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

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

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

Investigation of two-pore K+ (TPK) channels in Triticum aestivum L. suggests their role in stress response

Two-pore K+ (TPK) channels are voltage-independent and involved in stress response in plants. Herein, we identified 12 TaTPK genes located on nine chromosomes in the Triticum aestivum genome. The majority of TaTPK genes comprised two exons. Each TaTPK channel comprised four transmembrane (TM) helices, N- and C-terminal ion-channel domains, two EF-hand domains and one 14-3-3 binding site. Additionally, highly conserved 'GYGD' motif responsible for K+ ion specificity, was found in between the TMs in both the ion-channel domains. Nine TaTPK channels were predicted to be localised at the plasma membrane, while three were vacuolar. The protein-protein and protein-chemical interactions indicated the coordinated functioning of the TaTPK channels with the other K+ transporters and their possible interaction with the Ca2+-signaling pathway. Expression studies suggested their importance in both vegetative and reproductive tissues development. Significantly modulated expression of various TaTPK genes during heat, drought, combined heat and drought and salt stresses, and after fungal infestation, depicted their function in stress responses. The miRNAs and transcription factors interaction analyses suggested their role in the hormone, light, growth and development-related, and stress-responsive signaling cascades. The current study suggested vital functions of various TaTPK genes, especially in stress response, and would provide an opportunity for their detailed characterization in future studies.

A Survey of the Transcriptomic Resources in Durum Wheat: Stress Responses, Data Integration and Exploitation

Durum wheat (Triticum turgidum subsp. durum (Desf.) Husn.) is an allotetraploid cereal crop of worldwide importance, given its use for making pasta, couscous, and bulgur. Under climate change scenarios, abiotic (e.g., high and low temperatures, salinity, drought) and biotic (mainly exemplified by fungal pathogens) stresses represent a significant limit for durum cultivation because they can severely affect yield and grain quality. The advent of next-generation sequencing technologies has brought a huge development in transcriptomic resources with many relevant datasets now available for durum wheat, at various anatomical levels, also focusing on phenological phases and environmental conditions. In this review, we cover all the transcriptomic resources generated on durum wheat to date and focus on the corresponding scientific insights gained into abiotic and biotic stress responses. We describe relevant databases, tools and approaches, including connections with other "omics" that could assist data integration for candidate gene discovery for bio-agronomical traits. The biological knowledge summarized here will ultimately help in accelerating durum wheat breeding.

MicroRNAs balance growth and salt stress responses in sweet sorghum

Salt stress is one of the major causes of reduced crop production, limiting agricultural development globally. Plants have evolved with complex systems to maintain the balance between growth and stress responses, where signaling pathways such as hormone signaling play key roles. Recent studies revealed that hormones are modulated by microRNAs (miRNAs). Previously, two sweet sorghum (Sorghum bicolor) inbred lines with different salt tolerance were identified: the salt-tolerant M-81E and the salt-sensitive Roma. The levels of endogenous hormones in M-81E and Roma varied differently under salt stress, showing a different balance between growth and stress responses. miRNA and degradome sequencing showed that the expression of many upstream transcription factors regulating signal transduction and hormone-responsive genes was directly induced by differentially expressed miRNAs, whose levels were very different between the two sweet sorghum lines. Furthermore, the effects of representative miRNAs on salt tolerance in sorghum were verified through a transformation system mediated by Agrobacterium rhizogenes. Also, miR-6225-5p reduced the level of Ca²⁺ in the miR-6225-5p-overexpressing line by inhibiting the expression of the Ca²⁺ uptake gene SbGLR3.1 in the root epidermis and affected salt tolerance in sorghum. This study provides evidence for miRNA-mediated growth and stress responses in sweet sorghum.

Wheat Omics: Advancements and Opportunities

Plant omics, which includes genomics, transcriptomics, metabolomics and proteomics, has played a remarkable role in the discovery of new genes and biomolecules that can be deployed for crop improvement. In wheat, great insights have been gleaned from the utilization of diverse omics approaches for both qualitative and quantitative traits. Especially, a combination of omics approaches has led to significant advances in gene discovery and pathway investigations and in deciphering the essential components of stress responses and yields. Recently, a Wheat Omics database has been developed for wheat which could be used by scientists for further accelerating functional genomics studies. In this review, we have discussed various omics technologies and platforms that have been used in wheat to enhance the understanding of the stress biology of the crop and the molecular mechanisms underlying stress tolerance.

Glutathione imparts stress tolerance against Alternaria brassicicola infection via miRNA mediated gene regulation

Glutathione (GSH) is well known to play a crucial role in imparting resistance against various pathogen invasions. Nevertheless, the role of GSH in regulating miRNA-mediated defense response is yet to be explored. To decipher the GSH-mediated regulation of miRNA expression during necrotrophic infection in Arabidopsis thaliana, wild-type Col-0 and AtECS1, the transgenic line exhibiting enhanced GSH content, were infected with necrotrophic pathogen Alternaria brassicicola. AtECS1 plants exhibited enhanced resistance as compared to wild-type. MiRNA next-generation sequencing (NGS) was performed to compare the miRNA expression in Col-0 and AtECS1 leaves. Under control condition, differentially expressed 96 known miRNAs and 17 novel miRNAs viz. ath-miR8167f, ath-miR1886.3, ath-miR3932b-5p, etc. were identified. However, under infected condition, 73 known and 43 novel differentially expressed miRNAs viz. ath-miR5652, ath-miR160b, ath-miR865-5p, etc. were identified. Functional annotation and enrichment analysis revealed that several miRNAs that target defense-related genes like leucine-rich repeat protein kinase, MYB transcription factors, TCP8, etc. were down regulated in the AtECS1 line, which, in turn, relieves the repression of their target gene expression, leading to resistance against infection. Together, the present investigation suggests that GSH plays a decisive role in modulating the miRNA-mediated regulation of defense-related genes during pathogen invasion.

