpin producing a 21-nt predominant miRNA, miRW1, and smaller numbers of related sRNAs associated with the nonglaucous phenotype. When Iw1 was introduced into glaucous bread wheat, miRW1 accumulated, W1-COE and its paralog W2-COE were down-regulated, and the phenotype was nonglaucous and β-diketone-depleted. The IR region of Iw1 has >94% identity to an IR region on chromosome 2 in Ae. tauschii that also produces miRW1 and lies within the marker-based location of Iw2 We propose the Iw loci arose from an inverted duplication of W1-COE and/or W2-COE in ancestral wheat to form evolutionarily young miRNA genes that act to repress the glaucous trait.

Characterization of miR061 and its target genes in grapevine responding to exogenous gibberellic acid

MicroRNAs (miRNAs), as an important growth regulator, are also involved in gibberellic acid (GA) signaling, revealing much relationship between miRNAs and GA in various plant responses. Grape is highly sensitive to GA₃, which plays a significant regulatory role in regulation of flower development, berry expansion, berry set, berry ripening, and seedlessness induction; further, it was found that grapevine miR061 (VvmiR061) is a GA₃ responsive miRNA. In this study, grapevine REV (VvREV) and HOX32 (VvHOX32), two target genes of VvmiR061, were predicted, verified, and cloned; homologous conservation was analyzed in various plants. The expression profiles of both VvmiR061 and its target genes (VvREV and VvHOX32) under GA₃ treatment were detected by qRT-PCR during grapevine flower and berry development. Results revealed that GA₃ treatment has upregulated the transcription of VvREV and VvHOX32, while it downregulated the expression of VvmiR061. The function of VvmiR061 in cleaving target genes VvREV and VvHOX32 was diminished by GA₃ treatment during flower developmental process. The results of this study exhibited the importance of VvmiR061 in regulating flower development and GA₃ signaling pathway and also contributed some to the knowledge of small RNA-mediated regulation in grape.

Response of microRNAs to cold treatment in the young spikes of common wheat

Background

MicroRNAs (miRNAs) are a class of small non-coding RNAs that play important roles in biotic and abiotic stresses by regulating their target genes. For common wheat, spring frost damage frequently occurs, especially when low temperature coincides with plants at early floral organ differentiation, which may result in significant yield loss. Up to date, the role of miRNAs in wheat response to frost stress is not well understood.

Results

We report here the sequencing of small RNA transcriptomes from the young spikes that were treated with cold stress and the comparative analysis with those of the control. A total of 192 conserved miRNAs from 105 families and nine novel miRNAs were identified. Among them, 34 conserved and five novel miRNAs were differentially expressed between the cold-stressed samples and the controls. The expression patterns of 18 miRNAs were further validated by quantitative real time polymerase chain reaction (qRT-PCR). Moreover, nearly half of the miRNAs were cross inducible by biotic and abiotic stresses when compared with previously published work. Target genes were predicted and validated by degradome sequencing. Gene Ontology (GO) enrichment analysis showed that the target genes of differentially expressed miRNAs were enriched for response to the stimulus, regulation of transcription, and ion transport functions. Since many targets of differentially expressed miRNAs were transcription factors that are associated with floral development such as ARF, SPB (Squamosa Promoter Binding like protein), MADS-box (MCM1, AG, DEFA and SRF), MYB, SPX (SYG1, Pho81 and XPR1), TCP (TEOSINTE BRANCHED, Cycloidea and PCF), and PPR (PentatricoPeptide Repeat) genes, cold-altered miRNA expression may cause abnormal reproductive organ development.

Conclusion

Analysis of small RNA transcriptomes and their target genes provide new insight into miRNA regulation in developing wheat inflorescences under cold stress. MiRNAs provide another layer of gene regulation in cold stress response that can be genetically manipulated to reduce yield loss in wheat.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3556-2) contains supplementary material, which is available to authorized users.

