A Role for Arabidopsis miR399f in Salt, Drought, and ABA Signaling

Non-coding RNAs in plant stress responses: molecular insights and agricultural applications

Non-coding RNAs (ncRNAs) have emerged as crucial regulators in plant responses to environmental stress, orchestrating complex networks that finetune gene expression under both abiotic and biotic challenges. To elucidate this intricate ncRNA crosstalk, this review comprehensively summarizes recent advances in understanding the mechanisms of key regulatory ncRNAs including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), tRNA derived fragments (tRFs) and small interfering RNAs (siRNAs) in mediating plant adaptations to stress conditions. We discuss molecular insights into how these ncRNAs modulate stress signalling pathways, control hormonal responses and interact through elaborate crosstalk mechanisms. We also emphasize emerging biotechnological strategies that leverage both innate and artificial ncRNAs as well as potential approaches for finetuning ncRNA levels to engineer stress-resilient crops. Collectively, continued advances in high-throughput sequencing, functional genomics and computational modelling will deepen our understanding of ncRNA network mediated stress responses, ultimately guiding the design of robust climate-resilient crops.

The interaction of nutrient uptake with biotic and abiotic stresses in plants

Plants depend heavily on efficient nutrient uptake and utilization for optimal growth and development. However, plants are constantly subjected to a diverse array of biotic stresses, such as pathogen infections, insect pests, and herbivory, as well as abiotic stress like drought, salinity, extreme temperatures, and nutrient imbalances. These stresses significantly impact the plant's ability to take up nutrient and use it efficiency. Understanding how plants maintain nutrient uptake and use efficiency under biotic and abiotic stress conditions is crucial for improving crop resilience and sustainability. This review explores the recent advancements in elucidating the mechanisms underlying nutrient uptake and utilization efficiency in plants under such stress conditions. Our aim is to offer a comprehensive perspective that can guide the breeding of stress-tolerant and nutrition-efficient crop varieties, ultimately contributing to the advancement of sustainable agriculture.

MicroRNA gatekeepers: Orchestrating rhizospheric dynamics

The rhizosphere plays a crucial role in plant growth and resilience to biotic and abiotic stresses, highlighting the complex communication between plants and their dynamic rhizosphere environment. Plants produce a wide range of signaling molecules that facilitate communication with various rhizosphere factors, yet our understanding of these mechanisms remains elusive. In addition to protein-coding genes, increasing evidence underscores the critical role of microRNAs (miRNAs), a class of non-coding single-stranded RNA molecules, in regulating plant growth, development, and responses to rhizosphere stresses under diverse biotic and abiotic factors. In this review, we explore the crosstalk between miRNAs and their target mRNAs, which influence the development of key plant structures shaped by the belowground environment. Moving forward, more focused studies are needed to clarify the functions and expression patterns of miRNAs, to uncover the common regulatory mechanisms that mediate plant tolerance to rhizosphere dynamics. Beyond that, we propose that using artificial miRNAs and manipulating the expression of miRNAs and their targets through overexpression or knockout/knockdown approaches could effectively investigate their roles in plant responses to rhizosphere stresses, offering significant potential for advancing crop engineering.

Cell-Type Specific miRNA Regulatory Network Responses to ABA Stress Revealed by Time Series Transcriptional Atlases in Arabidopsis

In plants, microRNAs (miRNAs) participate in complex gene regulatory networks together with the transcription factors (TFs) in response to biotic and abiotic stresses. To date, analyses of miRNAs-induced transcriptome remodeling are at the whole plant or tissue levels. Here, Arabidopsis's ABA-induced single-cell RNA-seq (scRNA-seq) is performed at different stages of time points-early, middle, and late. Single-cell level primary miRNAs (pri-miRNAs) atlas supported the rapid, dynamic, and cell-type specific miRNA responses under ABA treatment. MiRNAs respond rapidly and prior to target gene expression dynamics, and these rapid response miRNAs are highly cell-type specific, especially in mesophyll and vascular cells. MiRNA-TF-mRNA regulation modules are identified by identifying miRNA-contained feed-forward loops (M-FFLs) in the regulatory network, and regulatory networks with M-FFLs have higher co-expression and clustering coefficient (CC) values than those without M-FFLs, suggesting the hub role of miRNAs in regulatory networks. The cell-type-specific M-FFLs are regulated by these hub miRNAs rather than TFs through sc-RNA-seq network analysis. MiR858a-FBH3-MYB module inhibited the expression of MYB63 and MYB20, which related to the formation of plant secondary wall and the production of lignin, through M-FFL specifically in vascular. These results can provide prominent insights into miRNAs' dynamic and cell-type-specific roles in plant development and stress responses.

Progesterone Metabolism in Digitalis and Other Plants-60 Years of Research and Recent Results

5β-Cardenolides are pharmaceutically important metabolites from the specialized metabolism of Digitalis lanata. They were used over decades to treat cardiac insufficiency and supraventricular tachycardia. Since the 1960s, plant scientists have known that progesterone is an essential precursor of cardenolide formation. Therefore, biosynthesis of plant progesterone was mainly analyzed in species of the cardenolide-containing genus Digitalis during the following decades. Today, Digitalis enzymes catalyzing the main steps of progesterone biosynthesis are known. Most of them are found in a broad range of organisms. This review will summarize the findings of 60 years of research on plant progesterone metabolism with particular focus on the recent results in Digitalis lanata and other plants.

Insights into the Epigenetic Basis of Plant Salt Tolerance

The increasing salinity of agricultural lands highlights the urgent need to improve salt tolerance in crops, a critical factor for ensuring food security. Epigenetic mechanisms are pivotal in plant adaptation to salt stress. This review elucidates the complex roles of DNA methylation, histone modifications, histone variants, and non-coding RNAs in the fine-tuning of gene expression in response to salt stress. It emphasizes how heritable changes, which do not alter the DNA sequence but significantly impact plant phenotype, contribute to this adaptation. DNA methylation is notably prevalent under high-salinity conditions and is associated with changes in gene expression that enhance plant resilience to salt. Modifications in histones, including both methylation and acetylation, are directly linked to the regulation of salt-tolerance genes. The presence of histone variants, such as H2A.Z, is altered under salt stress, promoting plant adaptation to high-salinity environments. Additionally, non-coding RNAs, such as miRNAs and lncRNAs, contribute to the intricate gene regulatory network under salt stress. This review also underscores the importance of understanding these epigenetic changes in developing plant stress memory and enhancing stress tolerance.

Multi-omics integrative analysis provided new insights into alkaline stress in alfalfa

Saline-alkali stress is one of the main abiotic stresses that limits plant growth. Salt stress has been widely studied, but alkaline salt degradation caused by NaHCO3 has rarely been investigated. In the present study, the alfalfa cultivar 'Zhongmu No. 1' was treated with 50 mM NaHCO3 (0, 4, 8, 12 and 24 h) to study the resulting enzyme activity and changes in mRNA, miRNA and metabolites in the roots. The results showed that the enzyme activity changed significantly after alkali stress treatment. The genomic analysis revealed 14,970 differentially expressed mRNAs (DEMs), 53 differentially expressed miRNAs (DEMis), and 463 differentially accumulated metabolites (DAMs). Combined analysis of DEMs and DEMis revealed that 21 DEMis negatively regulated 42 DEMs. In addition, when combined with Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of DEMs and DAMs, we found that phenylpropanoid biosynthesis, flavonoid biosynthesis, starch and sucrose metabolism and plant hormone signal transduction played important roles in the alkali stress response. The results of this study further elucidated the regulatory mechanism underlying the plant response to alkali stress and provided valuable information for the breeding of new saline-alkaline tolerance plant varieties.

miRNAs: Primary modulators of plant drought tolerance

Drought is a principal environmental factor that affects the growth and development of plants. Accordingly, plants have evolved adaptive mechanisms to cope with adverse environmental conditions. One of the mechanisms is gene regulation mediated by microRNAs (miRNAs). miRNAs are regarded as primary modulators of gene expression at the post-transcriptional level and have been shown to participate in drought stress response, including ABA response, auxin signaling, antioxidant defense, and osmotic regulation through downregulating the corresponding targets. miRNA-based genetic reconstructions have the potential to improve the tolerance of plants to drought. However, there are few precise classification and discussion of miRNAs in specific response behaviors to drought stress and their applications. This review summarized and discussed the specific response behaviors of miRNAs under drought stress and the role of miRNAs as regulators in the response of plants to drought and highlighted that the modification of miRNAs might effectively improve the tolerance of plants to drought.