Plant responses to drought stress: microRNAs in action

Drought is common in most regions of the world, and it has a significant impact on plant growth and development. Plants, on the other hand, have evolved their own defense systems to deal with the extreme weather. The reprogramming of gene expression by microRNAs (miRNAs) is one of these defense mechanisms. miRNAs are short noncoding RNAs that have emerged as key post-transcriptional gene regulators in a variety of species. Drought stress modulates the expression of certain miRNAs that are functionally conserved across plant species. These characteristics imply that miRNA-based genetic changes might improve drought resistance in plants. This study highlights current knowledge of plant miRNA biogenesis, regulatory mechanisms and their role in drought stress responses. miRNAs functions and their adaptations by plants during drought stress has also been explained that can be exploited to promote drought-resistance among economically important crops.

Recent Developments in the Application of Plant Growth-Promoting Drought Adaptive Rhizobacteria for Drought Mitigation

Drought intensity that has increased as a result of human activity and global warming poses a serious danger to agricultural output. The demand for ecologically friendly solutions to ensure the security of the world's food supply has increased as a result. Plant growth-promoting rhizobacteria (PGPR) treatment may be advantageous in this situation. PGPR guarantees the survival of the plant during a drought through a variety of processes including osmotic adjustments, improved phytohormone synthesis, and antioxidant activity, among others and these mechanisms also promote the plant's development. In addition, new developments in omics technology have improved our understanding of PGPR, which makes it easier to investigate the genes involved in colonizing plant tissue. Therefore, this review addresses the mechanisms of PGPR in drought stress resistance to summarize the most current omics-based and molecular methodologies for exploring the function of drought-responsive genes. The study discusses a detailed mechanistic approach, PGPR-based bioinoculant design, and a potential roadmap for enhancing their efficacy in combating drought stress.

Physiological and molecular responses of Phalaris arundinacea under salt stress on the Tibet plateau

Phalaris arundinacea, with its characteristics of rapid growth and high biological yield, is regarded as an excellent forage grass in the Qinghai-Tibetan Plateau region of China. To explore the physiological and molecular response mechanism of Phalaris arundinacea under salt stress, we monitored the biomass and physiological indexes of two locally grown strains under conditions of exposure to 150 and 300 mM NaCl solution. Z0611 exhibited better salt stress tolerance than YS. Transcriptome sequencing analysis showed that YS and Z0611 had 1713 and 4290 differentially expressed genes (DEGs), respectively, including on metabolic processes, single-organism process, catalytic activity, and plant hormone signal transduction in the GO and KEGG databases. We also identified a large number of genes involved in hormone signaling, antioxidant systems, ion homeostasis, and photosynthetic systems. Our study provides physiological and molecular insight for establishing a salt resistance database and mining salt tolerance genes in Phalaris arundinacea, and also provides theoretical guidance for the restoration of saline-alkali land on the Qinghai-Tibet Plateau.

Integrate Small RNA and Degradome Sequencing to Reveal Drought Memory Response in Wheat (Triticum aestivum L.)

Drought has gradually become one of the most severe abiotic stresses on plants. Plants that experience stress training can exhibit enhanced stress tolerance. According to MicroRNA (miRNA) sequencing data, this study identified 195 candidate drought memory-related miRNAs in wheat, and targets of 64 (32.8%) candidate miRNAs were validated by degradome sequencing. Several drought memory-related miRNAs such as tae-miR9676-5p, tae-MIR9676-p3_1ss21GA, tae-miR171a, tae-miR531_L-2, tae-miR408_L-1, PC-3p-5049_3565, tae-miR396c-5p, tae-miR9778, tae-miR164a-5p, and tae-miR9662a-3p were validated as having a strong response to drought memory by regulating the expression of their target genes. In addition, overexpression of drought memory-related miRNA, tae-miR531_L-2, can remarkably improve the drought tolerance of transgenic Arabidopsisthaliana. Drought memory can regulate plant cellular signal transduction, plant biosynthetic processes, and other biological processes to cope with drought via transcriptional memory. In addition, drought memory-related miRNAs can promote starch and sucrose catabolism and soluble sugar accumulation and regulate proline homeostasis to improve plant drought resistance. Our results could contribute to an understanding of drought memory in wheat seedlings and may provide a new strategy for drought-resistant breeding.

Comparative Analysis of Coding and Non-Coding Features within Insect Tolerance Loci in Wheat with Their Homologs in Cereal Genomes

Food insecurity and malnutrition have reached critical levels with increased human population, climate fluctuations, water shortage; therefore, higher-yielding crops are in the spotlight of numerous studies. Abiotic factors affect the yield of staple food crops; among all, wheat stem sawfly (Cephus cinctus Norton) and orange wheat blossom midge (Sitodiplosis mosellana) are two of the most economically and agronomically harmful insect pests which cause yield loss in cereals, especially in wheat in North America. There is no effective strategy for suppressing this pest damage yet, and only the plants with intrinsic tolerance mechanisms such as solid stem phenotypes for WSS and antixenosis and/or antibiosis mechanisms for OWBM can limit damage. A major QTL and a causal gene for WSS resistance were previously identified in wheat, and 3 major QTLs and a causal gene for OWBM resistance. Here, we present a comparative analysis of coding and non-coding features of these loci of wheat across important cereal crops, barley, rye, oat, and rice. This research paves the way for our cloning and editing of additional WSS and OWBM tolerance gene(s), proteins, and metabolites.

Drought stress and plant ecotype drive microbiome recruitment in switchgrass rhizosheath

The rhizosheath, a layer of soil grains that adheres firmly to roots, is beneficial for plant growth and adaptation to drought environments. Switchgrass is a perennial C4 grass which can form contact rhizosheath under drought conditions. In this study, we characterized the microbiomes of four different rhizocompartments of two switchgrass ecotypes (Alamo and Kanlow) grown under drought or well-watered conditions via 16S ribosomal RNA amplicon sequencing. These four rhizocompartments, the bulk soil, rhizosheath soil, rhizoplane, and root endosphere, harbored both distinct and overlapping microbial communities. The root compartments (rhizoplane and root endosphere) displayed low-complexity communities dominated by Proteobacteria and Firmicutes. Compared to bulk soil, Cyanobacteria and Bacteroidetes were selectively enriched, while Proteobacteria and Firmicutes were selectively depleted, in rhizosheath soil. Taxa from Proteobacteria or Firmicutes were specifically selected in Alamo or Kanlow rhizosheath soil. Following drought stress, Citrobacter and Acinetobacter were further enriched in rhizosheath soil, suggesting that rhizosheath microbiome assembly is driven by drought stress. Additionally, the ecotype-specific recruitment of rhizosheath microbiome reveals their differences in drought stress responses. Collectively, these results shed light on rhizosheath microbiome recruitment in switchgrass and lay the foundation for the improvement of drought tolerance in switchgrass by regulating the rhizosheath microbiome.