Genome-wide analysis of miRNAs and Tasi-RNAs in Zea mays in response to phosphate deficiency

Globally important cereal crop maize provides important nutritions and starch in dietary foods. Low phosphate (LPi) availability in the soil frequently limits the maize quality and yield across the world. Small non-coding RNAs (Snc-RNAs) play crucial roles in growth and adaptation of plants to the environment. Snc-RNAs like microRNAs (miRs) and trans-acting small interfering RNAs (Tasi-Rs) play important functions in posttranscriptional regulation of gene expression, which controls plant development, reproduction, and biotic/abiotic stress responses. In order to identify the miR and Tasi-R alterations in leaf and root of maize in response to sufficient phosphate and LPi at 3LS and 4LS, the snc-RNA population libraries for 0th, 1st, 2nd, 4th, and 8th day were constructed. These libraries were used for genome-wide alignment and RNA-fold analysis for possible prediction of potential miRs and Tasi-Rs. This study reported 174 known and conserved differentially expressed miRs of 27 miR families of maize plant. In addition, leaf and root specific potential novel miRs representing 155 new families were also discovered. Differentially expressed conserved as well as novel miR functions in root and leaf during early stage of Pi starvation were extensively discussed. Leaf and root specific miRs as well as common miRs with their target genes, participating in different biological, cellular, and metabolic processes were explored. Further, four miR390-directed Tasi-Rs which belong to TAS3 gene family along with other orthologs of Tasi-Rs were also identified. Finally, the study provides an insight into the composite regulatory mechanism of miRs in maize in response to Pi deficiency.

Uncovering leaf rust responsive miRNAs in wheat (Triticum aestivum L.) using high-throughput sequencing and prediction of their targets through degradome analysis

Deep sequencing identified 497 conserved and 559 novel miRNAs in wheat, while degradome analysis revealed 701 targets genes. QRT-PCR demonstrated differential expression of miRNAs during stages of leaf rust progression. Bread wheat (Triticum aestivum L.) is an important cereal food crop feeding 30 % of the world population. Major threat to wheat production is the rust epidemics. This study was targeted towards identification and functional characterizations of micro(mi)RNAs and their target genes in wheat in response to leaf rust ingression. High-throughput sequencing was used for transcriptome-wide identification of miRNAs and their expression profiling in retort to leaf rust using mock and pathogen-inoculated resistant and susceptible near-isogenic wheat plants. A total of 1056 mature miRNAs were identified, of which 497 miRNAs were conserved and 559 miRNAs were novel. The pathogen-inoculated resistant plants manifested more miRNAs compared with the pathogen infected susceptible plants. The miRNA counts increased in susceptible isoline due to leaf rust, conversely, the counts decreased in the resistant isoline in response to pathogenesis illustrating precise spatial tuning of miRNAs during compatible and incompatible interaction. Stem-loop quantitative real-time PCR was used to profile 10 highly differentially expressed miRNAs obtained from high-throughput sequencing data. The spatio-temporal profiling validated the differential expression of miRNAs between the isolines as well as in retort to pathogen infection. Degradome analysis provided 701 predicted target genes associated with defense response, signal transduction, development, metabolism, and transcriptional regulation. The obtained results indicate that wheat isolines employ diverse arrays of miRNAs that modulate their target genes during compatible and incompatible interaction. Our findings contribute to increase knowledge on roles of microRNA in wheat-leaf rust interactions and could help in rust resistance breeding programs.