Identification and Analysis of the MIR399 Gene Family in Grapevine Reveal Their Potential Functions in Abiotic Stress

MiR399 plays an important role in plant growth and development. The objective of the present study was to elucidate the evolutionary characteristics of the MIR399 gene family in grapevine and investigate its role in stress response. To comprehensively investigate the functions of miR399 in grapevine, nine members of the Vvi-MIR399 family were identified based on the genome, using a miRBase database search, located on four chromosomes (Chr 2, Chr 10, Chr 15, and Chr 16). The lengths of the Vvi-miR399 precursor sequences ranged from 82 to 122 nt and they formed stable stem-loop structures, indicating that they could produce microRNAs (miRNAs). Furthermore, our results suggested that the 2 to 20 nt region of miR399 mature sequences were relatively conserved among family members. Phylogenetic analysis revealed that the Vvi-MIR399 members of dicots (Arabidopsis, tomato, and sweet orange) and monocots (rice and grapevine) could be divided into three clades, and most of the Vvi-MIR399s were closely related to sweet orange in dicots. Promoter analysis of Vvi-MIR399s showed that the majority of the predicted cis-elements were related to stress response. A total of 66.7% (6/9) of the Vvi-MIR399 promoters harbored drought, GA, and SA response elements, and 44.4% (4/9) of the Vvi-MIRR399 promoters also presented elements involved in ABA and MeJA response. The expression trend of Vvi-MIR399s was consistent in different tissues, with the lowest expression level in mature and young fruits and the highest expression level in stems and young leaves. However, nine Vvi-MIR399s and four target genes showed different expression patterns when exposed to low light, high light, heat, cold, drought, and salt stress. Interestingly, a putative target of Vvi-MIR399 targeted multiple genes; for example, seven Vvi-MIR399s simultaneously targeted VIT_213s0067g03280.1. Furthermore, overexpression of Vvi_MIR399e and Vvi_MIR399f in Arabidopsis enhanced tolerance to drought compared with wild-type (WT). In contrast, the survival rate of Vvi_MIR399d-overexpressed plants were zero after drought stress. In conclusion, Vvi-MIR399e and Vvi-MIR399f, which are related to drought tolerance in grapevine, provide candidate genes for future drought resistance breeding.

Integration of mRNA and miRNA analysis reveals the molecular mechanisms of sugar beet (Beta vulgaris L.) response to salt stress

The continuous increase of saline-alkali areas worldwide has led to the emergence of saline-alkali conditions, which are the primary abiotic stress or hindering the growth of plants. Beet is among the main sources of sugar, and its yield and sugar content are notably affected by saline-alkali stress. Despite sugar beet being known as a salt-tolerant crop, there are few studies on the mechanisms underlying its salt tolerance, and previous studies have mainly delineated the crop's response to stress induced by NaCl. Recently, advancements in miRNA-mRNA network analysis have led to an increased understanding of how plants, including sugar beet, respond to stress. In this study, seedlings of beet variety "N98122" were grown in the laboratory using hydroponics culture and were exposed to salt stress at 40 days of growth. According to the phenotypic adaptation of the seedlings' leaves from a state of turgidity to wilting and then back to turgidity before and after exposure, 18 different time points were selected to collect samples for analysis. Subsequently, based on the data of real-time quantitative PCR (qRT-PCR) of salt-responsive genes, the samples collected at the 0, 2.5, 7.5, and 16 h time points were subjected to further analysis with experimental materials. Next, mRNA-seq data led to the identification of 8455 differentially expressed mRNAs (DEMs) under exposure to salt stress. In addition, miRNA-seq based investigation retrieved 3558 miRNAs under exposure to salt stress, encompassing 887 known miRNAs belonging to 783 families and 2,671 novel miRNAs. With the integrated analysis of miRNA-mRNA network, 57 miRNA-target gene pairs were obtained, consisting of 55 DEMIs and 57 DEMs. Afterwards, we determined the pivotal involvement of aldh2b7, thic, and δ-oat genes in the response of sugar beet to the effect of salt stress. Subsequently, we identified the miRNAs novel-m035-5p and novel-m0365-5p regulating the aldh gene and miRNA novel-m0979-3p regulating the thic gene. The findings of miRNA and mRNA expression were validated by qRT-PCR.

MicroRNA2871b of Dongxiang Wild Rice (Oryza rufipogon Griff.) Negatively Regulates Cold and Salt Stress Tolerance in Transgenic Rice Plants

Cold and salt stresses are major environmental factors that constrain rice production. Understanding their mechanisms is important to enhance cold and salt stress tolerance in rice. MicroRNAs (miRNAs) are a class of non-coding RNAs with only 21-24 nucleotides that are gene regulators in plants and animals. Previously, miR2871b expression was suppressed by cold stress in Dongxiang wild rice (DXWR, Oryza rufipogon Griff.). However, its biological functions in abiotic stress responses remain elusive. In the present study, miR2871b of DWXR was overexpressed to investigate its function under stress conditions. When miR2871b of DWXR was introduced into rice plants, the transgenic lines were more sensitive to cold and salt stresses, and their tolerance to cold and salt stress decreased. The increased expression of miR2871b in rice plants also increased the levels of reactive oxygen species (ROS) and malondialdehyde (MDA); however, it markedly decreased the activities of peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT) and the contents of proline (Pro) and soluble sugar (SS). These data suggested that miR2871b of DXWR has negative regulatory effects on cold and salt stress tolerance. Meanwhile, 412 differentially expressed genes (DEGs) were found in rice transgenic plants using transcriptome sequencing, among which 266 genes were up-regulated and 146 genes were down-regulated. Furthermore, the upstream cis-acting elements and downstream targets of miR2871b were predicted and analyzed, and several critical acting elements (ABRE and TC-rich repeats) and potential target genes (LOC_Os03g41200, LOC_Os07g47620, and LOC_Os04g30260) were obtained. Collectively, these results generated herein further elucidate the vital roles of miR2871b in regulating cold and salt responses of DXWR.

Comparative Analysis of miRNA Expression Profiles under Salt Stress in Wheat

Salt stress is one of the important environmental factors that inhibit the normal growth and development of plants. Plants have evolved various mechanisms, including signal transduction regulation, physiological regulation, and gene transcription regulation, to adapt to environmental stress. MicroRNAs (miRNAs) play a role in regulating mRNA expression. Nevertheless, miRNAs related to salt stress are rarely reported in bread wheat (Triticum aestivum L.). In this study, using high-throughput sequencing, we analyzed the miRNA expression profile of wheat under salt stress. We identified 360 conserved and 859 novel miRNAs, of which 49 showed considerable changes in transcription levels after salt treatment. Among them, 25 were dramatically upregulated and 24 were downregulated. Using real-time quantitative PCR, we detected significant changes in the relative expression of miRNAs, and the results showed the same trend as the sequencing data. In the salt-treated group, miR109 had a higher expression level, while miR60 and miR202 had lower expression levels. Furthermore, 21 miRNAs with significant changes were selected from the differentially expressed miRNAs, and 1023 candidate target genes were obtained through the prediction of the website psRNATarget. Gene ontology (GO) analysis of the candidate target genes showed that the expressed miRNA may be involved in the response to biological processes, molecular functions, and cellular components. In addition, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis confirmed their important functions in RNA degradation, metabolic pathways, synthesis pathways, peroxisome, environmental adaptation, global and overview maps, and stress adaptation and the MAPK signal pathway. These findings provide a basis for further exploring the function of miRNA in wheat salt tolerance.