Tuning Beforehand: A Foresight on RNA Interference (RNAi) and In Vitro-Derived dsRNAs to Enhance Crop Resilience to Biotic and Abiotic Stresses

Crop yield is severely affected by biotic and abiotic stresses. Plants adapt to these stresses mainly through gene expression reprogramming at the transcriptional and post-transcriptional levels. Recently, the exogenous application of double-stranded RNAs (dsRNAs) and RNA interference (RNAi) technology has emerged as a sustainable and publicly acceptable alternative to genetic transformation, hence, small RNAs (micro-RNAs and small interfering RNAs) have an important role in combating biotic and abiotic stresses in plants. RNAi limits the transcript level by either suppressing transcription (transcriptional gene silencing) or activating sequence-specific RNA degradation (post-transcriptional gene silencing). Using RNAi tools and their respective targets in abiotic stress responses in many crops is well documented. Many miRNAs families are reported in plant tolerance response or adaptation to drought, salinity, and temperature stresses. In biotic stress, the spray-induced gene silencing (SIGS) provides an intelligent method of using dsRNA as a trigger to silence target genes in pests and pathogens without producing side effects such as those caused by chemical pesticides. In this review, we focus on the potential of SIGS as the most recent application of RNAi in agriculture and point out the trends, challenges, and risks of production technologies. Additionally, we provide insights into the potential applications of exogenous RNAi against biotic stresses. We also review the current status of RNAi/miRNA tools and their respective targets on abiotic stress and the most common responsive miRNA families triggered by stress conditions in different crop species.

Recognizing the hidden half in wheat: root system attributes associated with drought tolerance

Improving drought tolerance in wheat is crucial for maintaining productivity and food security. Roots are responsible for the uptake of water from soil, and a number of root traits are associated with drought tolerance. Studies have revealed many quantitative trait loci and genes controlling root development in plants. However, the genetic dissection of root traits in response to drought in wheat is still unclear. Here, we review crop root traits associated with drought, key genes governing root development in plants, and quantitative trait loci and genes regulating root system architecture under water-limited conditions in wheat. Deep roots, optimal root length density and xylem diameter, and increased root surface area are traits contributing to drought tolerance. In view of the diverse environments in which wheat is grown, the balance among root and shoot traits, as well as individual and population performance, are discussed. The known functions of key genes provide information for the genetic dissection of root development of wheat in a wide range of conditions, and will be beneficial for molecular marker development, marker-assisted selection, and genetic improvement in breeding for drought tolerance.

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.

Pan-Genome miRNomics in Brachypodium

Pan-genomes are efficient tools for the identification of conserved and varying genomic sequences within lineages of a species. Investigating genetic variations might lead to the discovery of genes present in a subset of lineages, which might contribute into beneficial agronomic traits such as stress resistance or yield. The content of varying genomic regions in the pan-genome could include protein-coding genes as well as microRNA(miRNAs), small non-coding RNAs playing key roles in the regulation of gene expression. In this study, we performed in silico miRNA identification from the genomic sequences of 54 lineages of Brachypodium distachyon, aiming to explore varying miRNA contents and their functional interactions. A total of 115 miRNA families were identified in 54 lineages, 56 of which were found to be present in all lineages. The miRNA families were classified based on their conservation among lineages and potential mRNA targets were identified. Obtaining information about regulatory mechanisms stemming from these miRNAs offers strong potential to provide a better insight into the complex traits that were potentially present in some lineages. Future work could lead us to introduce these traits to different lineages or other economically important plant species in order to promote their survival in different environmental conditions.

Nitrogen Starvation-Responsive MicroRNAs Are Affected by Transgenerational Stress in Durum Wheat Seedlings

Stress events have transgenerational effects on plant growth and development. In Mediterranean regions, water-deficit and heat (WH) stress is a frequent issue that negatively affects crop yield and quality. Nitrogen (N) is an essential plant macronutrient and often a yield-limiting factor for crops. Here, the response of durum wheat seedlings to N starvation under the transgenerational effects of WH stress was investigated in two genotypes. Both genotypes showed a significant reduction in seedling height, leaf number, shoot and root weight (fresh and dry), primary root length, and chlorophyll content under N starvation stress. However, in the WH stress-tolerant genotype, the percentage reduction of most traits was lower in progeny from the stressed parents than progeny from the control parents. Small RNA sequencing identified 1534 microRNAs in different treatment groups. Differentially expressed microRNAs (DEMs) were characterized subject to N starvation, parental stress and genotype factors, with their target genes identified in silico. GO and KEGG enrichment analyses revealed the biological functions, associated with DEM-target modules in stress adaptation processes, that could contribute to the phenotypic differences observed between the two genotypes. The study provides the first evidence of the transgenerational effects of WH stress on the N starvation response in durum wheat.

Multi-Omics Analysis of Small RNA, Transcriptome, and Degradome in T. turgidum-Regulatory Networks of Grain Development and Abiotic Stress Response

Crop reproduction is highly sensitive to water deficit and heat stress. The molecular networks of stress adaptation and grain development in tetraploid wheat (Triticum turgidum durum) are not well understood. Small RNAs (sRNAs) are important epigenetic regulators connecting the transcriptional and post-transcriptional regulatory networks. This study presents the first multi-omics analysis of the sRNAome, transcriptome, and degradome in T. turgidum developing grains, under single and combined water deficit and heat stress. We identified 690 microRNAs (miRNAs), with 84 being novel, from 118 sRNA libraries. Complete profiles of differentially expressed miRNAs (DEMs) specific to genotypes, stress types, and different reproductive time-points are provided. The first degradome sequencing report for developing durum grains discovered a significant number of new target genes regulated by miRNAs post-transcriptionally. Transcriptome sequencing profiled 53,146 T. turgidum genes, swith differentially expressed genes (DEGs) enriched in functional categories such as nutrient metabolism, cellular differentiation, transport, reproductive development, and hormone transduction pathways. miRNA-mRNA networks that affect grain characteristics such as starch synthesis and protein metabolism were constructed on the basis of integrated analysis of the three omics. This study provides a substantial amount of novel information on the post-transcriptional networks in T. turgidum grains, which will facilitate innovations for breeding programs aiming to improve crop resilience and grain quality.

