Characterization of drought- and heat-responsive microRNAs in switchgrass

Overlapping of copper-nanoparticles with microRNA reveals crippling of heat stress pathway in Solanum lycopersicum: Tomato case study

Despite the tangible benefits of copper nanoparticles (CuNPs) for plants, the increasing use of CuNPs poses a threat to plants and the environment. Although miRNAs have been shown to mediate heat shock and CuNPs by altering gene expression, no study has investigated how CuNPs in combination with heat shock (HS) affect the miRNA expression profile. Here, we exposed tomato plants to 0.01 CuONPs at 42 °C for 1 h after exposure. It was found that the expression levels of miR156a, miR159a and miR172a and their targets SPL3, MYB33 and AP2a were altered under CuNPs and HS + CuNPs. This alteration accelerated the change of vegetative phase and the process of leaf senescence. The overexpression of miR393 under CuNPs and HS + CuNPs could also be an indicator of the attenuation of leaf morphology. Interestingly, the down-regulation of Cu/ZnSOD1 and Cu/ZnSOD2 as target genes of miR398a, which showed strong abnormal expression, was replaced by FeSOD (FSD1), indicating the influence of CuNPs. In addition, CuNPs triggered the expression of some important genes of heat shock response, including HsFA2, HSP70-9 and HSP90-3, which showed lower expression compared to HS. Thus, CuNPs play an important role in altering the gene expression pathway during heat stress.

Genome-wide expression analysis of novel heat-responsive microRNAs and their targets in contrasting wheat genotypes at reproductive stage under terminal heat stress

Introduction

Heat stress at terminal stage of wheat is critical and leads to huge yield losses worldwide. microRNAs (miRNAs) play significant regulatory roles in gene expression associated with abiotic and biotic stress at the post-transcriptional level.

Methods

In the present study, we carried out a comparative analysis of miRNAs and their targets in flag leaves as well as developing seeds of heat tolerant (RAJ3765) and heat susceptible (HUW510) wheat genotypes under heat stress and normal conditions using small RNA and degradome sequencing.

Results and discussion

A total of 84 conserved miRNAs belonging to 35 miRNA families and 93 novel miRNAs were identified in the 8 libraries. Tae-miR9672a-3p, tae-miR9774, tae-miR9669-5p, and tae-miR5048-5p showed the highest expression under heat stress. Tae-miR9775, tae-miR9662b-3p, tae-miR1120a, tae-miR5084, tae-miR1122a, tae-miR5085, tae-miR1118, tae-miR1130a, tae-miR9678-3p, tae-miR7757-5p, tae-miR9668-5p, tae-miR5050, tae-miR9652-5p, and tae-miR9679-5p were expressed only in the tolerant genotype, indicating their role in heat tolerance. Comparison between heat-treated and control groups revealed that 146 known and 57 novel miRNAs were differentially expressed in the various tissues. Eight degradome libraries sequence identified 457 targets of the differentially expressed miRNAs. Functional analysis of the targets indicated their involvement in photosynthesis, spliceosome, biosynthesis of nucleotide sugars and protein processing in the endoplasmic reticulum, arginine and proline metabolism and endocytosis.

Conclusion

This study increases the number of identified and novel miRNAs along with their roles involved in heat stress response in contrasting genotypes at two developing stages of wheat.

Genome-wide profiling of histone (H3) lysine 4 (K4) tri-methylation (me3) under drought, heat, and combined stresses in switchgrass

BACKGROUND

Switchgrass (Panicum virgatum L.) is a warm-season perennial (C4) grass identified as an important biofuel crop in the United States. It is well adapted to the marginal environment where heat and moisture stresses predominantly affect crop growth. However, the underlying molecular mechanisms associated with heat and drought stress tolerance still need to be fully understood in switchgrass. The methylation of H3K4 is often associated with transcriptional activation of genes, including stress-responsive. Therefore, this study aimed to analyze genome-wide histone H3K4-tri-methylation in switchgrass under heat, drought, and combined stress.

RESULTS

In total, ~ 1.3 million H3K4me3 peaks were identified in this study using SICER. Among them, 7,342; 6,510; and 8,536 peaks responded under drought (DT), drought and heat (DTHT), and heat (HT) stresses, respectively. Most DT and DTHT peaks spanned 0 to + 2000 bases from the transcription start site [TSS]. By comparing differentially marked peaks with RNA-Seq data, we identified peaks associated with genes: 155 DT-responsive peaks with 118 DT-responsive genes, 121 DTHT-responsive peaks with 110 DTHT-responsive genes, and 175 HT-responsive peaks with 136 HT-responsive genes. We have identified various transcription factors involved in DT, DTHT, and HT stresses. Gene Ontology analysis using the AgriGO revealed that most genes belonged to biological processes. Most annotated peaks belonged to metabolite interconversion, RNA metabolism, transporter, protein modifying, defense/immunity, membrane traffic protein, transmembrane signal receptor, and transcriptional regulator protein families. Further, we identified significant peaks associated with TFs, hormones, signaling, fatty acid and carbohydrate metabolism, and secondary metabolites. qRT-PCR analysis revealed the relative expressions of six abiotic stress-responsive genes (transketolase, chromatin remodeling factor-CDH3, fatty-acid desaturase A, transmembrane protein 14C, beta-amylase 1, and integrase-type DNA binding protein genes) that were significantly (P < 0.05) marked during drought, heat, and combined stresses by comparing stress-induced against un-stressed and input controls.

CONCLUSION

Our study provides a comprehensive and reproducible epigenomic analysis of drought, heat, and combined stress responses in switchgrass. Significant enrichment of H3K4me3 peaks downstream of the TSS of protein-coding genes was observed. In addition, the cost-effective experimental design, modified ChIP-Seq approach, and analyses presented here can serve as a prototype for other non-model plant species for conducting stress studies.

Identification and expression analysis of miR396 and its target genes in Jerusalem artichoke under temperature stress

The highly conserved miR396 plays a pivotal role in the growth, development, and responses to abiotic and biotic stresses in plants. However, research on miR396 and its targets in Jerusalem artichoke remains largely unexplored. In this study, we employed bioinformatics and experimental techniques, such as cloning and qRT-PCR, to investigate the regulatory role of miR396 on its targets, leveraging our lab's transcriptomic and degradomic data of Jerusalem artichoke. Specifically, we initially cloned and characterized the precursors (htu-MIR396a/b/c) and mature sequences (htu-miR396a/b/c) of three miR396 isoforms. Subsequently, we identified nine target genes, including seven Growth-Regulating Factors (GRFs) (HtGRF3/4/6/9/10/12/13), one WRKY transcription factor (HtWRKY40), and one Scarecrow-like (SCL) transcription factor (HtSCL33). Finally, we conducted an analysis of their expression patterns across various tissues and their responses to temperature stress. Notably, htu-MIR396s exhibited high expression in seedling stems, while htu-miR396s predominantly expressed in seedling leaves. Moreover, HtWRKY40 and HtSCL33 displayed higher expression levels than HtGRFs in most tissues, except leaves. Remarkably, HtGRF4/6/10/12/13 exhibited higher expression in leaves than in roots and stems during seedling growth. Furthermore, during tuber development, HtGRF4/6/10, HtWRKY40, and HtSCL33 were highly expressed, while HtGRF3/9/12/13 showed relatively lower expression levels. Under heat stress (42℃), htu-MIR396 expression was up-regulated, and htu-miR396 showed dynamic expression patterns in seedlings, resulting in the induction of HtGRF4/6/10/12/13 in leaves and HtSCL33 in roots, while HtWRKY40 in leaves was repressed. Conversely, under cold stress (4℃), htu-MIR396s showed fluctuating expression levels, and htu-miR396s were up-regulated in seedlings. Notably, HtGRF4/13 and HtSCL33 in seedlings were reduced, whereas HtGRF6 in roots and HtWRKY40 in leaves were enhanced. These findings offer valuable insights into the functional roles of miR396-target interactions under abiotic stress in Jerusalem artichoke.