Flowering under enhanced ionising radiation conditions and its regulation through epigenetic mechanisms

As sessile organisms, plants have to deal with unfavourable conditions by acclimating or adapting in order to survive. Regulation of flower induction is one such mechanism to ensure reproduction and species survival. Flowering is a tightly regulated process under the control of a network of genes, which can be affected by environmental cues and stress. The effects of ionising radiation (IR) on flowering, however, have been poorly studied. Understanding the effects of ionising radiation on flowering, including the timing, gene pathways, and epigenetics involved, is crucial in the continuing effort of environmental radiation protection. The review shows that plants alter their flowering pattern in response to IR, with various flowering related genes (eg. FLOWERING LOCUS C (FLC), FLOWERING LOCUS T (FT), CONSTANS (CO), GIGANTEA (GI), APETALA1 (AP1), LEAFY (LFY)) and epigenetic processes (DNA methylation, and miRNA expression eg. miRNA169, miR156, miR172) being affected. Thereby, showing a hypothetical IR-induced flowering mechanism. Further research on the interaction between IR and flowering in plants is, however, needed to elucidate the mechanisms behind the stress-induced flowering response.

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.

Non-coding RNAs fine-tune the balance between plant growth and abiotic stress tolerance

To survive in adverse environmental conditions, plants have evolved sophisticated genetic and epigenetic regulatory mechanisms to balance their growth and abiotic stress tolerance. An increasing number of non-coding RNAs (ncRNAs), including small RNAs (sRNAs) and long non-coding RNAs (lncRNAs) have been identified as essential regulators which enable plants to coordinate multiple aspects of growth and responses to environmental stresses through modulating the expression of target genes at both the transcriptional and posttranscriptional levels. In this review, we summarize recent advances in understanding ncRNAs-mediated prioritization towards plant growth or tolerance to abiotic stresses, especially to cold, heat, drought and salt stresses. We highlight the diverse roles of evolutionally conserved microRNAs (miRNAs) and small interfering RNAs (siRNAs), and the underlying phytohormone-based signaling crosstalk in regulating the balance between plant growth and abiotic stress tolerance. We also review current discoveries regarding the potential roles of ncRNAs in stress memory in plants, which offer their descendants the potential for better fitness. Future ncRNAs-based breeding strategies are proposed to optimize the balance between growth and stress tolerance to maximize crop yield under the changing climate.

Effect of Zinc and Nickel Treatments on Improvement of the Osmotic Defense System of Wheat Plant Under Salinity Stress

The present experiments were performed to determine the effects of Zn (20 µM and 200 µM) and Ni (1 µM and 100 µM) on the growth and metabolic activities in the roots, shoots, and spikes of wheat ( Triticum aestivum L.) cv. Gimiza 11 grown under different salinity conditions. In addition to identifying the osmotic tolerance of wheat, the roles of Zn and Ni in alleviating osmotic stress were examined. The root was the organ most sensitive to osmotic stress, whereas the shoot was the most resistant, and the spike was the intermediate. These three organs negatively responded to increasing osmotic stress levels, as fresh and dry matter decreased, and related biochemical parameters were adversely affected. However, fresh and dry matter were generally elevated when plants were supplemented with Zn or Ni under increasing osmotic stress. The sensitivity of roots was associated with depletion in the concentrations of sugars and free proline, whereas soluble protein and amino acid levels were increased. The stress tolerance of shoots and spikes was accompanied by an increase in soluble sugars, soluble proteins, and proline, while amino acid levels increased in spikes only. The Na + and K + content in wheat plants increased with increasing NaCl-induced osmotic stress levels. In turn, the accumulation and partitioning of Na + and K + did not vary among the three organs, both at different salt concentrations and between Zn or Ni treatments. Moreover, the present results show that the concentrations of anthocyanins, flavonoids, and l -ascorbic acid increased under exposure to osmotic stress and did not change significantly under Zn or Ni treatments.

Integrated mRNA and microRNA expression analysis of root response to phosphate deficiency in Medicago sativa

The deficiency of available phosphate significantly limits plant growth and development. This study sought to investigate how alfalfa (Medicago sativa), a high-yielding and high-quality forage widely cultivated worldwide, responds to phosphate deficiency stress by integrating transcriptional and post-transcriptional data. In this study, 6,041 differentially expressed genes (DEGs) were identified in alfalfa roots under phosphate deficiency conditions. Furthermore, psRNATarget, RNAhybrid, and TargetFinder were used to predict the target genes of 137 differentially expressed miRNAs (DEMs) in the root. In total, 3,912 DEGs were predicted as target genes. Pearson correlation analysis revealed 423 pairs of miRNA-mRNA regulatory relationships. MiRNA negatively regulates mRNA involved in regulatory pathways of phosphate deficiency responses in alfalfa. miR156e targeted squamosa promoter-binding-like protein 13A (SPL13), miR160c targeted auxin response factor 18 (ARF18), and miR2587a controlled glycolysis and citrate cycle via Phosphoenolpyruvate carboxykinase (ATP) (PCKA). Novel-miR27 regulated SPX domain-containing protein that controls phosphate transport in alfalfa root, novel-miR3-targeted sulfoquinovosyl transferase SQD2 controlled sulfolipid synthesis and glutathione S-transferase (GST; mediated by miR169j/k and novel-miR159) regulated glutathione metabolism. miR399l regulated auxin-responsive protein SAUR72 involved in IAA signal transduction, while abscisic acid receptor PYL4 (regulated by novel-miR205 and novel-miR83) participated in ABA signal transduction. Combined miRNA-mRNA enrichment analysis showed that most miRNAs regulate the phosphate starvation response of alfalfa by modulating target genes involved in carbohydrate metabolism, sulfolipid metabolism, glutathione metabolism, and hormone signal transduction. Therefore, this study provides new insights into the post-transcriptional regulation mechanism of phosphate deficiency responses and new perspectives on phosphate assimilation pathways in alfalfa and other legumes.

MicroRNAs Mediated Plant Responses to Salt Stress

One of the most damaging issues to cultivatable land is soil salinity. While salt stress influences plant growth and yields at low to moderate levels, severe salt stress is harmful to plant growth. Mineral shortages and toxicities frequently exacerbate the problem of salinity. The growth of many plants is quantitatively reduced by various levels of salt stress depending on the stage of development and duration of stress. Plants have developed various mechanisms to withstand salt stress. One of the key strategies is the utilization of microRNAs (miRNAs) that can influence gene regulation at the post-transcriptional stage under different environmental conditions, including salinity. Here, we have reviewed the miRNA-mediated adaptations of various plant species to salt stress and other abiotic variables. Moreover, salt responsive (SR)-miRNAs, their targets, and corresponding pathways have also been discussed. The review article concludes by suggesting that the utilization of miRNAs may be a vital strategy to generate salt tolerant crops ensuring food security in the future.

One AP2/ERF Transcription Factor Positively Regulates Pi Uptake and Drought Tolerance in Poplar

Drought decreases the inorganic phosphate (Pi) supply of soil, resulting in Pi starvation of plants, but the molecular mechanism of how plants, especially the perennial trees, are tolerant to drought stress and Pi starvation, is still elusive. In this study, we identified an AP2/ERF transcription factor gene, PalERF2, from Populus alba var. pyramidalis, and it was induced by both mannitol treatment and Pi starvation. Overexpressing and knocking-down of PalERF2 both enhanced and attenuated tolerance to drought stress and Pi deficiency compared to WT, respectively. Moreover, the overexpression of PalERF2 up-regulated the expression levels of Pi starvation-induced (PSI) genes and increased Pi uptake under drought conditions; however, its RNAi poplar showed the opposite phenotypes. Subsequent analysis indicated that PalERF2 directly modulated expressions of drought-responsive genes PalRD20 and PalSAG113, as well as PSI genes PalPHL2 and PalPHT1;4, through binding to the DRE motifs on their promoters. These results clearly indicate that poplars can recruit PalERF2 to increase the tolerance to drought and also elevate Pi uptake under drought stress.