Water-deficit stress-responsive microRNAs and their targets in four durum wheat genotypes

MicroRNAs (miRNAs) guide regulation at the post-transcriptional level by inducing messenger RNA (mRNA) degradation or translational inhibition of their target protein-coding genes. Durum wheat miRNAs may contribute to the genotypic water-deficit stress response in different durum varieties. Further investigation of the interactive miRNA-target regulatory modules and experimental validation of their response to water stress will contribute to our understanding of the small RNA-mediated molecular networks underlying stress adaptation in durum wheat. In this study, a comprehensive genome-wide in silico analysis using the updated Triticum transcriptome assembly identified 2055 putative targets for 113 conserved durum miRNAs and 131 targets for four novel durum miRNAs that putatively contribute to genotypic stress tolerance. Predicted mRNA targets encode various transcription factors, binding proteins and functional enzymes, which play vital roles in multiple biological pathways such as hormone signalling and metabolic processes. Quantitative PCR profiling further characterised 43 targets and 5 miRNAs with stress-responsive and/or genotype-dependent differential expression in two stress-tolerant and two stress-sensitive durum genotypes subjected to pre-anthesis water-deficit stress. Furthermore, a 5' RLM-RACE approach validated nine mRNA targets cleaved by water-deficit stress-responsive miRNAs, which, to our knowledge, has not been previously reported in durum wheat. The present study provided experimental evidence of durum miRNAs and target genes in response to water-deficit stress in contrasting durum varieties, providing new insights into the regulatory roles of the miRNA-guided RNAi mechanism underlying stress adaptation in durum wheat.

The miRNAome of durum wheat: isolation and characterisation of conserved and novel microRNAs and their target genes

Background

The allotetraploid durum wheat [Triticum turgidum subsp. durum (Desf.) Husn.] is a highly economically important species especially in the Mediterranean basin. However, its genomics, transcriptomics and in particular microRNAome are still largely unknown.

Results

In the present work, two small RNA libraries from durum wheat Ciccio and Svevo cultivars were generated from different tissues at the late milk (Z77) developmental stage. A total of 167 conserved and 98 potential novel miRNAs were identified in the two libraries and interestingly, three novel miRNAs were found to be derived from ribosomal RNA. Putative target genes were predicted for conserved and novel miRNAs, the majority of which interact with nucleic acids, according to GO terms relative to molecular function. Quantitative qPCR analysis showed that several miRNAs identified were differentially expressed in the mature (Z77) developmental stage compared to young (Z14) tissues. Moreover, target gene expression analysis suggested that in roots, the putative genes encoding for the SQUAMOSA SPL2 and TGA1 proteins are regulated by ttu-miR156n, while MYB3 transcription factor by ttu-miR319f. Additionally, the Photosystem II P680 chlorophyll A apoprotein gene showed an expression level negatively correlated to that of ttu-novel-48 in leaves.

Conclusion

Our results suggest that, in durum wheat, these genes may play important roles in root/leaf development and are subjected to miRNA regulation. The prediction of novel miRNAs putatively derived from ribosomal RNA opens new perspectives on the study of plant miRNAs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2838-4) contains supplementary material, which is available to authorized users.

Characterization of wheat miRNAs and their target genes responsive to cadmium stress

A increasing number of microRNAs have been shown to play important regulatory roles in plant responses to various metal stresses. However, little information about miRNAs especially miRNAs responsive to cadmium (Cd) stress is available in wheat. To investigate the role of miRNAs in responses to Cd stress, wheat seedlings were subjected to 250 μM Cd solution for 6, 12, 24 and 48 h, and analyses of morphological and physiological changes as well as the expression of five miRNAs and their corresponding targets were carried out. Our results demonstrated that miRNAs and their targets were differentially expressed in leaves and roots of wheat seedlings exposed to Cd stress. Furthermore, miR398 may involve in oxidative stress tolerance by regulating its target CSD to participate in Cd stress. Among ten miRNA-target pairs studied, nine pairs showed complex regulation relationship in leaves and roots of wheat seedlings exposed to Cd stress. These findings suggested that miRNAs are involved in the mediation of Cd stress signaling responses in wheat. The characterization of the miRNAs and the associated targets in responses to Cd exposure provides a framework for understanding the molecular mechanism of heavy metal tolerance in plants.