miRNAs for crop improvement

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

Involvement of microRNA164 in responses to heat stress in Arabidopsis

MicroRNAs (miRNAs) are considered to be integral parts of plant stress regulatory networks. Under long-term heat stress, miR164 is induced. Conversely, its targets are repressed. Transgenic overexpressors (164OE) and mutants of MIR164 (mir164) were used to study miR164's functions during heat responses. Target gene expression decreased in 164OE transgenic plants and increased in mir164a-4 and mir164b mutants. Under heat stress, the mir164 mutants presented heat-sensitive phenotypes, while 164OE transgenic plants showed better thermotolerance than wild-type (WT) plants. Overexpression of miR164 decreased heat-inhibition of hypocotyl lengths. Under heat stress, miR164 target genes modulated the expression of chlorophyll b reductase and chlorophyll catabolic genes, reducing the chlorophyll a/b ratio. More H₂O₂ accumulated in the mir164 mutants under heat stress, which may have caused oxidative damage. In addition, expression of HSPs was altered in the experimental plants compared to that of the WT. Overall, miR164 influenced target gene expression, altering development, chlorophyll a/b ratio, H₂O₂-caused damage, and HSPs expression under long-term heat stress. These phenomena, in turn, likely influence the thermotolerance of plants.

Dynamic Regulation of Grapevine's microRNAs in Response to Mycorrhizal Symbiosis and High Temperature

MicroRNAs (miRNAs) are non-coding small RNAs that play crucial roles in plant development and stress responses and can regulate plant interactions with beneficial soil microorganisms such as arbuscular mycorrhizal fungi (AMF). To determine if root inoculation with distinct AMF species affected miRNA expression in grapevines subjected to high temperatures, RNA-seq was conducted in leaves of grapevines inoculated with either Rhizoglomus irregulare or Funneliformis mosseae and exposed to a high-temperature treatment (HTT) of 40 °C for 4 h per day for one week. Our results showed that mycorrhizal inoculation resulted in a better plant physiological response to HTT. Amongst the 195 identified miRNAs, 83 were considered isomiRs, suggesting that isomiRs can be biologically functional in plants. The number of differentially expressed miRNAs between temperatures was higher in mycorrhizal (28) than in non-inoculated plants (17). Several miR396 family members, which target homeobox-leucine zipper proteins, were only upregulated by HTT in mycorrhizal plants. Predicted targets of HTT-induced miRNAs in mycorrhizal plants queried to STRING DB formed networks for Cox complex, and growth and stress-related transcription factors such as SQUAMOSA promoter-binding-like-proteins, homeobox-leucine zipper proteins and auxin receptors. A further cluster related to DNA polymerase was found in R. irregulare inoculated plants. The results presented herein provide new insights into miRNA regulation in mycorrhizal grapevines under heat stress and can be the basis for functional studies of plant-AMF-stress interactions.

Overexpression of Mtr-miR319a Contributes to Leaf Curl and Salt Stress Adaptation in Arabidopsis thaliana and Medicago truncatula

Salt stress is a worldwide agronomic issue that limits crop yield and quality. Improving salt stress tolerance via genetic modification is the most efficient method to conquer soil salinization problems in crops. Crop miRNAs have been declared to be tightly associated with responding and adapting to salt stress and are advantageous for salt tolerance modification. However, very few studies have validated vital salt tolerance miRNAs and coupled potent target genes in Medicago species, the most economically important forage legume species. In this study, Mtr-miR319a, a miRNA that was identified from the previous next-generation sequencing assay of salt-treated Medicago truncatula, was overexpressed in M. truncatula and Arabidopsis thaliana, inducing the curly leaves and salt stress tolerance phenotypes. Combining the elevated expression level of Mtr-miR319a in the M. truncatula overexpression lines under normal and salt-treatment conditions, the regulatory roles of Mtr-miR319a in leaf development and salt stress adaptation were demonstrated. Several predicted target genes of Mtr-miR319a were also regulated by Mtr-miR319a and were associated with the aforementioned phenotypes in M. truncatula plants, most notably MtTCP4. Our study clarified the functional role of Mtr-miR319a and its target genes in regulating leaf development and defending salt stress, which can help to inform crop breeding efforts for improving salt tolerance via genetic engineering.

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.

Identification of microRNAs responsive to arbuscular mycorrhizal fungi in Panicum virgatum (switchgrass)

BACKGROUND

MicroRNAs (miRNAs) are important post-transcriptional regulators involved in the control of a range of processes, including symbiotic interactions in plants. MiRNA involvement in arbuscular mycorrhizae (AM) symbiosis has been mainly studied in model species, and our study is the first to analyze global miRNA expression in the roots of AM colonized switchgrass (Panicum virgatum), an emerging biofuel feedstock. AM symbiosis helps plants gain mineral nutrition from the soil and may enhance switchgrass biomass production on marginal lands. Our goals were to identify miRNAs and their corresponding target genes that are controlling AM symbiosis in switchgrass.

RESULTS

Through genome-wide analysis of next-generation miRNA sequencing reads generated from switchgrass roots, we identified 122 mature miRNAs, including 28 novel miRNAs. By comparing miRNA expression profiles of AM-inoculated and control switchgrass roots, we identified 15 AM-responsive miRNAs across lowland accession "Alamo", upland accession "Dacotah", and two upland/lowland F₁ hybrids. We used degradome sequencing to identify target genes of the AM-responsive miRNAs revealing targets of miRNAs residing on both K and N subgenomes. Notably, genes involved in copper ion binding were targeted by downregulated miRNAs, while upregulated miRNAs mainly targeted GRAS family transcription factors.

CONCLUSION

Through miRNA analysis and degradome sequencing, we revealed that both upland and lowland switchgrass genotypes as well as upland-lowland hybrids respond to AM by altering miRNA expression. We demonstrated complex GRAS transcription factor regulation by the miR171 family, with some miR171 family members being AM responsive while others remained static. Copper miRNA downregulation was common amongst the genotypes tested and we identified superoxide dismutases and laccases as targets, suggesting that these Cu-miRNAs are likely involved in ROS detoxification and lignin deposition, respectively. Other prominent targets of the Cu miRNAs were blue copper proteins. Overall, the potential effect of AM colonization on lignin deposition pathways in this biofuel crop highlights the importance of considering AM and miRNA in future biofuel crop development strategies.

MicroRNA398: A Master Regulator of Plant Development and Stress Responses

MicroRNAs (miRNAs) play crucial roles in plant development and stress responses, and a growing number of studies suggest that miRNAs are promising targets for crop improvement because they participate in the regulation of diverse, important agronomic traits. MicroRNA398 (miR398) is a conserved miRNA in plants and has been shown to control multiple stress responses and plant growth in a variety of species. There are many studies on the stress response and developmental regulation of miR398. To systematically understand its function, it is necessary to summarize the evolution and functional roles of miR398 and its target genes. In this review, we analyze the evolution of miR398 in plants and outline its involvement in abiotic and biotic stress responses, in growth and development and in model and non-model plants. We summarize recent functional analyses, highlighting the role of miR398 as a master regulator that coordinates growth and diverse responses to environmental factors. We also discuss the potential for fine-tuning miR398 to achieve the goal of simultaneously improving plant growth and stress tolerance.