Deciphering the role of miRNA in reprogramming plant responses to drought stress

Drought is the most prevalent environmental stress that affects plants' growth, development, and crop productivity. However, plants have evolved adaptive mechanisms to respond to the harmful effects of drought. They reprogram their: transcriptome, proteome, and metabolome that alter their cellular and physiological processes and establish cellular homeostasis. One of the crucial regulatory processes that govern this reprogramming is post-transcriptional regulation by microRNAs (miRNAs). miRNAs are small non-coding RNAs, involved in the downregulation of the target mRNA via translation inhibition/mRNA degradation/miRNA-mediated mRNA decay/ribosome drop off/DNA methylation. Many drought-inducible miRNAs have been identified and characterized in plants. Their main targets are regulatory genes that influence growth, development, osmotic stress tolerance, antioxidant defense, phytohormone-mediated signaling, and delayed senescence during drought stress. Overexpression of drought-responsive miRNAs (Osa-miR535, miR160, miR408, Osa-miR393, Osa-miR319, and Gma-miR394) in certain plants has led to tolerance against drought stress indicating their vital role in stress mitigation. Similarly, knock down (miR166/miR398c) or deletion (miR169 and miR827) of miRNAs has also resulted in tolerance to drought stress. Likewise, engineered Arabidopsis plants with miR165, miR166 using short tandem target mimic strategy, exhibited drought tolerance. Since miRNAs regulate the expression of an array of drought-responsive genes, they can act as prospective targets for genetic manipulations to enhance drought tolerance in crops and achieve sustainable agriculture. Further investigations toward functional characterization of diverse miRNAs, and understanding stress-responses regulated by these miRNAs and their utilization in biotechnological applications is highly recommended.

Integrated Analysis of Coding and Non-coding RNAs Reveals the Molecular Mechanism Underlying Salt Stress Response in Medicago truncatula

Salt stress is among the most severe abiotic stresses in plants worldwide. Medicago truncatula is a model plant for legumes and analysis of its response to salt stress is helpful for providing valuable insights into breeding. However, few studies have focused on illustrating the whole-transcriptome molecular mechanism underlying salt stress response in Medicago truncatula. Herein, we sampled the leaves of Medicago truncatula treated with water or NaCl and analyzed the characteristics of its coding and non-coding RNAs. We identified a total of 4,693 differentially expressed mRNAs (DEmRNAs), 505 DElncRNAs, 21 DEcircRNAs, and 55 DEmiRNAs. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses revealed that their functions were mostly associated with metabolic processes. We classified the lncRNAs and circRNAs into different types and analyzed their genomic distributions. Furthermore, we predicted the interactions between different RNAs based on the competing endogenous RNA (ceRNA) theory and identified multiple correlation networks, including 27 DEmiRNAs, 43 DEmRNAs, 19 lncRNAs, and 5 DEcircRNAs. In addition, we comprehensively analyzed the candidate DEmRNAs and ceRNAs and found that they were involved in Ca⁺ signaling, starch and sucrose biosynthesis, phenylpropanoid and lignin metabolism, auxin and jasmonate biosynthesis, and transduction pathways. Our integrated analyses in salt stress response in Medicago truncatula revealed multiple differentially expressed coding and non-coding RNAs, including mRNAs, lncRNAs, circRNAs, and miRNAs, and identified multiple DEmRNA and ceRNA interaction pairs that function in many pathways, providing insights into salt stress response in leguminous plants.

Genome-Wide Investigation of the MiR166 Family Provides New Insights into Its Involvement in the Drought Stress Responses of Tea Plants (Camellia sinensis (L.) O. Kuntze)

MicroRNA166 (miR166) is a highly conserved plant miRNA that plays a crucial role in plant growth and the resistance to various abiotic stresses. However, the miR166s in tea (Camellia sinensis (L.) O. Kuntze) have not been comprehensively identified and analyzed. This study identified 30 mature miR166s and twelve pre-miR166s in tea plants. An evolutionary analysis revealed that csn-miR166s originating from the 3′ arm of their precursors were more conserved than the csn-miR166s derived from the 5′ arm of their precursors. The twelve pre-miR166s in tea were divided into two groups, with csn-MIR166 Scaffold364-2 separated from the other precursors. The Mfold-based predictions indicated that the twelve csn-MIR166s formed typical and stable structures comprising a stem-loop hairpin, with minimum free energy ranging from −110.90 to −71.80 kcal/mol. An analysis of the CsMIR166 promoters detected diverse cis-acting elements, including those related to light responses, biosynthesis and metabolism, abiotic stress defenses, and hormone responses. There was no one-to-one relationship between the csn-miR166s and their targets, but most csn-miR166s targeted HD-Zip III genes. Physiological characterization of tea plants under drought stress showed that leaf water content proportionally decreased with the aggravation of drought stress. In contrast, tea leaves’ malondialdehyde (MDA) content proportionally increased. Moreover, the cleavage site of the ATHB-15-like transcript was identified according to a modified 5′ RNA ligase-mediated rapid amplification of cDNA ends. The RT-qPCR data indicated that the transcription of nine csn-miR166s was negatively correlated with their target gene.

Advances in the regulation of plant salt-stress tolerance by miRNA

Salt stress significantly affects the growth, development, yield, and quality of plants. MicroRNAs (miRNAs) are involved in various stress responses via target gene regulation. Their role in regulating salt stress has also received significant attention from researchers. Various transcription factor families are the common target genes of plant miRNAs. Thus, regulating the expression of miRNAs is a novel method for developing salt-tolerant crops. This review summarizes plant miRNAs that mediate salt tolerance, specifically miRNAs that have been utilized in genetic engineering to modify plant salinity tolerance. The molecular mechanism by which miRNAs mediate salt stress tolerance merits elucidation, and this knowledge will promote the development of miRNA-mediated salt-tolerant crops and provide new strategies against increasingly severe soil salinization.

MYB2 Is Important for Tapetal PCD and Pollen Development by Directly Activating Protease Expression in Arabidopsis

Tapetal programmed cell death (PCD) is a complex biological process that plays an important role in pollen formation and reproduction. Here, we identified the MYB2 transcription factor expressed in the tapetum from stage 5 to stage 11 that was essential for tapetal PCD and pollen development in Arabidopsis thaliana. Downregulation of MYB2 retarded tapetal degeneration, produced defective pollen, and decreased pollen vitality. EMSA and transcriptional activation analysis revealed that MYB2 acted as an upstream activator and directly regulated expression of the proteases CEP1 and βVPE. The expression of these proteases was lower in the buds of the myb2 mutant. Overexpression of either/both CEP1 or/and βVPE proteases partially recover pollen vitality in the myb2 background. Taken together, our results revealed that MYB2 regulates tapetal PCD and pollen development by directly activating expression of the proteases CEP1 and βVPE. Thus, a transcription factor/proteases regulatory and activated cascade was established for tapetal PCD during another development in Arabidopsis thaliana. Highlight: MYB2 is involved in tapetal PCD and pollen development by directly regulating expression of the protease CEP1 and βVPE and establishes a transcription factor/proteases regulatory and activated cascade.

Mechanisms of Abscisic Acid-Mediated Drought Stress Responses in Plants

Drought is one of the major constraints to rain-fed agricultural production, especially under climate change conditions. Plants evolved an array of adaptive strategies that perceive stress stimuli and respond to these stress signals through specific mechanisms. Abscisic acid (ABA) is a premier signal for plants to respond to drought and plays a critical role in plant growth and development. ABA triggers a variety of physiological processes such as stomatal closure, root system modulation, organizing soil microbial communities, activation of transcriptional and post-transcriptional gene expression, and metabolic alterations. Thus, understanding the mechanisms of ABA-mediated drought responses in plants is critical for ensuring crop yield and global food security. In this review, we highlighted how plants adjust ABA perception, transcriptional levels of ABA- and drought-related genes, and regulation of metabolic pathways to alter drought stress responses at both cellular and the whole plant level. Understanding the synergetic role of drought and ABA will strengthen our knowledge to develop stress-resilient crops through integrated advanced biotechnology approaches. This review will elaborate on ABA-mediated drought responses at genetic, biochemical, and molecular levels in plants, which is critical for advancement in stress biology research.

tae-miR399-UBC24 Module Enhances Freezing Tolerance in Winter Wheat via a CBF Signaling Pathway

Although the regulation of Pi homeostasis by miR399 has been studied in various plant species, its underlying molecular mechanism in response to freezing stress is still poorly understood. In this work, we found that the expression of tae-miR399 and its target gene TaUBC24 in the tillering nodes of the strong cold-resistant winter wheat cultivar Dongnongdongmai1 (Dn1) was not only significantly altered after severe winters but also responsive to short-term freezing stress. TaUBC24 physically interacted with TaICE1. Enhanced freezing tolerance was observed for tae-miR399-overexpressing Arabidopsis lines. Under freezing stress, overexpression of tae-miR399 ultimately decreased the expression of AtUBC24, inhibiting the degradation of AtICE1, which increased the expression of genes involved in the CBF signaling pathway and starch metabolism and promoted the activities of antioxidant enzymes. These results will improve our understanding of the molecular mechanism through which the miR399-UBC24 module plays a cardinal role in regulating plant freezing stress tolerance through mediation of downstream pathways.