Wheat miRNA ancestors: evident by transcriptome analysis of A, B, and D genome donors

MicroRNAs are critical players of post-transcriptional gene regulation with profound effects on the fundamental processes of cellular life. Their identification and characterization, together with their targets, hold great significance in exploring and exploiting their roles on a functional context, providing valuable clues into the regulation of important biological processes, such as stress tolerance or environmental adaptation. Wheat is a hardy crop, extensively harvested in temperate regions, and is a major component of the human diet. With the advent of the next generation sequencing technologies considerably decreasing sequencing costs per base-pair, genomic, and transcriptomic data from several wheat species, including the progenitors and wild relatives have become available. In this study, we performed in silico identification and comparative analysis of microRNA repertoires of bread wheat (Triticum aestivum L.) and its diploid progenitors and relatives, Aegilops sharonensis, Aegilops speltoides, Aegilops tauschii, Triticum monococcum, and Triticum urartu through the utilization of publicly available transcriptomic data. Over 200 miRNA families were identified, majority of which have not previously been reported. Ancestral relationships expanded our understanding of wheat miRNA evolution, while T. monococcum miRNAs delivered important clues on the effects of domestication on miRNA expression. Comparative analyses on wild Ae. sharonensis accessions highlighted candidate miRNAs that can be linked to stress tolerance. The miRNA repertoires of bread wheat and its diploid progenitors and relatives provide important insight into the diversification and distribution of miRNA genes, which should contribute to the elucidation of miRNA evolution of Poaceae family. A thorough understanding of the convergent and divergent expression profiles of miRNAs in different genetic backgrounds can provide unique opportunities to modulation of gene regulation for better crop performance.

Topological characteristics of target genes regulated by abiotic-stress-responsible miRNAs in a rice interactome network

A great number of microRNAs (miRNAs) have been identified in responding and acting in gene regulatory networks associated with plant tolerance to abiotic stress conditions, such as drought, salinity, and high temperature. The topological exploration of target genes regulated by abiotic-stress-responsible miRNAs (ASRmiRs) in a network facilitates to discover the molecular basis of plant abiotic stress response. This study was based on the staple food rice (Oryza sativa) in which ASRmiRs were manually curated. After having compared the topological properties of target genes (stress-miR-targets) with those (non-stress-miR-targets) not regulated by ASRmiRs in a rice interactome network, we found that stress-miR-targets exhibited distinguishable topological properties. The interaction probability analysis and k-core decomposition showed that stress-miR-targets preferentially interacted with non-stress-miR-targets and located at the peripheral positions in the network. Our results indicated an obvious topological distinction between the two types of genes, reflecting the specific mechanisms of action of stress-miR-targets in rice abiotic stress response. Also, the results may provide valuable clues to elucidate molecular mechanisms of crop response to abiotic stress.

Dissecting miRNAs in Wheat D Genome Progenitor, Aegilops tauschii

As the post-transcriptional regulators of gene expression, microRNAs or miRNAs comprise an integral part of understanding how genomes function. Although miRNAs have been a major focus of recent efforts, miRNA research is still in its infancy in most plant species. Aegilops tauschii, the D genome progenitor of bread wheat, is a wild diploid grass exhibiting remarkable population diversity. Due to the direct ancestry and the diverse gene pool, A. tauschii is a promising source for bread wheat improvement. In this study, a total of 87 Aegilops miRNA families, including 51 previously unknown, were computationally identified both at the subgenomic level, using flow-sorted A. tauschii 5D chromosome, and at the whole genome level. Predictions at the genomic and subgenomic levels suggested A. tauschii 5D chromosome as rich in pre-miRNAs that are highly associated with Class II DNA transposons. In order to gain insights into miRNA evolution, putative 5D chromosome miRNAs were compared to its modern ortholog, Triticum aestivum 5D chromosome, revealing that 48 of the 58 A. tauschii 5D miRNAs were conserved in orthologous T. aestivum 5D chromosome. The expression profiles of selected miRNAs (miR167, miR5205, miR5175, miR5523) provided the first experimental evidence for miR5175, miR5205 and miR5523, and revealed differential expressional changes in response to drought in different genetic backgrounds for miR167 and miR5175. Interestingly, while miR5523 coding regions were present and expressed as pre-miR5523 in both T. aestivum and A. tauschii, the expression of mature miR5523 was observed only in A. tauschii under normal conditions, pointing out to an interference at the downstream processing of pre-miR5523 in T. aestivum. Overall, this study expands our knowledge on the miRNA catalog of A. tauschii, locating a subset specifically to the 5D chromosome, with ample functional and comparative insight which should contribute to and complement efforts to develop drought tolerant wheat varieties.