Research advances in function and regulation mechanisms of plant small heat shock proteins (sHSPs) under environmental stresses

Plants respond to various stresses by triggering the expression of genes that encode proteins involved in plant growth, fruit ripening, cellular protein homeostasis, and tolerance systems. sHSPs, a subfamily of heat shock proteins (HSPs), can be expressed in plants to inhibit abnormal aggregation of proteins and protect normal proteins by interacting with folding target proteins, protect cell integrity, and improve resistance under various adverse conditions. Thus, sHSPs have significant influences on seed germination and plant development. In this review, the classification, structure, and functions of sHSP family members in plants are systematically summarized, with emphasis on their roles in promoting fruit ripening and plant growth by reducing the accumulation of ROS, improving the survival rate of plants and the antioxidant activity, and protecting photosynthesis under biotic and abiotic stresses. Meanwhile, the production and regulatory mechanisms of sHSPs are described in detail. Heat shock factors, long non-coding RNA (lncRNAs), microRNA (miRNAs), and FK506 binding proteins are related to the production process of sHSPs. Molecular chaperone complex HSP70/100, plastidic proteins, and abscisic acid (ABA) are involved in the regulatory mechanisms of sHSPs. Besides, scientific efforts and practices for improving plant stress resistance have carried out the constitutive expression of sHSPs in transgenic plants in recent years. It is a powerful path for inducing the protective mechanisms of plants under various stresses. Therefore, exploring the role of sHSPs in the plant defense system paves a way for comprehensively unraveling plant tolerance in response to biotic and abiotic stress.

Thermo-Priming Mediated Cellular Networks for Abiotic Stress Management in Plants

Plants can adapt to different environmental conditions and can survive even under very harsh conditions. They have developed elaborate networks of receptors and signaling components, which modulate their biochemistry and physiology by regulating the genetic information. Plants also have the abilities to transmit information between their different parts to ensure a holistic response to any adverse environmental challenge. One such phenomenon that has received greater attention in recent years is called stress priming. Any milder exposure to stress is used by plants to prime themselves by modifying various cellular and molecular parameters. These changes seem to stay as memory and prepare the plants to better tolerate subsequent exposure to severe stress. In this review, we have discussed the various ways in which plants can be primed and illustrate the biochemical and molecular changes, including chromatin modification leading to stress memory, with major focus on thermo-priming. Alteration in various hormones and their subsequent role during and after priming under various stress conditions imposed by changing climate conditions are also discussed.

A Multi-Level Iterative Bi-Clustering Method for Discovering miRNA Co-regulation Network of Abiotic Stress Tolerance in Soybeans

Although growing evidence shows that microRNA (miRNA) regulates plant growth and development, miRNA regulatory networks in plants are not well understood. Current experimental studies cannot characterize miRNA regulatory networks on a large scale. This information gap provides an excellent opportunity to employ computational methods for global analysis and generate valuable models and hypotheses. To address this opportunity, we collected miRNA-target interactions (MTIs) and used MTIs from Arabidopsis thaliana and Medicago truncatula to predict homologous MTIs in soybeans, resulting in 80,235 soybean MTIs in total. A multi-level iterative bi-clustering method was developed to identify 483 soybean miRNA-target regulatory modules (MTRMs). Furthermore, we collected soybean miRNA expression data and corresponding gene expression data in response to abiotic stresses. By clustering these data, 37 MTRMs related to abiotic stresses were identified, including stress-specific MTRMs and shared MTRMs. These MTRMs have gene ontology (GO) enrichment in resistance response, iron transport, positive growth regulation, etc. Our study predicts soybean MTRMs and miRNA-GO networks under different stresses, and provides miRNA targeting hypotheses for experimental analyses. The method can be applied to other biological processes and other plants to elucidate miRNA co-regulation mechanisms.

Identification and Characterization of circRNAs under Drought Stress in Moso Bamboo (Phyllostachys edulis)

Circular RNAs (circRNAs) are a class of endogenous noncoding RNAs formed by 3′-5′ ligation during splicing. They play an important role in the regulation of transcription and miRNA in eukaryotes. Drought is one of the detrimental abiotic stresses that limit plant growth and productivity. How circRNAs influence the response to drought stress in moso bamboo (Phyllostachys edulis) remains elusive. In this study, we investigate the expression pattern of circRNAs in moso bamboo at 6 h, 12 h, 24 h and 48 h after drought treatment by deep sequencing and bioinformatics analysis and identify 4931 circRNAs, 52 of which are differentially expressed (DEcircRNAs) in drought-treated and untreated moso bamboo. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of the host genes that generate the DEcircRNAs indcate that these DEcircRNAs are predicted to be involved in biochemical processes in response to drought, such as ubiquitin-mediated proteolysis, calcium-dependent protein kinase phosphorylation, amino acid biosynthesis and plant hormone signal transduction including abscisic acid. In addition, some circRNAs are shown to act as sponges for 291 miRNAs. Taken together, our results characterize the transcriptome profiles of circRNAs in drought responses and provide new insights into resistance breeding of moso bamboo.

Global analysis of switchgrass (Panicum virgatum L.) transcriptomes in response to interactive effects of drought and heat stresses

BACKGROUND

Sustainable production of high-quality feedstock has been of great interest in bioenergy research. Despite the economic importance, high temperatures and water deficit are limiting factors for the successful cultivation of switchgrass in semi-arid areas. There are limited reports on the molecular basis of combined abiotic stress tolerance in switchgrass, particularly the combination of drought and heat stress. We used transcriptomic approaches to elucidate the changes in the response of switchgrass to drought and high temperature simultaneously.

RESULTS

We conducted solely drought treatment in switchgrass plant Alamo AP13 by withholding water after 45 days of growing. For the combination of drought and heat effect, heat treatment (35 °C/25 °C day/night) was imposed after 72 h of the initiation of drought. Samples were collected at 0 h, 72 h, 96 h, 120 h, 144 h, and 168 h after treatment imposition, total RNA was extracted, and RNA-Seq conducted. Out of a total of 32,190 genes, we identified 3912, as drought (DT) responsive genes, 2339 and 4635 as, heat (HT) and drought and heat (DTHT) responsive genes, respectively. There were 209, 106, and 220 transcription factors (TFs) differentially expressed under DT, HT and DTHT respectively. Gene ontology annotation identified the metabolic process as the significant term enriched in DTHT genes. Other biological processes identified in DTHT responsive genes included: response to water, photosynthesis, oxidation-reduction processes, and response to stress. KEGG pathway enrichment analysis on DT and DTHT responsive genes revealed that TFs and genes controlling phenylpropanoid pathways were important for individual as well as combined stress response. For example, hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase (HCT) from the phenylpropanoid pathway was induced by single DT and combinations of DTHT stress.

CONCLUSION

Through RNA-Seq analysis, we have identified unique and overlapping genes in response to DT and combined DTHT stress in switchgrass. The combination of DT and HT stress may affect the photosynthetic machinery and phenylpropanoid pathway of switchgrass which negatively impacts lignin synthesis and biomass production of switchgrass. The biological function of genes identified particularly in response to DTHT stress could further be confirmed by techniques such as single point mutation or RNAi.

Drought tolerance improvement in Solanum lycopersicum: an insight into "OMICS" approaches and genome editing

Solanum lycopersicum (tomato) is an internationally acclaimed vegetable crop that is grown worldwide. However, drought stress is one of the most critical challenges for tomato production, and it is a crucial task for agricultural biotechnology to produce drought-resistant cultivars. Although breeders have done a lot of work on the tomato to boost quality and quantity of production and enhance resistance to biotic and abiotic stresses, conventional tomato breeding approaches have been limited to improving drought tolerance because of the intricacy of drought traits. Many efforts have been made to better understand the mechanisms involved in adaptation and tolerance to drought stress in tomatoes throughout the years. "Omics" techniques, such as genomics, transcriptomics, proteomics, and metabolomics in combination with modern sequencing technologies, have tremendously aided the discovery of drought-responsive genes. In addition, the availability of biotechnological tools, such as plant transformation and the recently developed genome editing system for tomatoes, has opened up wider opportunities for validating the function of drought-responsive genes and the generation of drought-tolerant varieties. This review highlighted the recent progresses for tomatoes improvement against drought stress through "omics" and "multi-omics" technologies including genetic engineering. We have also discussed the roles of non-coding RNAs and genome editing techniques for drought stress tolerance improvement in tomatoes.