A comprehensive overview of miRNA targeting drought stress resistance in plants

MicroRNAs (miRNAs) are essential nonprotein-coding genes. In a range of organisms, miRNAs has been reported to play an essential role in regulating gene expressions at post-transcriptional level. They participate in most of the stress responsive processes in plants. Drought is an ultimate abiotic stress that affects the crop production. Therefore understanding drought stress responses are essential to improve the production of agricultural crops. Throughout evolution, plants have developed their own defense systems to cope with the adversities of environmental stresses. Among defensive mechanisms include the regulations of gene expression by miRNAs. Drought stress regulates the expression of some of the functionally conserved miRNAs in different plants. The given properties of miRNAs provide an insight to genetic alterations and enhancing drought resistance in cereal crops. The current review gives a summary to regulatory mechanisms in plants as well as miRNAs response to drought stresses in cereal crops. Some possible approaches and guidelines for the exploitation of drought stress miRNA responses to improve cereal crops are also described.

miRNAs play critical roles in response to abiotic stress by modulating cross-talk of phytohormone signaling

One of the most interesting signaling molecules that regulates a wide array of adaptive stress responses in plants are the micro RNAs (miRNAs) that are a unique class of non-coding RNAs constituting novel mechanisms of post-transcriptional gene regulation. Recent studies revealed the role of miRNAs in several biotic and abiotic stresses by regulating various phytohormone signaling pathways as well as by targeting a number of transcription factors (TFs) and defense related genes. Phytohormones are signal molecules modulating the plant growth and developmental processes by regulating gene expression. Studies concerning miRNAs in abiotic stress response also show their vital roles in abiotic stress signaling. Current research indicates that miRNAs may act as possible candidates to create abiotic stress tolerant crop plants by genetic engineering. Yet, the detailed mechanism governing the dynamic expression networks of miRNAs in response to stress tolerance remains unclear. In this review, we provide recent updates on miRNA-mediated regulation of phytohormones combating various stress and its role in adaptive stress response in crop plants.

Integrated analysis of miRNA-mRNA regulatory networks of potato (Solanum tuberosum L.) in response to cadmium stress

Cadmium (Cd) stress is a ubiquitous abiotic stress affecting plant growth worldwide and negatively impacting crop yield and food safety. Potato is the most important non-grain crop globally, but there is limited research available on the response of this crop to Cd stress. This study explored the coping mechanism for Cd stress in potato through analyses of miRNA and mRNA. Tissue culture seedlings (20-day-old) of potato variety 'Atlantic' were cultured for up to 48 h in liquid medium containing 5 mmol/L CdCl2, and phenotypic, physiological, and transcriptomic changes were observed at specific times. With the extension of Cd stress time, the potato leaves gradually wilted and curled, and root salicylic acid (SA), glutathione (GSH), and lignin contents and peroxidase (POD) activity increased, while indole-3-acetic acid (IAA) and zeatin (ZT) contents decreased. Using miRNA-seq, 161 existing miRNAs, 383 known miRNAs, and 7361 novel miRNAs were identified, and, 18 miRNAs were differentially expressed in response to Cd stress. Based on mRNA-seq, 7340 differentially expressed mRNAs (DEGs) were found. Through mRNA-miRNA integrated analysis, miRNA-target gene pairs consisting of 23 DEGs and 33 miRNAs were identified. Furthermore, "glutathione metabolism" "plant hormone signal transduction" and "phenylpropanoid biosynthesis" were established as crucial pathways in the Cd stress response of potato. Novel miRNAs novel-m3483-5p and novel-m2893-5p participate in these pathways through targeted regulation of cinnamic alcohol dehydrogenase (CAD; PG0005359) and alanine aminotransferase (POP; PG0024281), respectively. This study provides information that will help elucidate the complex mechanism of the Cd stress response in potato. Moreover, candidate miRNAs and mRNAs could yield new strategies for the development of Cd-tolerant potato breeding.

Updates on the Role of ABSCISIC ACID INSENSITIVE 5 (ABI5) and ABSCISIC ACID-RESPONSIVE ELEMENT BINDING FACTORs (ABFs) in ABA Signaling in Different Developmental Stages in Plants

The core abscisic acid (ABA) signaling pathway consists of receptors, phosphatases, kinases and transcription factors, among them ABA INSENSITIVE 5 (ABI5) and ABRE BINDING FACTORs/ABRE-BINDING PROTEINs (ABFs/AREBs), which belong to the BASIC LEUCINE ZIPPER (bZIP) family and control expression of stress-responsive genes. ABI5 is mostly active in seeds and prevents germination and post-germinative growth under unfavorable conditions. The activity of ABI5 is controlled at transcriptional and protein levels, depending on numerous regulators, including components of other phytohormonal pathways. ABFs/AREBs act redundantly in regulating genes that control physiological processes in response to stress during vegetative growth. In this review, we focus on recent reports regarding ABI5 and ABFs/AREBs functions during abiotic stress responses, which seem to be partially overlapping and not restricted to one developmental stage in Arabidopsis and other species. Moreover, we point out that ABI5 and ABFs/AREBs play a crucial role in the core ABA pathway’s feedback regulation. In this review, we also discuss increased stress tolerance of transgenic plants overexpressing genes encoding ABA-dependent bZIPs. Taken together, we show that ABI5 and ABFs/AREBs are crucial ABA-dependent transcription factors regulating processes essential for plant adaptation to stress at different developmental stages.

Identification of microRNAs and their target genes related to needle discoloration of evergreen tree Chinese cedar (Cryptomeria fortunei) in cold winters

Comparative analysis of miRNAs and their gene targets between the evergreen and yellowish-brown Cryptomeria fortunei phenotypes in cold winters suggests a possible role of miRNA-regulated pathways in needle color. Cryptomeria fortunei (Chinese cedar) is a conifer tree of considerable economic, ornamental and ecological importance. Despite the evergreen nature of C. fortunei, most needles turn yellowish- or reddish-brown in winter. The roles of microRNAs (miRNAs) in regulating pigment biosynthesis in color-leafed plants have been widely investigated. However, whether or not an miRNA-mediated staged discoloration mechanism exists in evergreen C. fortunei is currently unknown. In this study, we deciphered the microRNAs landscape in overwintering C. fortunei needles using high-throughput sequencing. A total of 517 known and 212 novel miRNA mature/star sequences, including 233 differentially expressed miRNAs, were identified. Based on integrated transcriptome and miRNA analysis, 2702 target unigenes of the miRNAs were predicted and these targets were significantly enriched in pigment-related biosynthesis pathways. A miRNA-target pigment biosynthesis regulatory network was then constructed, and its module miRNA (ath-miR858b, aly-miR858-3p, cme-miR828 and novel33_mature)-MYBs (v-myb avian myeloblastosis viral oncogene homolog) appeared to be a key factor regulating needle discoloration in C. fortunei. These miRNA-MYBs were further confirmed by degradome sequencing. Overall, these findings provide new insight into the posttranscriptional regulatory mechanism of leaf/needle discoloration in gymnosperms and may contribute to the miRNA-mediated genetic improvement of evergreen C. fortunei needles.