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.

Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era

Abiotic stresses are among the principal limiting factors for productivity in agriculture. In the current era of continuous climate changes, the understanding of the molecular aspects involved in abiotic stress response in plants is a priority. The rise of -omics approaches provides key strategies to promote effective research in the field, facilitating the investigations from reference models to an increasing number of species, tolerant and sensitive genotypes. Integrated multilevel approaches, based on molecular investigations at genomics, transcriptomics, proteomics and metabolomics levels, are now feasible, expanding the opportunities to clarify key molecular aspects involved in responses to abiotic stresses. To this aim, bioinformatics has become fundamental for data production, mining and integration, and necessary for extracting valuable information and for comparative efforts, paving the way to the modeling of the involved processes. We provide here an overview of bioinformatics resources for research on plant abiotic stresses, describing collections from -omics efforts in the field, ranging from raw data to complete databases or platforms, highlighting opportunities and still open challenges in abiotic stress research based on -omics technologies.

Transgenerational Effects of Water-Deficit and Heat Stress on Germination and Seedling Vigour-New Insights from Durum Wheat microRNAs

Water deficiency and heat stress can severely limit crop production and quality. Stress imposed on the parents during reproduction could have transgenerational effects on their progeny. Seeds with different origins can vary significantly in their germination and early growth. Here, we investigated how water-deficit and heat stress on parental durum wheat plants affected seedling establishment of the subsequent generation. One stress-tolerant and one stress-sensitive Australian durum genotype were used. Seeds were collected from parents with or without exposure to stress during reproduction. Generally, stress on the previous generation negatively affected seed germination and seedling vigour, but to a lesser extent in the tolerant variety. Small RNA sequencing utilising the new durum genome assembly revealed significant differences in microRNA (miRNA) expression in the two genotypes. A bioinformatics approach was used to identify multiple miRNA targets which have critical molecular functions in stress adaptation and plant development and could therefore contribute to the phenotypic differences observed. Our data provide the first confirmation of the transgenerational effects of reproductive-stage stress on germination and seedling establishment in durum wheat. New insights gained on the epigenetic level indicate that durum miRNAs could be key factors in optimising seed vigour for breeding superior germplasm and/or varieties.

Transcriptome Analysis Implicates Involvement of Long Noncoding RNAs in Cytoplasmic Male Sterility and Fertility Restoration in Cotton

The cytoplasmic male sterility (CMS)/restorer-of-fertility system is an important tool to exploit heterosis during commercially hybrid seed production. The importance of long noncoding RNAs (lncRNAs) in plant development is recognized, but few analyses of lncRNAs during anther development of three-line hybrid cotton (CMS-D2 line A, maintainer line B, restorer-of-fertility line R) have been reported. Here, we performed transcriptome sequencing during anther development in three-line hybrid cotton. A total of 80,695 lncRNAs were identified, in which 43,347 and 44,739 lncRNAs were differentially expressed in A–B and A–R comparisons, respectively. These lncRNAs represent functional candidates involved in CMS and fertility restoration. GO analysis indicated that cellular hormone metabolic processes and oxidation–reduction reaction processes might be involved in CMS, and cellular component morphogenesis and small molecular biosynthetic processes might participate in fertility restoration. Additionally, 63 lncRNAs were identified as putative precursors of 35 miRNAs, and quantitative reverse transcription polymerase chain reaction (qRT-PCR) showed a similar expression pattern to RNA-seq data. Furthermore, construction of lncRNA regulatory networks indicated that several miRNA–lncRNA–mRNA networks might be involved in CMS and fertility restoration. Our findings provide systematic identification of lncRNAs during anther development and lays a solid foundation for the regulatory mechanisms and utilization in hybrid cotton breeding.

RNAseq analysis reveals drought-responsive molecular pathways with candidate genes and putative molecular markers in root tissue of wheat

Drought is one of the major impediments in wheat productivity. Traditional breeding and marker assisted QTL introgression had limited success. Available wheat genomic and RNA-seq data can decipher novel drought tolerance mechanisms with putative candidate gene and marker discovery. Drought is first sensed by root tissue but limited information is available about how roots respond to drought stress. In this view, two contrasting genotypes, namely, NI5439 41 (drought tolerant) and WL711 (drought susceptible) were used to generate ~78.2 GB data for the responses of wheat roots to drought. A total of 45139 DEGs, 13820 TF, 288 miRNAs, 640 pathways and 435829 putative markers were obtained. Study reveals use of such data in QTL to QTN refinement by analysis on two model drought-responsive QTLs on chromosome 3B in wheat roots possessing 18 differentially regulated genes with 190 sequence variants (173 SNPs and 17 InDels). Gene regulatory networks showed 69 hub-genes integrating ABA dependent and independent pathways controlling sensing of drought, root growth, uptake regulation, purine metabolism, thiamine metabolism and antibiotics pathways, stomatal closure and senescence. Eleven SSR markers were validated in a panel of 18 diverse wheat varieties. For effective future use of findings, web genomic resources were developed. We report RNA-Seq approach on wheat roots describing the drought response mechanisms under field drought conditions along with genomic resources, warranted in endeavour of wheat productivity.