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 RNAs: The Essential Regulators in Plant Thermotolerance

Small RNAs (sRNAs) are a class of non-coding RNAs that consist of 21-24 nucleotides. They have been extensively investigated as critical regulators in a variety of biological processes in plants. sRNAs include two major classes: microRNAs (miRNAs) and small interfering RNAs (siRNAs), which differ in their biogenesis and functional pathways. Due to global warming, high-temperature stress has become one of the primary causes for crop loss worldwide. Recent studies have shown that sRNAs are involved in heat stress responses in plants and play essential roles in high-temperature acclimation. Genome-wide studies for heat-responsive sRNAs have been conducted in many plant species using high-throughput sequencing. The roles for these sRNAs in heat stress response were also unraveled subsequently in model plants and crops. Exploring how sRNAs regulate gene expression and their regulatory mechanisms will broaden our understanding of sRNAs in thermal stress responses of plant. Here, we highlight the roles of currently known miRNAs and siRNAs in heat stress responses and acclimation of plants. We also discuss the regulatory mechanisms of sRNAs and their targets that are responsive to heat stress, which will provide powerful molecular biological resources for engineering crops with improved thermotolerance.

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.

Current status of microRNA-mediated regulation of drought stress responses in cereals

Drought is one of the most important abiotic stress factors impeding crop productivity. With the uncovering of their role as potential regulators of gene expression, microRNAs (miRNAs) have been recognized as new targets for developing stress resistance. MicroRNAs are small noncoding RNAs whose abundance is significantly altered under stress conditions. Interestingly, plant miRNAs predominantly targets transcription factors (TFs), and some of which are also the most critical drought-responsive genes that in turn could regulate the expression of numerous loci with drought-adaptive potential. The phytohormone ABA plays important roles in regulating stomatal conductance and in initiating an adaptive response to drought stress. miRNAs are implicated in regulating ABA-(abscisic acid) and non-ABA-mediated drought resistance pathways. For instance, miR159-MYB module and miR169-NFYA module participates in an ABA-dependent pathway, whereas several other ABA-independent miRNA-target modules (miR156-SPL; miR393-TIR1; miR160-ARF10, ARF16, ARF17; miR167-ARF6 and ARF8; miR390/TAS3siRNA-ARF2, ARF3, ARF4) collectively regulate drought responses in plants. Overall, miRNA-mediated drought response manifests diverse molecular, biochemical and physiological processes. Because of their immense role in controlling gene expression, miRNA manipulation has significant potential to augment plant tolerance to drought stress. This review compiles the current understanding of drought-responsive miRNAs in major cereals. Also, potential miRNA manipulation strategies currently in use along with the challenges and future perspectives are discussed.

Identification and characterization of heat-responsive microRNAs at the booting stage in two rice varieties, 9311 and Nagina 22

MicroRNAs (miRNAs) are small, non-coding, regulatory RNAs that play important roles in abiotic stress responses in plants, but their regulatory roles in the adaptive response to heat stress at the booting stage in two rice varieties, 9311 and Nagina 22, remain largely unknown. In this study, 464 known miRNAs and 123 potential novel miRNAs were identified. Of these miRNAs, a total of 90 differentially expressed miRNAs were obtained with 9311 libraries as the control group, of which 54 were upregulated and 36 were downregulated. To gain insight into functional significance, 2773 potential target genes of these 90 differentially expressed miRNAs were predicted. GO enrichment analysis showed that the predicted target genes of differentially expressed miRNAs included NACs, LACs, CSD, and Hsp40. KEGG pathway analysis showed that the target genes of these differentially expressed miRNAs were significantly enriched in the plant hormone signal transduction pathway. The expression levels of 10 differentially expressed miRNAs and their target genes obtained by qRT-PCR were largely consistent with the sequencing results. This study lays a foundation for the elucidation of the miRNA-mediated regulatory mechanisms in rice at elevated temperatures.

Sequence and functional analysis of MIR319 promoter homologs from Brassica juncea reveals regulatory diversification and altered expression under stress

KEY MESSAGE

Extensive regulatory divergence during development, abiotic stress and ABA regime observed amongst promoter homologs and homeologs of MIR319 from Brassica juncea. Gene duplication followed by sub-functionalization, neo-functionalization, and pseudogenization are routes to functional and adaptive diversification. The influence of polyploidy on protein-coding genes is well investigated but little is known about their impact on transcriptional regulation of MIRNA gene family. The present study was therefore performed with an aim to uncover regulatory diversification of MIR319 homologs and homeologs in Brassica juncea. We employed comparative genomics to identify and isolate six promoter homologs of MIR319 from B. juncea. Regulatory diversification was studied using analysis of reporter activity driven by BjMIR319 promoters in a heterologous system employing promoter-reporter fusion constructs. MIR319 is known to play important roles in leaf and flower development, and multiple stress responses. Reporter activity was therefore monitored during development, hormonal and stress regimes. In-silico analyses revealed differential distribution of cis-regulatory motifs and functional analysis revealed distinct spatiotemporal expression patterns. The significance of presence of selected cis-regulatory motifs corresponding to heat, cold, salt and ABA stress were further functionally validated. It was observed that promoter of Bj -MIR319a-A01 was upregulated in response to cold and salt stress, while promoter of Bj -MIR319c-A04 (D1) and Bj -MIR319c-A05 (FL) were downregulated in response to high temperature. In summary, comparative analysis of homologous promoters from Brassica juncea, an allopolyploid revealed extensive sequence and functional diversity. Spatiotemporal activity of reporter gene driven by BjMIR319 promoter was distinct, and partially overlapping with from those reported previously for A. thaliana. The present study clearly demonstrates regulatory divergence amongst promoter homologs of MIR319 in Brassica juncea during development and stress response, and underlines the urgent need for dissection of promoter function and detailed characterization including identification of interacting trans-factors. Genbank accession numbers: MT379853-MT379858.

Priming by High Temperature Stress Induces MicroRNA Regulated Heat Shock Modules Indicating Their Involvement in Thermopriming Response in Rice

Rice plants often encounter high temperature stress, but the associated coping strategies are poorly understood. It is known that a prior shorter exposure to high temperature, called thermo-priming, generally results in better adaptation of the plants to subsequent exposure to high temperature stress. High throughput sequencing of transcript and small RNA libraries of rice seedlings primed with short exposure to high temperature followed by high temperature stress and from plants exposed to high temperature without priming was performed. This identified a number of transcripts and microRNAs (miRs) that are induced or down regulated. Among them osa-miR531b, osa-miR5149, osa-miR168a-5p, osa-miR1846d-5p, osa-miR5077, osa-miR156b-3p, osa-miR167e-3p and their respective targets, coding for heat shock activators and repressors, showed differential expression between primed and non-primed plants. These findings were further validated by qRT-PCR. The results indicate that the miR-regulated heat shock proteins (HSPs)/heat shock transcription factors (HSFs) may serve as important regulatory nodes which are induced during thermo-priming for plant survival and development under high temperatures.