Identification of Novel miRNAs and Their Target Genes in the Response to Abscisic Acid in Arabidopsis

miRNAs are involved in various biological processes, including adaptive responses to abiotic stress. To understand the role of miRNAs in the response to ABA, ABA-responsive miRNAs were identified by small RNA sequencing in wild-type Arabidopsis, as well as in abi1td, mkkk17, and mkkk18 mutants. We identified 10 novel miRNAs in WT after ABA treatment, while in abi1td, mkkk17, and mkkk18 mutants, three, seven, and nine known miRNAs, respectively, were differentially expressed after ABA treatment. One novel miRNA (miRn-8) was differentially expressed in the mkkk17 mutant. Potential target genes of the miRNA panel were identified using psRNATarget. Sequencing results were validated by quantitative RT-PCR of several known and novel miRNAs in all genotypes. Of the predicted targets of novel miRNAs, seven target genes of six novel miRNAs were further validated by 5' RLM-RACE. Gene ontology analyses showed the potential target genes of ABA-responsive known and novel miRNAs to be involved in diverse cellular processes in plants, including development and stomatal movement. These outcomes suggest that a number of the identified miRNAs have crucial roles in plant responses to environmental stress, as well as in plant development, and might have common regulatory roles in the core ABA signaling pathway.

Multiple Functions of MYB Transcription Factors in Abiotic Stress Responses

Plants face a more volatile environment than other organisms because of their immobility, and they have developed highly efficient mechanisms to adapt to stress conditions. Transcription factors, as an important part of the adaptation process, are activated by different signals and are responsible for the expression of stress-responsive genes. MYB transcription factors, as one of the most widespread transcription factor families in plants, participate in plant development and responses to stresses by combining with MYB cis-elements in promoters of target genes. MYB transcription factors have been extensively studied and have proven to be critical in the biosynthesis of secondary metabolites in plants, including anthocyanins, flavonols, and lignin. Multiple studies have now shown that MYB proteins play diverse roles in the responses to abiotic stresses, such as drought, salt, and cold stresses. However, the regulatory mechanism of MYB proteins in abiotic stresses is still not well understood. In this review, we will focus mainly on the function of Arabidopsis MYB transcription factors in abiotic stresses, especially how MYB proteins participate in these stress responses. We also pay attention to how the MYB proteins are regulated in these processes at both the transcript and protein levels.

Variation of PHT families adapts salt cress to phosphate limitation under salinity

Salt cress (Eutrema salsugineum) presents relatively high phosphate (Pi) use efficiency cy in its natural habitat. Phosphate Transporters (PHTs) play critical roles in Pi acquisition and homeostasis. Here, a comparative study of PHT families between salt cress and Arabidopsis was performed. A total of 27 putative PHT genes were identified in E. salsugineum genome. Notably, seven tandem genes encoding PHT1;3 were found, and function analysis in Arabidopsis indicated at least six EsPHT1;3s participated in Pi uptake. Meanwhile, different expression profiles of PHT genes between the two species under Pi limitation and salt stress were documented. Most PHT1 genes were down-regulated in Arabidopsis while up-regulated in salt cress under salinity, among which EsPHT1;9 was further characterized. EsPHT1;9 was involved in root-to-shoot Pi translocation. Particularly, the promoter of EsPHT1;9 outperformed that of AtPHT1;9 in promoting Pi translocation, K⁺ /Na⁺ ratio, thereby salt tolerance. Through cis-element analysis, we identified a bZIP transcription factor EsABF5 negatively regulating EsPHT1;9 and plant tolerance to low-Pi and salt stress. Altogether, more copies and divergent transcriptional regulation of PHT genes contribute to salt cress adaptation to the co-occurrence of salinity and Pi limitation, which add our knowledge on the evolutionary and molecular component of multistress- tolerance of this species.

Chloroplast Localized FIBRILLIN11 Is Involved in the Osmotic Stress Response during Arabidopsis Seed Germination

Simple Summary

The FIBRILLIN11 (FBN11) of Arabidopsis has a lipid-binding FBN domain and a kinase domain. FBN11 is present in chloroplasts and is involved in salt and osmotic stress responses during seed germination. In mannitol, the seed germination rate of the fbn11 mutants significantly reduced compared to that of the wild type. The ABA-dependent and -independent stress response regulating genes were differentially expressed in fbn11 mutants and wild-type when grown in mannitol supplemented medium. These results suggest that chloroplast localized FBN11 is involved in mediating osmotic stress tolerance through the signaling pathway that regulates the stress response in the nucleus.

Abstract

Plants live in ever-changing environments, facing adverse environmental conditions including pathogen infection, herbivore attack, drought, high temperature, low temperature, nutrient deficiency, toxic metal soil contamination, high salt, and osmotic imbalance that inhibit overall plant growth and development. Plants have evolved mechanisms to cope with these stresses. In this study, we found that the FIBRILLIN11 (FBN11) gene in Arabidopsis, which has a lipid-binding FBN domain and a kinase domain, is involved in the plant’s response to abiotic stressors, including salt and osmotic stresses. FBN11 protein localizes to the chloroplast. FBN11 gene expression significantly changed when plants were exposed to the abiotic stress response mediators such as abscisic acid (ABA), sodium chloride (NaCl), and mannitol. The seed germination rates of fbn11 homozygous mutants in different concentrations of mannitol and NaCl were significantly reduced compared to wild type. ABA-dependent and -independent stress response regulatory genes were differentially expressed in the fbn11 mutant compared with wild type when grown in mannitol medium. These results suggest a clear role for chloroplast-localized FBN11 in mediating osmotic stress tolerance via the stress response regulatory signaling pathway in the nucleus.

Integration of mRNA and miRNA analysis reveals the molecular mechanism of potato (Solanum tuberosum L.) response to alkali stress

The continuing increase in the global saline-alkali land area has made saline-alkali stress the principal abiotic stress limiting plant growth. Potato is the most important non-grain crop, and its production is also severely limited by saline-alkali stress. However, few studies have addressed the mechanism of saline-alkali tolerance of potato with a focus on its response to neutral salt NaCl stress, or its response to alkali stress. Recently, miRNA-mRNA analyses have helped advance our understanding of how plants respond to stress. Here, we have characterized the morphological, physiological, and transcriptome changes of tissue culture seedlings of potato variety "Qingshu No. 9" treated with NaHCO₃ (for 0, 2, 6, and 24 h). We found that the leaves of tissue culture seedlings wilted and withered under alkali stress, and the contents of ABA, BRs, trehalose, and lignin in roots increased significantly. The contents of GAs decreased significantly. Subsequently, miRNA-seq analysis results identified 168 differentially expressed miRNAs (DEMIs) under alkali stress, including 21 exist miRNAs and 37 known miRNAs from 47 families and 110 novel miRNAs. The mRNA-seq results identified 5731 differentially expressed mRNAs (DEMs) under alkali stress. By miRNA-mRNA integrated analysis, were obtained 33 miRNA-target gene pairs composed of 20 DEMIs and 33 DEMs. Next, we identified the "phenylpropanoid biosynthesis", "plant hormone signal transduction", and "starch and sucrose metabolism" pathways as necessary for potato to respond to alkali stress. miR4243-x and novel-m064-5p were involved in the response of potato to alkali stress by their negative regulatory effects on shikimate O-hydroxycinnamoyltransferase (HCT) and sucrose-phosphate synthase (SPS) genes, respectively. The expression results of miRNA and mRNA were verified by quantitative real-time PCR (qRT-PCR). Our results clarify the mechanism of potato response to alkali stress at the miRNA level, providing new insights into the molecular mechanisms of potato's response to alkali stress. We report many candidate miRNAs and mRNAs for molecular-assisted screening and salt-alkali resistance breeding.