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 microRNAS differentially regulated by water deficit in relation to mycorrhizal treatment in wheat

Arbuscular mycorrhizal fungi (AMF) are soil microrganisms that establish symbiosis with plants positively influencing their resistance to abiotic stresses. The aim of this work was to identify wheat miRNAs differentially regulated by water deficit conditions in presence or absence of AMF treatment. Small RNA libraries were constructed for both leaf and root tissues considering four conditions: control (irrigated) or water deficit in presence/absence of mycorrhizal (AMF) treatment. A total of 12 miRNAs were significantly regulated by water deficit in leaves: five in absence and seven in presence of AMF treatment. In roots, three miRNAs were water deficit-modulated in absence of mycorrhizal treatment while six were regulated in presence of it. The most represented miRNA family was miR167 that was regulated by water deficit in both leaf and root tissues. Interestingly, miR827-5p was differentially regulated in leaves in the absence of mycorrhizal treatment while it was water deficit-modulated in roots irrespective of AMF treatment. In roots, water deficit repressed miR827-5p, miR394, miR6187, miR167e-3p, and miR9666b-3p affecting transcription, RNA synthesis, protein synthesis, and protein modifications. In leaves, mycorrhizae modulated miR5384-3p and miR156e-3p affecting trafficking and cell redox homeostasis. DNA replication and transcription regulation should be targeted by the repression of miR1432-5p and miR166h-3p. This work provided interesting insights into the post-transcriptional mechanisms of wheat responses to water deficit in relation to mycorrhizal symbiosis.

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.

Transcriptome-wide identification and characterization of microRNAs responsive to phosphate starvation in Populus tomentosa

miRNAs (microRNAs) are ~ 21-nt non-coding small RNAs (sRNAs) that play crucial regulatory roles in plant biotic and abiotic stress responses. Phosphorus (Pi) deficiency constrains plant growth and reduces yields worldwide. To identify tree miRNAs and evaluate their functions in the response to low Pi, we identified 261 known and 31 candidate novel miRNA families from three sRNA libraries constructed from Populus tomentosa subjected to sufficient or Pi deficiency condition or to restoration of a sufficient Pi level after Pi deficiency. Pi deficiency resulted in significant changes in the abundance of TPM (transcript per million) of 65 known and 3 novel miRNAs. Interestingly, four miRNAs responsive to low N-miR167, miR394, miR171, and miR857-were found to be involved in the response to low Pi. Thirty-five known and one novel miRNAs responded dynamically to Pi fluctuations, suggesting their involvement in the response to Pi deficiency. miRNA clusters comprising 36 miRNAs were identified in 10 chromosomes. Intriguingly, nine pairs of sense and antisense miRNAs transcribed from the same loci were detected in P. tomentosa, which is the first such report in woody plants. Moreover, target genes of the known miRNAs and novel miRNA candidates with significantly changed abundance were predicted, and their functions were annotated. Degradome sequencing supported the identified targets of miRNAs in P. tomentosa. These findings will enhance our understanding of universal and specific molecular regulatory mechanisms of trees under nutrition stress and may facilitate improvement of the Pi utilization efficiency of woody plants.

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.

MicroRNAome Profile of Euphorbia kansui in Response to Methyl Jasmonate

miRNAs play vital regulatory roles in different plant developmental stages and in plant response to biotic and abiotic stresses. However, information is limited on the miRNA regulatory mechanism to methyl jasmonate (MeJA). In this study, we used the microRNAome profile to illustrate the relevant regulatory mechanisms of Euphorbia kansui in response to methyl jasmonate (MeJA) through Illumina RNA-Seq. As a result, we identified 875 miRNAs corresponding to 11,277 target mRNAs, among them, 168 known miRNA families representing 6019 target mRNAs sequences were obtained. 452 miRNA-mRNA pairs presented an anti-correlationship (Cor < −0.50 and p-value of correlation ≤ 0.05). The miRNA with a fold change ≥ 2 and a p (p-Value) < 0.05 in pairwise comparison were identified as significant differentially expressed miRNAs (DEMs). The DEMs in MeJA treatment of 0, 24, 36 and 48 h were compared by using Short Time Expression Miner (STEM) cluster and 4 significant gene profiles (p-value ≤ 0.02) were identified. Through the kyoto encyclopedia of genes and genomes (KEGG) pathway and gene ontology (GO) enrichment analysis on all miRNA targets, we identified 33 mRNAs in terpenoid biosynthesis, which were regulated by miRNAs under MeJA treatment, so the miRNA maybe involved in the response of E. kansui plant to exogenous MeJA and the results would provide very useful information on illustrating the regulatory mechanism of E. kansui and also provide an overall view of the miRNAs response to MeJA stress of a non-model plant.

High-throughput sequencing and differential expression analysis of miRNAs in response to Brassinosteroid treatment in Arabidopsis thaliana

Brassinosteroids are a class of phytohormones that play crucial roles in improving stress tolerance in plants. Many biochemical and physiological changes in response to abiotic stress are related to regulation of gene expression and accumulation of associated proteins. MicroRNAs (miRNAs) are class of small non-coding RNAs that regulate gene expression post-transcriptionally. Roles of these regulatory RNAs in brassinosteroid (BR) signalling have however remained elusive. In this study using high-throughput small RNA sequencing method, we present a comprehensive compilation of BR-induced differentially expressed microRNAs in root and shoots of Arabidopsis thaliana seedlings. We identified 229 known miRNAs belonging to 102 families and 27 novel miRNAs that express in response to exogenous BR treatment. Out of 102 families, miRNAs belonging to known 48 families and out of 27 novel miRNAs, 23 were observed to be differentially expressed in response to BR treatment. Among the conserved miRNAs, all members of miR169 were observed to be downregulated in both shoot and root samples. While, auxin-responsive factors were predicted to be direct targets of some novel miRNAs that are upregulated in shoots and suppressed in roots. The BR-responsive tissue-specific miRNome characterized in this study can be used as a starting point by investigators for functional validation studies that will shed light on the underlying molecular mechanism of BR-mediated stress tolerance at the level of post-transcriptional gene regulation.