MicroRNAs: Potential Targets for Developing Stress-Tolerant Crops

Crop yield is challenged every year worldwide by changing climatic conditions. The forecasted climatic scenario urgently demands stress-tolerant crop varieties to feed the ever-increasing global population. Molecular breeding and genetic engineering approaches have been frequently exploited for developing crops with desired agronomic traits. Recently, microRNAs (miRNAs) have emerged as powerful molecules, which potentially serve as expression markers during stress conditions. The miRNAs are small non-coding endogenous RNAs, usually 20-24 nucleotides long, which mediate post-transcriptional gene silencing and fine-tune the regulation of many abiotic- and biotic-stress responsive genes in plants. The miRNAs usually function by specifically pairing with the target mRNAs, inducing their cleavage or repressing their translation. This review focuses on the exploration of the functional role of miRNAs in regulating plant responses to abiotic and biotic stresses. Moreover, a methodology is also discussed to mine stress-responsive miRNAs from the enormous amount of transcriptome data available in the public domain generated using next-generation sequencing (NGS). Considering the functional role of miRNAs in mediating stress responses, these molecules may be explored as novel targets for engineering stress-tolerant crop varieties.

Novel insights into expansion and functional diversification of MIR169 family in tomato

MAIN CONCLUSION

Expansion of MIR169 members by duplication and new mature forms, acquisition of new promoters, differential precursor-miRNA processivity and engaging novel targets increase the functional diversification of MIR169 in tomato. MIR169 family is an evolutionarily conserved miRNA family in plants. A systematic in-depth analysis of MIR169 family in tomato is lacking. We report 18 miR169 precursors, annotating new loci for MIR169a, b and d, as well as 3 novel mature isoforms (MIR169f/g/h). The family has expanded by both tandem- and segmental-duplication events during evolution. A tandem-pair MIR169b/b-1 and MIR169b-2/h is polycistronic in nature coding for three MIR169b isoforms and a new variant miR169h, that is evidently absent in the wild relatives S. pennellii and S. pimpinellifolium. Seven novel miR169 targets including RNA-binding protein, protein-phosphatase, aminotransferase, chaperone, tetratricopeptide-repeat-protein, and transcription factors ARF-9B and SEPELLATA-3 were established by efficient target cleavage in the presence of specific precursors as well as increased target abundance upon miR169 chelation by short-tandem-target-mimic construct in transient assays. Comparative antagonistic expression profiles of MIR169:target pairs suggest MIR169 family as ubiquitous regulator of various abiotic stresses (heat, cold, dehydration and salt) and developmental pathways. This regulation is partly brought about by acquisition of new promoters as demonstrated by promoter MIR169:GUS reporter assays as well as differential processivity of different precursors and miRNA cleavage efficiencies. Thus, the current study augments the functional horizon of MIR169 family with applications for stress tolerance in crops.

MiR319 mediated salt tolerance by ethylene

Salinity-induced accumulation of certain microRNAs accompanied by gaseous phytohormone ethylene production has been recognized as a mechanism of plant salt tolerance. MicroRNA319 (miR319) has been characterized as an important player in abiotic stress resistance in some C3 plants, such as Arabidopsis thaliana and rice. However, its role in the dedicated biomass plant switchgrass (Panicum virgatum L.), a C4 plant, has not been reported. Here, we show crosstalk between miR319 and ethylene (ET) for increasing salt tolerance. By overexpressing Osa-MIR319b and a target mimicry form of miR319 (MIM319), we showed that miR319 positively regulated ET synthesis and salt tolerance in switchgrass. By experimental treatments, we demonstrated that ET-mediated salt tolerance in switchgrass was dose-dependent, and miR319 regulated the switchgrass salt response by fine-tuning ET synthesis. Further experiments showed that the repression of a miR319 target, PvPCF5, in switchgrass also led to enhanced ethylene accumulation and salt tolerance in transgenic plants. Genome-wide transcriptome analysis demonstrated that overexpression of miR319 (OE-miR319) down-regulated the expression of key genes in the methionine (Met) cycle but promoted the expression of genes in ethylene synthesis. The results enrich our understanding of the synergistic effects of the miR319-PvPCF5 module and ethylene synthesis in the salt tolerance of switchgrass, a C4 bioenergy plant.

Non-coding RNAs: Functional roles in the regulation of stress response in Brassica crops

Brassica crops face a combination of different abiotic and biotic stresses in the field that can reduce plant growth and development by affecting biochemical and morpho-physiological processes. Emerging evidence suggests that non-coding RNAs (ncRNAs), especially microRNAs (miRNAs) and long ncRNAs (lncRNAs), play a significant role in the modulation of gene expression in response to plant stresses. Recent advances in computational and experimental approaches are of great interest for identifying and functionally characterizing ncRNAs. While progress in this field is limited, numerous ncRNAs involved in the regulation of gene expression in response to stress have been reported in Brassica. In this review, we summarize the modes of action and functions of stress-related miRNAs and lncRNAs in Brassica as well as the approaches used to identify ncRNAs.

Early Response of Radish to Heat Stress by Strand-Specific Transcriptome and miRNA Analysis

Radish is a crucial vegetable crop of the Brassicaceae family with many varieties and large cultivated area in China. Radish is a cool season crop, and there are only a few heat tolerant radish varieties in practical production with little information concerning the related genes in response to heat stress. In this work, some physiological parameter changes of young leaves under short-term heat stress were detected. Furthermore, we acquired 1802 differentially expressed mRNAs (including encoding some heat shock proteins, heat shock factor and heat shock-related transcription factors), 169 differentially expressed lncRNAs and three differentially expressed circRNAs (novel_circ_0000265, novel_circ_0000325 and novel_circ_0000315) through strand-specific RNA sequencing technology. We also found 10 differentially expressed miRNAs (ath-miR159b-3p, athmiR159c, ath-miR398a-3p, athmiR398b-3p, ath-miR165a-5p, ath-miR169g-3p, novel_86, novel_107, novel_21 and ath-miR171b-3p) by small RNA sequencing technology. Through function prediction and enrichment analysis, our results suggested that the significantly possible pathways/complexes related to heat stress in radish leaves were circadian rhythm-plant, photosynthesis-antenna proteins, photosynthesis, carbon fixation in photosynthetic organisms, arginine and proline metabolism, oxidative phosphorylation, peroxisome and plant hormone signal transduction. Besides, we identified one lncRNA-miRNA-mRNAs combination responsive to heat stress. These results will be helpful for further illustration of molecular regulation networks of how radish responds to heat stress.

Identification and characterization of Populus microRNAs in response to plant growth-promoting endophytic Streptomyces sp. SSD49

Endophytic Streptomyces sp. SSD49 inhibited eight pathogens, including the human opportunistic pathogenic microorganisms, the plant pathogenic fungi and bacteria. The growth of soybeans, tomatoes, peppers and Populus tomentosa seedings inoculated with SSD49 are remarkably promoted. Here, we constructed two P. tomentosa seedling microRNA (miRNA) libraries inoculated with (PS30d) and without SSD49 (PC30d) to explore the molecular regulatory roles in the plant response to the beneficial bacteria. Totals of 314 known and 144 novel miRNAs were identified, among which 27 known and 11 novel miRNA had significantly different expression. The targets of up-regulated miR160, miR156, ptc114 and down-regulated miR319 and other differential expressed miRNAs primarily regulated genes encoding transcription factors (auxin response factor, small auxin-up RNA, and GRAS proteins), disease resistance proteins, phytohormone oxidase, and response regulators, which could promote plant growth, influence disease resistance and miRNA biosynthesis in P. tomentosa. This is the first report on the genome-wide identification of biocontrol endophytic Streptomyces inoculation-responsive miRNAs using small RNA sequencing in P. tomentosa and these findings provide new insight into understanding the biocontrol effects of endophytic Streptomyces.