A Comprehensive Prescription for Plant miRNA Identification

microRNAs (miRNAs) are tiny ribo-regulatory molecules involved in various essential pathways for persistence of cellular life, such as development, environmental adaptation, and stress response. In recent years, miRNAs have become a major focus in molecular biology because of their functional and diagnostic importance. This interest in miRNA research has resulted in the development of many specific software and pipelines for the identification of miRNAs and their specific targets, which is the key for the elucidation of miRNA-modulated gene expression. While the well-recognized importance of miRNAs in clinical research pushed the emergence of many useful computational identification approaches in animals, available software and pipelines are fewer for plants. Additionally, existing approaches suffers from mis-identification and annotation of plant miRNAs since the miRNA mining process for plants is highly prone to false-positives, particularly in cereals which have a highly repetitive genome. Our group developed a homology-based in silico miRNA identification approach for plants, which utilizes two Perl scripts "SUmirFind" and "SUmirFold" and since then, this method helped identify many miRNAs particularly from crop species such as Triticum or Aegliops. Herein, we describe a comprehensive updated guideline by the implementation of two new scripts, "SUmirPredictor" and "SUmirLocator," and refinements to our previous method in order to identify genuine miRNAs with increased sensitivity in consideration of miRNA identification problems in plants. Recent updates enable our method to provide more reliable and precise results in an automated fashion in addition to solutions for elimination of most false-positive predictions, miRNA naming and miRNA mis-annotation. It also provides a comprehensive view to genome/transcriptome-wide location of miRNA precursors as well as their association with transposable elements. The "SUmirPredictor" and "SUmirLocator" scripts are freely available together with a reference high-confidence plant miRNA list.

Root precursors of microRNAs in wild emmer and modern wheats show major differences in response to drought stress

MicroRNAs, small regulatory molecules with significant impacts on the transcriptional network of all living organisms, have been the focus of several studies conducted mostly on modern wheat cultivars. In this study, we investigated miRNA repertoires of modern durum wheat and its wild relatives, with differing degrees of drought tolerance, to identify miRNA candidates and their targets involved in drought stress response. Root transcriptomes of Triticum turgidum ssp. durum variety Kızıltan and two Triticum turgidum ssp. dicoccoides genotypes TR39477 and TTD-22 under control and drought conditions were assembled from individual RNA-Seq reads and used for in silico identification of miRNAs. A total of 66 miRNAs were identified from all species, across all conditions, of which 46 and 38 of the miRNAs identified from modern durum wheat and wild genotypes, respectively, had not been previously reported. Genotype- and/or stress-specific miRNAs provide insights into our understanding of the complex drought response. Particularly, miR1435, miR5024, and miR7714, identified only from drought-stress roots of drought-tolerant genotype TR39477, can be candidates for future studies to explore and exploit the drought response to develop tolerant varieties.

MicroRNA nomenclature and the need for a revised naming prescription

A central environment and interface for microRNA (miRNA) registry and repository and a general standardized framework for their systematic annotation was established over a decade ago. However, the numbers of experimentally and computationally identified miRNAs are swiftly accumulating, and new aspects of miRNA-mediated gene regulation are being revealed. Currently, it is of great significance that the annotation framework should be redefined to include newly discovered miRNA species such as the variants of mature miRNAs (isomiRNAs), and organellar miRNAs: cipomiRNAs and mitomiRNAs. It is also of great importance that key terminology referring to the novelty, evolutionary history or biogenesis of miRNAs, as well as the confidence of their identification are standardized in the literature and disseminated in a central miRNA registry. Here, we review the status of miRNA nomenclature, curation and critical points of need for a revision of miRNA nomenclature and terminology.