Discovery and profiling of small RNAs from Puccinia triticina by deep sequencing and identification of their potential targets in wheat

Cross-kingdom RNAi is a well-documented phenomenon where sRNAs generated by host and pathogens may govern resistance or susceptible phenotypes during host-pathogen interaction. With the first example of the direct involvement of fungal generated sRNAs in virulence of plant pathogenic fungi Botrytis cinerea and recently from Puccinia striiformis f. sp. tritici, we attempted to identify sRNAs in Puccinia triticina (P. triticina). Four sRNA libraries were prepared and sequenced using Illumina sequencing technology and a total of ~ 1-1.28 million potential sRNAs and two microRNA-like small RNA (mil-RNAs) candidates were identified. Computational prediction of targets using a common set of sRNAs and P. triticina mil-RNAs (pt-mil-RNAs) within P. triticina and wheat revealed the majority of the targets as repetitive elements in P. triticina whereas in wheat, the target genes were identified to be involved in many biological processes including defense-related pathways. We found 9 receptor-like kinases (RLKs) and 14 target genes of each related to reactive oxygen species (ROS) pathway and transcription factors respectively, including significant numbers of target genes from various other categories. Expression analysis of twenty selected sRNAs, targeting host genes pertaining to ROS related, disease resistance, metabolic processes, transporter, apoptotic inhibitor, and transcription factors along with two pt-mil-RNAs by qRT-PCR showed distinct patterns of expression of the sRNAs in urediniospore-specific libraries. In this study, for the first time, we report identification of novel sRNAs identified in P. triticina including two pt-mil-RNAs that may play an important role in biotrophic growth and pathogenicity.

Chromosome-based survey sequencing reveals the genome organization of wild wheat progenitor Triticum dicoccoides

Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is the progenitor of wheat. We performed chromosome-based survey sequencing of the 14 chromosomes, examining repetitive sequences, protein-coding genes, miRNA/target pairs and tRNA genes, as well as syntenic relationships with related grasses. We found considerable differences in the content and distribution of repetitive sequences between the A and B subgenomes. The gene contents of individual chromosomes varied widely, not necessarily correlating with chromosome size. We catalogued candidate agronomically important loci, along with new alleles and flanking sequences that can be used to design exome sequencing. Syntenic relationships and virtual gene orders revealed several small-scale evolutionary rearrangements, in addition to providing evidence for the 4AL-5AL-7BS translocation in wild emmer wheat. Chromosome-based sequence assemblies contained five novel miRNA families, among 59 families putatively encoded in the entire genome which provide insight into the domestication of wheat and an overview of the genome content and organization.

Characterization of miRNAs and their target genes in He-Ne laser pretreated wheat seedlings exposed to drought stress

Drought stress is considered a critical environmental factor that negatively affects wheat growth and development, which causes considerable losses in wheat yields worldwide. More recently, numerous microRNAs (miRNAs) have been found to be involved in wheat responses to drought stresses. However, there is little information regarding the effects of He-Ne laser irradiation on the expression traits of miRNAs and their targets in wheat seedlings exposed to drought stress. In the current study, therefore, a combination of physiological and molecular approaches was used to assess the effect of He-Ne laser irradiation on the expression of miRNAs and their targets in wheat seedlings exposed to drought stress. Our results demonstrated that drought stress significantly reduced plant height, root length, shoot and root fresh weight, relative water content, the expression level and activity of superoxide dismutase (SOD), enhanced malondialdehyde (MDA) concentration in the wheat seedlings. However, He-Ne laser irradiation significantly enhanced the activities of SOD, ascorbate peroxidase (APX), peroxidase (POD) and relative water content, and reduced MDA concentration of seedlings by regulating gene expression for SOD, POD, APX. In addition, in comparison with drought stress alone, miR160, miR164 and miR398 transcripts were down-regulated, and expression levels of its targets auxin response factor (ARF22), NAC domain transcription factor and Cu/Zn superoxide dismutases (CSD) were up-regulated in He-Ne laser irradiated seedlings exposed to drought stress. These results suggested that He-Ne laser irradiation could possible protection of drought stress, at least partially, by increasing the transcript levels and activities of SOD, POD and APX, and decreasing the transcript levels of miR160, miR164 and miR398. To the best of our knowledge, this is the first study to present biochemical and molecular evidence supporting the effect of He-Ne laser irradiation on the alleviation of drought stress in wheat seedlings mediated by miRNA expression.

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.

Regulation mechanism of microRNA in plant response to abiotic stress and breeding

microRNAs (miRNAs) in plants are a class of small RNAs consisting of approximately 21-24 nucleotides. The mature miRNA binds to the target mRNA through the formation of a miRNA-induced silencing complex (MIRISC), and cleaves or inhibits translation, thereby achieving negative regulation of the target gene. Based on miRNA plays an important role in regulating plant gene expression, studies on the prediction, identification, function and evolution of plant miRNAs have been carried out. In addition, many researches prove that miRNAs are also involved in many kinds of abiotic and biotic stress, under abiotic stress, plants can express some miRNA, and act on stress-related target genes, which can make plants adapt to stress in physiological response. In this review, the synthetic pathway and mechanism of plant miRNA are briefly described, and we discuss the biological functions and regulatory mechanisms of miRNAs responding to abiotic stresses including low temperature, salt, drought stress and breeding to lay the foundation for further exploring the mechanism of action of miRNAs in stress resistance of plant. And analyze its utilization prospects in plant stress resistance research.

Multiple Regression Analysis Reveals MicroRNA Regulatory Networks in Oryza sativa under Drought Stress

Drought is a major abiotic stress that reduces rice development and yield. miRNAs (microRNAs) are known to mediate posttranscriptional regulation under drought stress. Although the importance of individual miRNAs has been established, the crosstalks between miRNAs and mRNAs remain unearthed. Here we performed microarray analysis of miRNAs and matched mRNA expression profiles of drought-treated rice cultivar Nipponbare. Drought-responsive miRNA-mRNA regulations were identified by a combination of a partial least square (PLS) regression approach and sequence-based target prediction. A drought-induced network with 13 miRNAs and 58 target mRNAs was constructed, and four miRNA coregulatory modules were revealed. Functional analysis suggested that drought-response miRNA targets are enriched in hormone signaling, lipid and carbohydrate metabolism, and antioxidant defense. 13 candidate miRNAs and target genes were validated by RT-qPCR, hierarchical clustering, and ROC analysis. Two target genes (DWARF-3 and P0651G05.2) of miRNA coregulatory modules were further verified by RLM-5' RACE. Together, our integrative study of miRNA-mRNA interaction provided attractive candidates that will help elucidate the drought-response mechanisms in Oryza sativa.