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

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

Integration of mRNA and miRNA Analysis Reveals the Molecular Mechanism of Cotton Response to Salt Stress

To identify the regulatory network of known and novel microRNAs (miRNAs) and their targets responding to salt stress, a combined analysis of mRNA libraries, small RNA libraries, and degradome libraries were performed. In this study, we used unique molecular identifiers (UMIs), which are more sensitive, accurate, and reproducible than traditional methods of sequencing, to quantify the number of molecules and correct for amplification bias. We identified a total of 312 cotton miRNAs using seedlings at 0, 1, 3, and 6 h after NaCl treatment, including 80 known ghr-miRNAs and 232 novel miRNAs and found 155 miRNAs that displayed significant differential expression under salt stress. Among them, fifty-nine differentially expressed miRNAs were simultaneously induced in two or three tissues, while 66, 11, and 19 were specifically expressed in the roots, leaves, and stems, respectively. It is indicated there were different populations of miRNAs against salt stress in roots, leaves and stems. 399 candidate targets of salt-induced miRNAs showed significant differential expression before and after salt treatment, and 72 targets of 25 miRNAs were verified by degradome sequencing data. Furthermore, the regulatory relationship of miRNA-target gene was validated experimentally via 5'RLM-RACE, proving our data reliability. Gene ontology and KEGG pathway analysis found that salt-responsive miRNA targets among the differentially expressed genes were significantly enriched, and mainly involved in response to the stimulus process and the plant hormone signal transduction pathway. Furthermore, the expression levels of newly identified miRNA mir1 and known miRNAs miR390 and miR393 gradually decreased when subjected to continuous salt stress, while overexpression of these miRNAs both increased sensitivity to salt stress. Those newly identified miRNAs and mRNA pairs were conducive to genetic engineering and better understanding the mechanisms responding to salt stress in cotton.

Genome-Wide Identification of Key Candidate microRNAs and Target Genes Associated with Peanut Drought Tolerance

Peanut is an important crash crop worldwide, and it is often threatened by drought stress due to unexpected extreme weather events. In this work, NH5 and FH18 were selected as drought-tolerant and drought-sensitive varieties, respectively. Comparison of their physiological responses revealed that NH5 showed less wilting, higher relative water content and lower water loss rate of detached leaves, lower electrolyte leakage, and stronger antioxidant ability under drought stress than did FH18. Based on comparative transcriptomic analysis, 5376 differentially expressed mRNAs were commonly identified in the two varieties, and 2993 genes specifically changed in the drought-tolerant variety and were mainly enriched in photosynthesis-antenna proteins and photosynthetic pathways. Furthermore, 73 microRNAs (miRNAs) were differentially expressed in the drought tolerance variety specifically under drought stress; of these, two key candidate miRNAs, novel miR_416 and novel miR_73, were identified, and the majority of their target genes were enriched in phenylpropanoid biosynthesis, linoleic acid metabolism, and cutin, suberine, and wax biosynthesis. This study lays the foundation for the analysis of the molecular mechanism of drought tolerance and promotes the genetic improvement of peanut drought tolerance.

Root Adaptation via Common Genetic Factors Conditioning Tolerance to Multiple Stresses for Crops Cultivated on Acidic Tropical Soils

Crop tolerance to multiple abiotic stresses has long been pursued as a Holy Grail in plant breeding efforts that target crop adaptation to tropical soils. On tropical, acidic soils, aluminum (Al) toxicity, low phosphorus (P) availability and drought stress are the major limitations to yield stability. Molecular breeding based on a small suite of pleiotropic genes, particularly those with moderate to major phenotypic effects, could help circumvent the need for complex breeding designs and large population sizes aimed at selecting transgressive progeny accumulating favorable alleles controlling polygenic traits. The underlying question is twofold: do common tolerance mechanisms to Al toxicity, P deficiency and drought exist? And if they do, will they be useful in a plant breeding program that targets stress-prone environments. The selective environments in tropical regions are such that multiple, co-existing regulatory networks may drive the fixation of either distinctly different or a smaller number of pleiotropic abiotic stress tolerance genes. Recent studies suggest that genes contributing to crop adaptation to acidic soils, such as the major Arabidopsis Al tolerance protein, AtALMT1, which encodes an aluminum-activated root malate transporter, may influence both Al tolerance and P acquisition via changes in root system morphology and architecture. However, trans-acting elements such as transcription factors (TFs) may be the best option for pleiotropic control of multiple abiotic stress genes, due to their small and often multiple binding sequences in the genome. One such example is the C2H2-type zinc finger, AtSTOP1, which is a transcriptional regulator of a number of Arabidopsis Al tolerance genes, including AtMATE and AtALMT1, and has been shown to activate AtALMT1, not only in response to Al but also low soil P. The large WRKY family of transcription factors are also known to affect a broad spectrum of phenotypes, some of which are related to acidic soil abiotic stress responses. Hence, we focus here on signaling proteins such as TFs and protein kinases to identify, from the literature, evidence for unifying regulatory networks controlling Al tolerance, P efficiency and, also possibly drought tolerance. Particular emphasis will be given to modification of root system morphology and architecture, which could be an important physiological "hub" leading to crop adaptation to multiple soil-based abiotic stress factors.

PLATZ2 negatively regulates salt tolerance in Arabidopsis seedlings by directly suppressing the expression of the CBL4/SOS3 and CBL10/SCaBP8 genes

Although the salt overly sensitive (SOS) pathway plays essential roles in conferring salt tolerance in Arabidopsis thaliana, the regulatory mechanism underlying SOS gene expression remains largely unclear. In this study, AtPLATZ2 was found to function as a direct transcriptional suppressor of CBL4/SOS3 and CBL10/SCaBP8 in the Arabidopsis salt stress response. Compared with wild-type plants, transgenic plants constitutively overexpressing AtPLATZ2 exhibited increased sensitivity to salt stress. Loss of function of PLATZ2 had no observed salt stress phenotype in Arabidopsis, while the double mutant of PLATZ2 and PLATZ7 led to weaker salt stress tolerance than wild-type plants. Overexpression of AtPLATZ2 in transgenic plants decreased the expression of CBL4/SOS3 and CBL10/SCaBP8 under both normal and saline conditions. AtPLATZ2 directly bound to A/T-rich sequences in the CBL4/SOS3 and CBL10/SCaBP8 promoters in vitro and in vivo, and inhibited CBL4/SOS3 promoter activity in the plant leaves. The salt sensitivity of #11 plants constitutively overexpressing AtPLATZ2 was restored by the overexpression of CBL4/SOS3 and CBL10/SCaBP8. Salt stress-induced Na+ accumulation in both the shoots and roots was more exaggerated in AtPLATZ2-overexpressing plants than in the wild type. The salt stress-induced Na+ accumulation in #11 seedlings was also rescued by the overexpression of CBL4/SOS3 and CBL10/SCaBP8. Furthermore, the transcription of AtPLATZ2 was induced in response to salt stress. Collectively, these results suggest that AtPLATZ2 suppresses plant salt tolerance by directly inhibiting CBL4/SOS3 and CBL10/SCaBP8, and functions redundantly with PLATZ7.

Emerging Connections between Small RNAs and Phytohormones

Small RNAs (sRNAs), mainly including miRNAs and siRNAs, are ubiquitous in eukaryotes. sRNAs mostly negatively regulate gene expression via (post-)transcriptional gene silencing through DNA methylation, mRNA cleavage, or translation inhibition. The mechanisms of sRNA biogenesis and function in diverse biological processes, as well as the interactions between sRNAs and environmental factors, like (a)biotic stress, have been deeply explored. Phytohormones are central in the plant's response to stress, and multiple recent studies highlight an emerging role for sRNAs in the direct response to, or the regulation of, plant hormonal pathways. In this review, we discuss recent progress on the unraveling of crossregulation between sRNAs and nine plant hormones.

The miR399-CsUBC24 Module Regulates Reproductive Development and Male Fertility in Citrus

MicroRNA399 (miR399) regulates phosphate homeostasis in plants by down-regulating the expression of PHOSPHATE2 (PHO2, or UBC24 encoding the ubiquitin-conjugating E2 enzyme). We previously identified CsmiR399a.1 in a small RNA sequencing screen of a male-sterile somatic cytoplasmic hybrid (or cybrid) of pummelo (Citrus grandis). Here, we report that miR399 affects reproductive development and male fertility in citrus. Down-regulation of CsmiR399a.1 using a short tandem target mimic (STTM) led to abnormal floral development, inhibition of anther dehiscence, and decreased pollen fertility. When grown in inorganic phosphate (Pi)-sufficient conditions, CsmiR399a.1-STTM plants had lower total phosphorus content in their leaves than the wild type and showed typical symptoms of Pi deficiency. In CsmiR399a.1-STTM plants, the expression of genes involved in starch metabolism and Pi homeostasis was significantly different than in the wild type. Thus, we conclude that miR399-STTM mimicked Pi deficiency, disturbed starch metabolism, and was responsible for pollen grain collapse in the transgenic lines. We identified CsUBC24, a citrus homolog of Arabidopsis (Arabidopsis thaliana) AtUBC24 (PHO2), as a target of CsmiR399a.1 that physically interacts with the floral development regulators SEPALLATA family (CsSEP1.1, CsSEP1.2, and CsSEP3) and the anther dehiscence regulator INDUCER OF CBF EXPRESSION1 (CsICE1). We hypothesize that CsUBC24 downregulates the CsSEPs, which disrupts the floral meristem identity regulatory network and leads to developmental abnormalities in flowers. By interacting with CsICE1, CsUBC24 disturbs stomate function on the anther surface, which inhibits anther dehiscence. These findings indicate that a miR399-based mechanism influences both reproductive development and male fertility in citrus.