Identification of microRNA-target modules from rice variety Pusa Basmati-1 under high temperature and salt stress

High temperature and salinity stress are major factors limiting the growth and productivity of rice crop on a global scale. It is therefore an essential prerequisite to understand the molecular genetic regulation of plant responses to dual stresses. MicroRNAs (miRs) are recognized as key controllers of gene expression which act mainly at the post-transcriptional level to regulate various aspects of plant development. The present study attempts to investigate the miR circuits that are modulated in response to high temperature and salinity stress in rice. To gain insights into the pathway, preliminary miR profiles were generated using the next-generation sequencing (NGS) datasets. The identified molecules were filtered on the basis of fold differential regulation under high temperature, and time kinetics of their expression under the two individual stresses was followed to capture the regulatory windows. The analysis revealed the involvement of common miR regulatory nodes in response to two different abiotic stresses, thereby broadening our perspective about the stress-mediated regulatory mechanisms operative in rice.

Osa-miR398b boosts H2 O2 production and rice blast disease-resistance via multiple superoxide dismutases

miRNAs contribute to plant resistance against pathogens. Previously, we found that the function of miR398b in immunity in rice differs from that in Arabidopsis. However, the underlying mechanisms are unclear. In this study, we characterized the mutants of miR398b target genes and demonstrated that multiple superoxide dismutase genes contribute to miR398b-regulated rice immunity against the blast fungus Magnaporthe oryzae. Out of the four target genes of miR398b, mutations in Cu/Zn-Superoxidase Dismutase1 (CSD1), CSD2 and Os11g09780 (Superoxide DismutaseX, SODX) led to enhanced resistance to M. oryzae and increased hydrogen peroxide (H₂ O₂ ) accumulation. By contrast, mutations in Copper Chaperone for Superoxide Dismutase (CCSD) resulted in enhanced susceptibility. Biochemical studies revealed that csd1, csd2 and sodx displayed altered expression of CSDs and other superoxide dismutase (SOD) family members, leading to increased total SOD enzyme activity that positively contributed to higher H₂ O₂ production. By contrast, the ccsd mutant showed CSD protein deletion, resulting in decreased CSD and total SOD enzyme activity. Our results demonstrate the roles of different SODs in miR398b-regulated resistance to rice blast disease, and uncover an integrative regulatory network in which miR398b boosts total SOD activity to upregulate H₂ O₂ concentration and thereby improve disease resistance.

Genome-Wide Analysis of the TCP Gene Family in Switchgrass (Panicum virgatum L.)

The plant-specific transcription factor TCPs play multiple roles in plant growth, development, and stress responses. However, a genome-wide analysis of TCP proteins and their roles in salt stress has not been declared in switchgrass (Panicum virgatum L.). In this study, 42 PvTCP genes (PvTCPs) were identified from the switchgrass genome and 38 members can be anchored to its chromosomes unevenly. Nine PvTCPs were predicted to be microRNA319 (miR319) targets. Furthermore, PvTCPs can be divided into three clades according to the phylogeny and conserved domains. Members in the same clade have the similar gene structure and motif localization. Although all PvTCPs were expressed in tested tissues, their expression profiles were different under normal condition. The specific expression may indicate their different roles in plant growth and development. In addition, approximately 20 cis-acting elements were detected in the promoters of PvTCPs, and 40% were related to stress response. Moreover, the expression profiles of PvTCPs under salt stress were also analyzed and 29 PvTCPs were regulated after NaCl treatment. Taken together, the PvTCP gene family was analyzed at a genome-wide level and their possible functions in salt stress, which lay the basis for further functional analysis of PvTCPs in switchgrass.

Banana sRNAome and degradome identify microRNAs functioning in differential responses to temperature stress

Background

Temperature stress is a major environmental factor affecting not only plant growth and development, but also fruit postharvest life and quality. MicroRNAs (miRNAs) are a class of non-coding small RNAs that play important roles in various biological processes. Harvested banana fruit can exhibit distinct symptoms in response to different temperature stresses, but the underlying miRNA-mediated regulatory mechanisms remained unknown.

Results

Here, we profiled temperature-responsive miRNAs in banana, using deep sequencing and computational and molecular analyses. In total 113 known miRNAs and 26 novel banana-specific miRNAs were identified. Of these miRNAs, 42 miRNAs were expressed differentially under cold and heat stresses. Degradome sequencing identified 60 target genes regulated by known miRNAs and half of these targets were regulated by 15 temperature-responsive miRNAs. The correlative expression patterns between several miRNAs and their target genes were further validated via qRT-PCR. Our data showed that miR535 and miR156 families may derive from a common ancestor during evolution and jointly play a role in fine-tuning SPL gene expression in banana. We also identified the miRNA-triggered phased secondary siRNAs in banana and found miR393-TIR1/AFB phasiRNA production displaying cold stress-specific enrichment.

Conclusions

Our results provide a foundation for understanding the miRNA-dependent temperature stress response in banana. The characterized correlations between miRNAs and their response to temperature stress could serve as markers in the breeding programs or tools for improving temperature tolerance of banana.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5395-1) contains supplementary material, which is available to authorized users.

miRNomes involved in imparting thermotolerance to crop plants

Thermal stress is one of the challenges to crop plants that negatively impacts crop yield. To overcome this ever-growing problem, utilization of regulatory mechanisms, especially microRNAs (miRNAs), that provide efficient and precise regulation in a targeted manner have been found to play determining roles. Besides their roles in plant growth and development, many recent studies have shown differential regulation of several miRNAs during abiotic stresses including heat stress (HS). Thus, understanding the underlying mechanism of miRNA-mediated gene expression during HS will enable researchers to exploit this regulatory mechanism to address HS responses. This review focuses on the miRNAs and regulatory networks that were involved in physiological, metabolic and morphological adaptations during HS in plant, specifically in crops. Illustrated examples including, the miR156-SPL, miR169-NF-YA5, miR395-APS/AST, miR396-WRKY, etc., have been discussed in specific relation to the crop plants. Further, we have also discussed the available plant miRNA databases and bioinformatics tools useful for miRNA identification and study of their regulatory role in response to HS. Finally, we have briefly discussed the future prospects about the miRNA-related mechanisms of HS for improving thermotolerance in crop plants.

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.

Analysis of Brachypodium miRNA targets: evidence for diverse control during stress and conservation in bioenergy crops

BACKGROUND

Since the proposal of Brachypodium distachyon as a model for the grasses, over 500 Bdi-miRNAs have been annotated in miRBase making Brachypodium second in number only to rice. Other monocots, such as switchgrass, are completely absent from the miRBase database. While a significant number of miRNAs have been identified which are highly conserved across plants, little research has been done with respect to the conservation of miRNA targets. Plant responses to abiotic stresses are regulated by diverse pathways many of which involve miRNAs; however, it can be difficult to identify miRNA guided gene regulation when the miRNA is not the primary regulator of the target mRNA.

RESULTS

To investigate miRNA target conservation and stress response involvement, a set of PARE (Parallel Analysis of RNA Ends) libraries totaling over two billion reads was constructed and sequenced from Brachypodium, switchgrass, and sorghum representing the first report of RNA degradome data from the latter two species. Analysis of this data provided not only PARE evidence for miRNA guided cleavage of over 7000 predicted target mRNAs in Brachypodium, but also evidence for miRNA guided cleavage of over 1000 homologous transcripts in sorghum and switchgrass. A pipeline was constructed to compare RNA-seq and PARE data made from Brachypodium plants exposed to various abiotic stress conditions. This resulted in the identification of 44 miRNA targets which exhibit stress regulated cleavage. Time course experiments were performed to reveal the relationship between miR393ab, miR169a, miR394ab, and their respective targets throughout the first 36 h of the cold stress response in Brachypodium.