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.

Shifting the limits in wheat research and breeding using a fully annotated reference genome

An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.

Transcriptional regulation of osmotic stress tolerance in wheat (Triticum aestivum L.)

The current review provides an updated, new insights into the regulation of transcription mediated underlying mechanisms of wheat plants to osmotic stress perturbations. Osmotic stress tolerance mechanisms being complex are governed by multiple factors at physiological, biochemical and at the molecular level, hence approaches like "OMICS" that can underpin mechanisms behind osmotic tolerance in wheat is of paramount importance. The transcription factors (TFs) are a class of molecular proteins, which are involved in regulation, modulation and orchestrating the responses of plants to a variety of environmental stresses. Recent reports have provided novel insights on the role of TFs in osmotic stress tolerance via direct molecular links. However, our knowledge on the regulatory role TFs during osmotic stress tolerance in wheat remains limited. The present review in its first part sheds light on the importance of studying the role of osmotic stress tolerance in wheat plants and second aims to decipher molecular mechanisms of TFs belonging to several classes, including DREB, NAC, MYB, WRKY and bHLH, which have been reported to engage in osmotic stress mediated gene expression in wheat and third part covers the systems biology approaches to understand the transcriptional regulation of osmotic stress and the role of long non-coding RNAs in response to osmotic stress with special emphasis on wheat. The current concept may lead to an understanding in molecular regulation and signalling interaction of TFs under osmotic stress to clarify challenges and problems for devising potential strategies to improve complex regulatory events involved in plant tolerance to osmotic stress adaptive pathways in wheat.

Transcriptome analysis reveals new microRNAs-mediated pathway involved in anther development in male sterile wheat

Background

337S is a novel bi-pole-photo-thermo-sensitive genic male sterile line in wheat, and sensitive to both long day length/high temperature and short day length/low temperature condition. Although the regulatory function of MicroRNAs (miRNAs) in reproductive development has been increasingly studied, their roles in pre-meiotic and meiotic cells formation of plants have not been clearly explored. Here, we explored the roles of miRNAs in regulating male sterility of 337S at short day length/low temperature condition.

Results

Small RNA sequencing and degradome analyses were employed to identify miRNAs and their targets in the 337S whose meiotic cells collapsed rapidly during male meiotic prophase, resulting in failure of meiosis at SL condition. A total of 102 unique miRNAs were detected. Noticeably, the largest miRNA family was MiR1122. The target CCR4-associated factor 1 (CAF1) of miR2275, a subunit of the Carbon Catabolite Repressed 4-Negative on TATA-less (CCR4-NOT) complex, contributes to the process of early meiosis, and was first identified here. Further studies showed that the expression of several pivotal anther-related miRNAs was altered in 337S at SL condition, especially tae-miR1127a, which may be related to male sterility of 337S. Here, we also identified a new member of SWI/SNF factors SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A, member 3-like 3 (SMARCA3L3) targeted by tae-miR1127a, whose function might be involved in faithful progression of meiosis in male reproductive cells.

Conclusion

The miRNA-target interactions of tae-miR2275-CAF1 and tae-miR1127a-SMARCA3L3 might be involved in regulating male fertility in 337S. Our results also implied that multiple roles for SMARCA3L3 and CAF1 in DNA repair and transcriptional regulation jointly orchestrated a tight and orderly system for maintaining chromatin and genome integrity during meiosis.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4727-5) contains supplementary material, which is available to authorized users.

Lateral Root Development in Potato Is Mediated by Stu-mi164 Regulation of NAC Transcription Factor

The NAC designation is derived from petunia (Petunia hybrida) gene NO APICAL MERISTEM (NAM) and Arabidopsis genes ATAF1/ATAF2 and CUP-SHAPED COTYLEDON2 (CUC2), which belongs to the family of plant-specific transcription factors (TFs), and plays important role in plant development processes, such as response to biotic and abiotic stress, and hormone signaling. MicroRNAs (miRNAs) are a class of small, non-coding endogenous RNAs which play versatile and significant role in plant stress response and development via negatively affecting gene expression at a post-transcriptional level. Here, we showed that Stu-mi164 had a complementary sequence in the CDS sequence of potato NAC TFs, and that NAC expression exhibited significant differences under osmotic stress. We measured expression levels of the Stu-mi164 target gene StNAC262 between control and PEG-treated plants using real-time PCR, and the results demonstrated that they had inverse relationship. We suggested that Stu-miR164 might drive overexpression of NAC gene under osmotic stress in potato. To confirm the regulation of NAC TFs by Stu-mi164, we developed transgenic plants, using Agrobacterium tumefaciens-mediated transformation, of the potato cultivars "Gannongshu 2" and "Kexin 3" overexpressing the Stu-mi164 or the TF StNAC262. Real-time PCR analysis of transgenic potato plants under osmotic (PEG) stress, showed that potato plants overexpressing Stu-mi164 had reduced expression of StNAC262 and their osmotic resistance decreased. Furthermore, these plants had low number of lateral roots although the same length as the control. Our findings support the regulatory role of Stu-miRNAs in controlling plant response to osmotic stress via StNAC262.

A large-scale multiomics analysis of wheat stem solidness and the wheat stem sawfly feeding response, and syntenic associations in barley, Brachypodium, and rice

The wheat stem sawfly (WSS), Cephus cinctus Norton (Hymenoptera: Cephidae), is an important pest of wheat and other cereals, threatening the quality and quantity of grain production. WSS larvae feed and develop inside the stem where they are protected from the external environment; therefore, pest management strategies primarily rely on host plant resistance. A major locus on the long arm of wheat chromosome 3B underlies most of the variation in stem solidness; however, the impact of stem solidness on WSS feeding has not been completely characterized. Here, we used a multiomics approach to examine the response to WSS in both solid- and semi-solid-stemmed wheat varieties. The combined transcriptomic, proteomic, and metabolomic data revealed that two important molecular pathways, phenylpropanoid and phosphate pentose, are involved in plant defense against WSS. We also detected a general downregulation of several key defense transcripts, including those encoding secondary metabolites such as DIMBOA, tricetin, and lignin, which suggested that the WSS larva might interfere with plant defense. We comparatively analyzed the stem solidness genomic region known to be associated with WSS tolerance in wild emmer, durum, and bread wheats, and described syntenic regions in the close relatives barley, Brachypodium, and rice. Additionally, microRNAs identified from the same genomic region revealed potential regulatory pathways associated with the WSS response. We propose a model outlining the molecular responses of the WSS–wheat interactions. These findings provide insight into the link between stem solidness and WSS feeding at the molecular level.