Apple SERRATE negatively mediates drought resistance by regulating MdMYB88 and MdMYB124 and microRNA biogenesis

The function of serrate (SE) in miRNA biogenesis in Arabidopsis is well elucidated, whereas its role in plant drought resistance is largely unknown. In this study, we report that MdSE acts as a negative regulator of apple (Malus × domestica) drought resistance by regulating the expression levels of MdMYB88 and MdMYB124 and miRNAs, including mdm-miR156, mdm-miR166, mdm-miR172, mdm-miR319, and mdm-miR399. MdSE interacts with MdMYB88 and MdMYB124, two positive regulators of apple drought resistance. MdSE decreases the transcript and protein levels of MdMYB88 and MdMYB124, which directly regulate the expression of MdNCED3, a key enzyme in abscisic acid (ABA) biosynthesis. Furthermore, MdSE is enriched in the same region of the MdNECD3 promoter where MdMYB88/MdMYB124 binds. Consistently, MdSE RNAi transgenic plants are more sensitive to ABA-induced stomatal closure, whereas MdSE OE plants are less sensitive. In addition, under drought stress, MdSE is responsible for the biogenesis of mdm-miR399, a negative regulator of drought resistance, and negatively regulates miRNAs, including mdm-miR156, mdm-miR166, mdm-miR172, and mdm-miR319, which are positive regulators of drought resistance. Taken together, by revealing the negative role of MdSE, our results broaden our understanding of the apple drought response and provide a candidate gene for apple drought improvement through molecular breeding.

Genome-Wide Identification and Characterization of Drought Stress Responsive microRNAs in Tibetan Wild Barley

Drought stress is a major obstacle to agricultural production. Tibetan wild barley with rich genetic diversity is useful for drought-tolerant improvement of cereals. MicroRNAs (miRNAs) play critical roles in controlling gene expression in response to various environment perturbations in plants. However, the genome-wide expression profiles of miRNAs and their targets in response to drought stress are largely unknown in wild barley. In this study, a polyethylene glycol (PEG) induced drought stress hydroponic experiment was performed, and the expression profiles of miRNAs from the roots of two contrasting Tibetan wild barley genotypes XZ5 (drought-tolerant) and XZ54 (drought-sensitive), and one cultivated barley Tadmor (drought-tolerant) generated by high-throughput sequencing were compared. There were 69 conserved miRNAs and 1574 novel miRNAs in the dataset of three genotypes under control and drought conditions. Among them, seven conserved miRNAs and 36 novel miRNAs showed significantly genotype-specific expression patterns in response to drought stress. And 12 miRNAs were further regarded as drought tolerant associated miRNAs in XZ5, which mostly participate in gene expression, metabolism, signaling and transportation, suggesting that they and their target genes play important roles in plant drought tolerance. This is the first comparation study on the miRNA transcriptome in the roots of two Tibetan wild barley genotypes differing in drought tolerance and one drought tolerant cultivar in response to PEG treatment. Further results revealed the candidate drought tolerant miRNAs and target genes in the miRNA regulation mechanism in wild barley under drought stress. Our findings provide valuable understandings for the functional characterization of miRNAs in drought tolerance.

Phosphate excess increases susceptibility to pathogen infection in rice

Phosphorus (P) is an essential nutrient for plant growth and productivity. Due to soil fixation, however, phosphorus availability in soil is rarely sufficient to sustain high crop yields. The overuse of fertilizers to circumvent the limited bioavailability of phosphate (Pi) has led to a scenario of excessive soil P in agricultural soils. Whereas adaptive responses to Pi deficiency have been deeply studied, less is known about how plants adapt to Pi excess and how Pi excess might affect disease resistance. We show that high Pi fertilization, and subsequent Pi accumulation, enhances susceptibility to infection by the fungal pathogen Magnaporthe oryzae in rice. This fungus is the causal agent of the blast disease, one of the most damaging diseases of cultivated rice worldwide. Equally, MIR399f overexpression causes an increase in Pi content in rice leaves, which results in enhanced susceptibility to M. oryzae. During pathogen infection, a weaker activation of defence-related genes occurs in rice plants over-accumulating Pi in leaves, which is in agreement with the phenotype of blast susceptibility observed in these plants. These data support that Pi, when in excess, compromises defence mechanisms in rice while demonstrating that miR399 functions as a negative regulator of rice immunity. The two signalling pathways, Pi signalling and defence signalling, must operate in a coordinated manner in controlling disease resistance. This information provides a basis to understand the molecular mechanisms involved in immunity in rice plants under high Pi fertilization, an aspect that should be considered in management of the rice blast disease.

Cloning and characterization of two chlorophyll A/B binding protein genes and analysis of their gene family in Camellia sinensis

In this study, two chlorophyll A/B binding protein (CAB) genes (CsCP1 and CsCP2) in tea plant were cloned. The proteins encoded by these genes belong to the external or internal antenna proteins of PS II, respectively. They may be the targets of physiological regulation for tea leaf cell PS II because they all contain multiple functional domains and modifiable sites. The CAB gene family in the tea genome consists of 25 homologous genes. We measured the expression patterns of ten genes in the CsCP1 and CsCP2 subfamily under six different stresses. CsCP1 expression was inhibited in response to 6 kinds of stress; CsCP2 expression was slightly upregulated only after cold stress and ABA treatment. However, the expression levels of CSA016997 and CSA030476 were upregulated significantly in the six stresses. The results suggested that the 10 CAB genes may have different functions in tea leaves. Moreover, changes in the expression of the 10 genes under stress appear to be related to ABA- and MeJA-dependent signalling pathways, and their responses to MeJA treatment is faster than those to ABA. In addition, we introduced our experiences for cloning the genes in the context of complex genomes.

Comparative transcriptome study of switchgrass (Panicum virgatum L.) homologous autopolyploid and its parental amphidiploid responding to consistent drought stress

BACKGROUND

Newly formed polyploids may experience short-term adaptative changes in their genome that may enhance the resistance of plants to stress. Considering the increasingly serious effects of drought on biofuel plants, whole genome duplication (WGD) may be an efficient way to proceed with drought resistant breeding. However, the molecular mechanism of drought response before/after WGD remains largely unclear.

RESULT

We found that autoploid switchgrass (Panicum virgatum L.) 8X Alamo had higher drought tolerance than its parent amphidiploid 4X Alamo using physiological tests. RNA and microRNA sequencing at different time points during drought were then conducted on 8X Alamo and 4X Alamo switchgrass. The specific differentially expressed transcripts (DETs) that related to drought stress (DS) in 8X Alamo were enriched in ribonucleoside and ribonucleotide binding, while the drought-related DETs in 4X Alamo were enriched in structural molecule activity. Ploidy-related DETs were primarily associated with signal transduction mechanisms. Weighted gene co-expression network analysis (WGCNA) detected three significant DS-related modules, and their DETs were primarily enriched in biosynthesis process and photosynthesis. A total of 26 differentially expressed microRNAs (DEmiRs) were detected, and among them, sbi-microRNA 399b was only expressed in 8X Alamo. The targets of microRNAs that were responded to polyploidization and drought stress all contained cytochrome P450 and superoxide dismutase genes.

CONCLUSIONS

This study explored the drought response of 8X and 4X Alamo switchgrass on both physiological and transcriptional levels, and provided experimental and sequencing data basis for a short-term adaptability study and drought-resistant biofuel plant breeding.