Plant miRNAs: biogenesis, organization and origins

MicroRNAs, or miRNAs, are posttranscriptional regulators of gene expression. A wealth of observations and findings suggest highly complex, multicomponent, and intermingled pathways governing miRNA biogenesis and miRNA-mediated gene silencing. Plant miRNA genes are usually found as individual entities scattered around the intergenic and-to a much lesser extent-intragenic space, while miRNA gene clusters, formed by tandem or segmental duplications, also exist in plant genomes. Genome duplications are proposed to contribute to miRNA family expansions, as well. Evolutionarily young miRNAs retaining extensive homology to their loci of origin deliver important clues into miRNA origins and evolution. Additionally, imprecisely processed miRNAs evidence noncanonical routes of biogenesis, which may affect miRNA expression levels or targeting capabilities. Majority of the knowledge regarding miRNAs comes from model plant species. As ongoing research progressively expands into nonmodel systems, our understanding of miRNAs and miRNA-related pathways changes which opens up new perspectives and frontiers in miRNA research.

Molecular organization and comparative analysis of chromosome 5B of the wild wheat ancestor Triticum dicoccoides

Wild emmer wheat, Triticum turgidum ssp. dicoccoides is the wild relative of Triticum turgidum, the progenitor of durum and bread wheat, and maintains a rich allelic diversity among its wild populations. The lack of adequate genetic and genomic resources, however, restricts its exploitation in wheat improvement. Here, we report next-generation sequencing of the flow-sorted chromosome 5B of T. dicoccoides to shed light into its genome structure, function and organization by exploring the repetitive elements, protein-encoding genes and putative microRNA and tRNA coding sequences. Comparative analyses with its counterparts in modern and wild wheats suggest clues into the B-genome evolution. Syntenic relationships of chromosome 5B with the model grasses can facilitate further efforts for fine-mapping of traits of interest. Mapping of 5B sequences onto the root transcriptomes of two additional T. dicoccoides genotypes, with contrasting drought tolerances, revealed several thousands of single nucleotide polymorphisms, of which 584 shared polymorphisms on 228 transcripts were specific to the drought-tolerant genotype. To our knowledge, this study presents the largest genomics resource currently available for T. dicoccoides, which, we believe, will encourage the exploitation of its genetic and genomic potential for wheat improvement to meet the increasing demand to feed the world.

From Genetics to Functional Genomics: Improvement in Drought Signaling and Tolerance in Wheat

Drought being a yield limiting factor has become a major threat to international food security. It is a complex trait and drought tolerance response is carried out by various genes, transcription factors (TFs), microRNAs (miRNAs), hormones, proteins, co-factors, ions, and metabolites. This complexity has limited the development of wheat cultivars for drought tolerance by classical breeding. However, attempts have been made to fill the lost genetic diversity by crossing wheat with wild wheat relatives. In recent years, several molecular markers including single nucleotide polymorphisms (SNPs) and quantitative trait loci (QTLs) associated with genes for drought signaling pathways have been reported. Screening of large wheat collections by marker assisted selection (MAS) and transformation of wheat with different genes/TFs has improved drought signaling pathways and tolerance. Several miRNAs also provide drought tolerance to wheat by regulating various TFs/genes. Emergence of OMICS techniques including transcriptomics, proteomics, metabolomics, and ionomics has helped to identify and characterize the genes, proteins, metabolites, and ions involved in drought signaling pathways. Together, all these efforts helped in understanding the complex drought tolerance mechanism. Here, we have reviewed the advances in wide hybridization, MAS, QTL mapping, miRNAs, transgenic technique, genome editing system, and above mentioned functional genomics tools for identification and utility of signaling molecules for improvement in wheat drought tolerance.