Comparative metabolite profiling of drought stress in roots and leaves of seven Triticeae species

BACKGROUND

Drought is a lifestyle disease. Plant metabolomics has been exercised for understanding the fine-tuning of the potential pathways to surmount the adverse effects of drought stress. A broad spectrum of morphological and metabolic responses from seven Triticeae species including wild types with different drought tolerance/susceptibility level was investigated under control and water scarcity conditions.

RESULTS

Significant morphological parameters measured were root length, surface area, average root diameter and overall root development. Principal Component Analysis, Partial Least-Squares-Discriminant Analysis and Hierarchical Cluster Analysis were applied to the metabolomic data obtained by Gas Chromatography-Mass Spectrometry technique in order to determine the important metabolites of the drought tolerance across seven different Triticeae species. The metabolites showing significant accumulation under the drought stress were considered as the key metabolites and correlated with potential biochemical pathways, enzymes or gene locations for a better understanding of the tolerance mechanisms. In all tested species, 45 significantly active metabolites with possible roles in drought stress were identified. Twenty-one metabolites out of forty-five including sugars, amino acids, organic acids and low molecular weight compounds increased in both leaf and root samples of TR39477, IG132864 and Bolal under the drought stress, contrasting to TTD-22, Tosunbey, Ligustica and Meyeri samples. Three metabolites including succinate, aspartate and trehalose were selected for further genome analysis due to their increased levels in TR39477, IG132864, and Bolal upon drought stress treatment as well as their significant role in energy producing biochemical pathways.

CONCLUSION

These results demonstrated that the genotypes with high drought tolerance skills, especially wild emmer wheat, have a great potential to be a genetic model system for experiments aiming to validate metabolomics-genomics networks.

Ectopic expression of CSD1 and CSD2 targeting genes of miR398 in grapevine is associated with oxidative stress tolerance

MicroRNAs (miRNAs) are endogenous small RNAs of -21 nucleotides that play an important role in diverse plant physiological processes at the post-transcriptional level by directing mRNA cleavage or translational inhibition. Previous studies have indicated that down-regulation of miR398 in response to oxidative stress allows up-regulation of the two target genes, cytosolic CSD1 and chloroplastic CSD2 (copper/zinc superoxide dismutase), resulting in protecting the plants to tolerate oxidative stress. In this study, we provide evidence that grapevine miR398 (Vv-miR398), by regulating the expression of its target genes, VvCSD1 and VvCSD2, mediates responses of grapevine to copper (Cu) stress which have been magnified due to increase in Cu-containing pesticide application. The expression of Vv-miR398 was inhibited by different concentrations of Cu stress; on the other hand, there was a steady increase in the activity of VvCSD1 and VvCSD2 genes. The function of VvCSD1 and VvCSD2 under Cu stress was thoroughly examined by overexpressing the use of the VvCSD1 and VvCSD2 in transgenic tobacco (Nicotiana tabacum). We found that both the overexpressed transgenic lines had lower Cu sensitivity and higher Cu tolerance compared with the wild type. In addition, lower levels of ROS and higher levels of SOD activities were accumulated in the transgenic lines in comparison with the wild type under the higher Cu conditions. Furthermore, these transgenic tobacco lines also recorded a higher UV and salt tolerance than the WT plants. These results suggested that overexpressing the VvCSDs will enhance the ROS-scavenging systems and protect the plant against more oxidative damage. Also, more investigations in this line are needed that would provide significant improvements in our understanding the resistance of fruit crops to environmental stress.

Redox and Ionic Homeostasis Regulations against Oxidative, Salinity and Drought Stress in Wheat (A Systems Biology Approach)

Systems biology and omics has provided a comprehensive understanding about the dynamics of the genome, metabolome, transcriptome, and proteome under stress. In wheat, abiotic stresses trigger specific networks of pathways involved in redox and ionic homeostasis as well as osmotic balance. These networks are considerably more complicated than those in model plants, and therefore, counter models are proposed by unifying the approaches of omics and stress systems biology. Furthermore, crosstalk among these pathways is monitored by the regulation and streaming of transcripts and genes. In this review, we discuss systems biology and omics as a promising tool to study responses to oxidative, salinity, and drought stress in wheat.

Assembly and Annotation of Transcriptome Provided Evidence of miRNA Mobility between Wheat and Wheat Stem Sawfly

Wheat Stem Sawfly (WSS), Cephus Cinctus Norton (Hymenoptera: Cephidae), is one of the most important pests, causing yield and economic losses in wheat and barley. The lack of information about molecular mechanisms of WSS for defeating plant's resistance prevents application of effective pest control strategies therefore, it is essential to identify the genes and their regulators behind WSS infestations. Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are recognized with their regulatory functions on gene expression, tuning protein production by controlling transcriptional and post-transcriptional activities. A transcriptome-guided approach was followed in order to identify miRNAs, lncRNAs, and mRNA of WSS, and their interaction networks. A total of 1,893 were presented here as differentially expressed between larva and adult WSS insects. There were 11 miRNA families detected in WSS transcriptome. Together with the annotation of 1,251 novel mRNAs, the amount of genetic information available for WSS was expanded. The network between WSS miRNAs, lncRNAs, and mRNAs suggested miRNA-mediated regulatory roles of lncRNAs as competing endogenous RNAs. In the light of the previous evidence that small RNA molecules of a pathogen could suppress the immune response of host plant, we analyzed the putative interactions between larvae and wheat at the miRNA level. Overall, this study provides a profile of larva and adult WSS life stages in terms of coding and non-coding elements. These findings also emphasize the potential roles of wheat and larval miRNAs in wheat resistance to infestation and in the suppression of resistance which is critical for the development of effective pest control strategies.

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.