CONCLUSIONS

Knowledge gained from this study provides considerable insight into the RNA degradomes and the breadth of miRNA target conservation among these three species. Additionally, associations of a number of miRNAs and target mRNAs with the stress responses have been revealed which could aid in the development of stress tolerant transgenic crops.

Cross-species multiple environmental stress responses: An integrated approach to identify candidate genes for multiple stress tolerance in sorghum (Sorghum bicolor (L.) Moench) and related model species

BACKGROUND

Crop response to the changing climate and unpredictable effects of global warming with adverse conditions such as drought stress has brought concerns about food security to the fore; crop yield loss is a major cause of concern in this regard. Identification of genes with multiple responses across environmental stresses is the genetic foundation that leads to crop adaptation to environmental perturbations.

METHODS

In this paper, we introduce an integrated approach to assess candidate genes for multiple stress responses across-species. The approach combines ontology based semantic data integration with expression profiling, comparative genomics, phylogenomics, functional gene enrichment and gene enrichment network analysis to identify genes associated with plant stress phenotypes. Five different ontologies, viz., Gene Ontology (GO), Trait Ontology (TO), Plant Ontology (PO), Growth Ontology (GRO) and Environment Ontology (EO) were used to semantically integrate drought related information.

RESULTS

Target genes linked to Quantitative Trait Loci (QTLs) controlling yield and stress tolerance in sorghum (Sorghum bicolor (L.) Moench) and closely related species were identified. Based on the enriched GO terms of the biological processes, 1116 sorghum genes with potential responses to 5 different stresses, such as drought (18%), salt (32%), cold (20%), heat (8%) and oxidative stress (25%) were identified to be over-expressed. Out of 169 sorghum drought responsive QTLs associated genes that were identified based on expression datasets, 56% were shown to have multiple stress responses. On the other hand, out of 168 additional genes that have been evaluated for orthologous pairs, 90% were conserved across species for drought tolerance. Over 50% of identified maize and rice genes were responsive to drought and salt stresses and were co-located within multifunctional QTLs. Among the total identified multi-stress responsive genes, 272 targets were shown to be co-localized within QTLs associated with different traits that are responsive to multiple stresses. Ontology mapping was used to validate the identified genes, while reconstruction of the phylogenetic tree was instrumental to infer the evolutionary relationship of the sorghum orthologs. The results also show specific genes responsible for various interrelated components of drought response mechanism such as drought tolerance, drought avoidance and drought escape.

CONCLUSIONS

We submit that this approach is novel and to our knowledge, has not been used previously in any other research; it enables us to perform cross-species queries for genes that are likely to be associated with multiple stress tolerance, as a means to identify novel targets for engineering stress resistance in sorghum and possibly, in other crop species.

Enhanced Cold Tolerance and Tillering in Switchgrass (Panicum virgatum L.) by Heterologous Expression of Osa-miR393a

The microRNA393 (miR393) family is one of the conserved miRNA families in the plant kingdom. MiR393 was reported to regulate rice tillering and abiotic stress resistance positively through an auxin signaling pathway. However, little is known about the function of miR393 in switchgrass (Panicum virgatum L.), an important bioenergy C4 grass plant. We tested the expression level of miR393 and its four putative target genes (PvAFB1, PvAFB2, PvAFB3 and PvTIR1) in switchgrass, and found that these genes all responded to cold stress and exogenous 1-naphthaleneacetic acid (NAA) treatment. To investigate the function of miR393 in switchgrass, we enhanced miR393 expression by introducing an Osa-miR393a gene into switchgrass. The results showed that cold tolerance of the transgenic T0 and T1 generation plants was highly improved. Cold tolerance-related genes PvCOR47, PvICE1 and PvRAV1 were negatively regulated by exogenous NAA, and the expression of these genes was significantly higher in transgenic plants than in wild-type plants. The transgenic T1 seedlings were more tolerant to exogenous NAA treatment, accumulating less H2O2 after cold treatments. It was also observed that the miR393/target module regulates cold tolerance responses in Arabidopsis. In addition, transgenic plants overexpressing miR393 had significantly more tillers and higher biomass yield per plant in greenhouse and field tests. Forage quality analyses revealed that the soluble sugar contents of transgenic plants were increased markedly. Overall, the results suggested that overexpression of miR393 improved cold tolerance and tillering of switchgrass through regulation of auxin signaling transduction.

Small RNAs in regulating temperature stress response in plants

Due to global climate change, temperature stress has become one of the primary causes of crop losses worldwide. Much progress has been made in unraveling the complex stress response mechanisms in plants, particularly in the identification of temperature stress responsive protein-coding genes. Recently discovered microRNAs (miRNAs) and endogenous small-interfering RNAs (siRN As) have also been demonstrated as important players in plant temperature stress response. Using high-throughput sequencing, many small RNAs, especially miRNAs, have been identified to be triggered by cold or heat. Subsequently, several studies have shown an important functional role for these small RNAs in cold or heat tolerance. These findings greatly broaden our understanding of endogenous small RNAs in plant stress response control. Here, we highlight new findings regarding the roles of miRNAs and siRNAs in plant temperature stress response and acclimation. We also review the current understanding of the regulatory mechanisms of small RNAs in temperature stress response, and explore the outlook for the use of these small RNAs in molecular breeding for improvement of temperature stress tolerance in plants.

High throughput sequencing of small RNAs reveals dynamic microRNAs expression of lipid metabolism during Camellia oleifera and C. meiocarpa seed natural drying

BACKGROUND

Camellia species are ancient oilseed plants with a history of cultivation over two thousand years. Prior to oil extraction, natural seed drying is often practiced, a process affecting fatty acid quality and quantity. MicroRNAs (miRNA) of lipid metabolism associated with camellia seed natural drying are unexplored. To obtain insight into the function of miRNAs in lipid metabolism during natural drying, Illumina sequencing of C. oleifera and C. meiocarpa small-RNA was conducted.

RESULTS

A total of 274 candidate miRNAs were identified and 3733 target unigenes were annotated by performing a BLASTX. Through integrated GO and KEGG function annotation, 23 miRNA regulating 131 target genes were identified as lipid metabolism, regulating fatty acid biosynthesis, accumulation and catabolism. We observed one, two, and four miRNAs of lipid metabolism which were specially expressed in C. Meiocarpa, C. oleifera, and the two species collectively, respectively. At 30% moisture contents, C. meiocarpa and C. oleifer produced nine and eight significant differentially expressed miRNAs, respectively, with high fatty acid synthesis and accumulation activities. Across the two species, 12 significant differentially expressed miRNAs were identified at the 50% moisture content.

CONCLUSIONS

Sequencing of small-RNA revealed the presence of 23 miRNAs regulating lipid metabolism in camellia seed during natural drying and permitted comparative miRNA profiles between C. Meiocarpa and C. oleifera. Furthermore, this study successfully identified the best drying environment at which the quantity and quality of lipid in camellia seed are at its maximum.

Genome-wide identification of heat stress-responsive small RNAs in tall fescue (Festuca arundinacea) by high-throughput sequencing

MicroRNAs (miRNAs) play vital roles in the adaptive response of plants to various abiotic and biotic stresses. Tall fescue (Festuca arundinacea Schreb.) is a major cool-season forage and turf grass species which is severely influenced by heat stress. To unravel possible heat stress-responsive miRNAs, high-throughput sequencing was employed for heat-tolerant PI578718 and heat-sensitive PI234881 genotypes growing in presence and absence of heat stress (40°C for 36h). By searching against the miRBase database, among 1421 reference monocotyledon miRNAs, more than 850 were identified in all samples. Among these miRNAs, 1.46% and 2.29% were differentially expressed in PI234881 and PI578718 under heat stress, respectively, and most of them were down-regulated. In addition, a total of 170 novel miRNAs belonging to 145 miRNA families were identified. Furthermore, putative targets of differentially expressed miRNAs were predicted. The regulation of selected miRNAs by heat stress was revalidated through quantitative reverse transcription PCR (qRT-PCR) analysis. Most of these miRNAs shared similar expression patterns; however, some showed distinct expression patterns under heat stress, with their putative targets displaying different transcription levels. This is the first genome-wide miRNA identification in tall fescue. miRNAs specific to PI578718, or those that exhibited differential expression profiles between the two genotypes under high temperature, were probably associated with the variation in thermotolerance of tall fescue. The differentially expressed miRNAs between these two tall fescue genotypes and their putative targeted genes will provide essential information for further study on miRNAs mediating heat response and facilitate to improve turf grass breeding.

Characterization and Function of MicroRNA∗s in Plants

MicroRNAs, a group of non-coding RNA molecules, play essential roles in a wide range of cellular processes in different molecules, cells, and organisms. In plants, microRNAs are a class of 20- to 24-nucleotides endogenous small RNAs that repress gene expression. The microRNA guide strand (miRNA) and its complementary strand (miRNA^∗) both originate from the miRNA/miRNA^∗ duplex. Generally, the guide strands act as post-transcriptional regulators that suppress gene expression by cleaving their target mRNA transcripts, whereas the complementary strands were thought to be degraded as 'passenger strands.' However, the complementary strand has been confirmed to possess significant biological functionality in recent reports. In this review, we summarized the binding characteristics of the miRNA^∗ strands with ARGONAUTE proteins, their tissue-specific accumulations and their biological functions, illustrating the essential roles of miRNA^∗s in biological processes and therefore providing directions for further exploration.

MicroRNA, a new target for engineering new crop cultivars

Global sustainable development depends on, at least partially, the sustainable development of crop reproduction that provides food, cloth and bioenergy as well certain drugs. During thousands of years of human history, many crops have been domesticated for feeding the world. Perfectly, in the past 2 decades, scientists have innovated biotechnological tools for improving crop yield and quality. For sustainable development, more targets and tools are needed to develop. Among these, microRNA (miRNA) is becoming an emerging target for engineering new crop cultivars with high yield and quality as well tolerance to environmental abiotic and biotic stresses. miRNAs are an extensive class of small regulatory RNAs, which play essential roles in all plant biological and metabolic processes, not only in plant development and growth but also in compound biosynthesis and response to various environmental stress. miRNA-based biotechnology is becoming a new strategy for crop improvement, which will play important role in future agricultural sustainable development.

Regulation of Non-coding RNAs in Heat Stress Responses of Plants

Heat stress is an important factor limiting plant growth, development, and productivity; thus, plants have evolved special adaptive mechanisms to cope with high-temperature stress. Non-coding RNAs (ncRNAs) are a class of regulatory RNAs that play an important role in many biological processes. Recently developed advanced technologies, such as genome-wide transcriptomic analysis, have revealed that abundant ncRNAs are expressed under heat stress. Although this area of research is still in its infancy, an increasing number of several classes of regulatory ncRNA (i.e., miRNA, siRNA, and lncRNA) related to heat stress responses have been reported. In this mini-review, we discuss our current understanding of the role of ncRNAs in heat stress responses in plants, especially miRNAs, siRNAs, and their targets. For example, the miR398-CSD/CCS-HSF, miR396-WRKY6, miR159-GAMYB, and TAS1-HTT-HSF pathways regulate plant heat tolerance. We highlight the hormone/development-related miRNAs involved in heat stress, and discuss the regulatory networks of miRNA-targets. We also note that DNA methylation and alternative splicing could affect miRNA expression under heat stress, and some lncRNAs could respond to heat stress. Finally, we briefly discuss future prospects concerning the ncRNA-related mechanisms of heat stress responses in plants.

Identification of Circular RNAs and Their Targets in Leaves of Triticum aestivum L. under Dehydration Stress

Circular RNAs (circRNAs) are a type of newly identified non-coding RNAs through high-throughput deep sequencing, which play important roles in miRNA function and transcriptional controlling in human, animals, and plants. To date, there is no report in wheat seedlings regarding the circRNAs identification and roles in the dehydration stress response. In present study, the total RNA was extracted from leaves of wheat seedlings under dehydration-stressed and well-watered conditions, respectively. Then, the circRNAs enriched library based deep sequencing was performed and the circRNAs were identified using bioinformatics tools. Around 88 circRNAs candidates were isolated in wheat seedlings leaves while 62 were differentially expressed in dehydration-stressed seedlings compared to well-watered control. Among the dehydration responsive circRNAs, six were found to act as 26 corresponding miRNAs sponges in wheat. Sixteen circRNAs including the 6 miRNAs sponges and other 10 randomly selected ones were further validated to be circular by real-time PCR assay, and 14 displayed consistent regulation patterns with the transcriptome sequencing results. After Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the targeted mRNAs functions, the circRNAs were predicted to be involved in dehydration responsive process, such as photosynthesis, porphyrin, and chlorophyll metabolism, oxidative phosphorylation, amino acid biosynthesis, and metabolism, as well as plant hormone signal transduction, involving auxin, brassinosteroid, and salicylic acid. Herein, we revealed a possible connection between the regulations of circRNAs with the expressions of functional genes in wheat leaves associated with dehydration resistance.

MicroRNA390-Directed TAS3 Cleavage Leads to the Production of tasiRNA-ARF3/4 During Somatic Embryogenesis in Dimocarpus longan Lour

Trans-acting short-interfering RNAs (tasiRNAs) originate from TAS3 families through microRNA (miRNA) 390-guided cleavage of primary transcripts and target auxin response factors (ARF3/-4), which are involved in the normal development of lateral roots and flowers in plants. However, their roles in embryo development are still unclear. Here, the pathway miR390-TAS3-ARF3/-4 was identified systematically for the first time during somatic embryo development in Dimocarpus longan. We identified the miR390 primary transcript and promoter. The promoter contained cis-acting elements responsive to stimuli such as light, salicylic acid, anaerobic induction, fungal elicitor, circadian control, and heat stress. The longan TAS3 transcript, containing two miR390-binding sites, was isolated; the miR390- guided cleavage site located near the 3' end of the TAS3 transcript was verified. Eight TAS3-tasiRNAs with the 21-nucleotides phase were found among longan small RNA data, further confirming that miR390-directed TAS3 cleavage leads to the production of tasiRNA in longan. Among them, TAS3_5'D5+ and 5'D6+ tasiRNAs were highly abundant, and verified to target ARF3 and -4, implying that miR390-guided TAS3 cleavage with 21-nucleotides phase leading to the production of tasiRNA-ARF is conserved in plants. Pri-miR390 was highly expressed in friable-embryogenic callus (EC), and less expressed in incomplete compact pro-embryogenic cultures, while miR390 showed its lowest expression in EC and highest expression in torpedo-shaped embryos (TEs). DlTAS3 and DlARF4 both exhibited their lowest expressions in EC, and reached their peaks in the globular embryos stage, which were mainly inversely proportional to the expression of miR390, especially at the globular embryos to cotyledonary embryos (CEs) stages. While DlARF3 showed little variation from the EC to TEs stages, and exhibited its lowest expression in the CEs stage. There was a general lack of correlation between the expressions of DlARF3 and miR390. In addition, pri-miR390, DlTAS3, DlARF3 and -4 were up-regulated by 2,4-D in a concentration-dependent manner. They were also preferentially expressed in roots, pulp, and seeds of 'Sijimi' longan, implying their extended roles in the development of longan roots and fruit. This study provided insights into a possible role of miR390-tasiRNAs-ARF in plant somatic embryo development.