Alfalfa response to heat stress is modulated by microRNA156

Overexpression of SQUAMOSA promoter binding protein-like 4a (NtSPL4a) alleviates Cd toxicity in Nicotiana tabacum

Squamosa Promoter Binding Protein-Like (SPL) plays a crucial role in regulating plant development and combating stress, yet its mechanism in regulating resistance to Cd toxicity remains unclear. In this study, we cloned a nuclear-localized transcription factor, NtSPL4a, from the tobacco cultivar TN90. Transient co-expression results showed that miR156 significantly reduced the expression of NtSPL4a by binding to the 3'-UTR of its transcript. We obtained transgenic tobacco overexpressing NtSPL4a (including the 3'-UTR) and NtSPL4aΔ (lacking the 3'-UTR) through Agrobacterium-mediated genetic transformation. Compared to the wild type (WT), overexpression of NtSPL4a/NtSPL4aΔ shortened the flowering time and exhibited a more developed root system. The transgenic tobacco showed significantly reduced Cd content, being 85.1% (OE-NtSPL4a) and 46.7% (OE-NtSPL4aΔ) of WT, respectively. Moreover, the upregulation of NtSPL4a affected the mineral nutrient homeostasis in transgenic tobacco. Additionally, overexpression of NtSPL4a/NtSPL4aΔ effectively alleviated leaf chlorosis and oxidative stress induced by Cd toxicity. One possible reason is that the overexpression of NtSPL4a/NtSPL4aΔ can effectively promote the accumulation of non-enzymatic antioxidants. A comparative transcriptomic analysis was performed between transgenic tobacco and WT to further unravel the global impacts brought by NtSPL4a. The tobacco overexpressing NtSPL4a had 183 differentially expressed genes (77 upregulated, 106 downregulated), while the tobacco overexpressing NtSPL4aΔ had 594 differentially expressed genes (244 upregulated, 350 downregulated) compared to WT. These differentially expressed genes mainly included transcription factors, metal transport proteins, flavonoid biosynthesis pathway genes, and plant stress-related genes. Our study provides new insights into the role of the transcript factor SPL in regulating Cd tolerance.

The complex transcriptional regulation of heat stress response in maize

As one of the most important food and feed crops worldwide, maize suffers much more tremendous damages under heat stress compared to other plants, which seriously inhibits plant growth and reduces productivity. To mitigate the heat-induced damages and adapt to high temperature environment, plants have evolved a series of molecular mechanisms to sense, respond and adapt high temperatures and heat stress. In this review, we summarized recent advances in molecular regulations underlying high temperature sensing, heat stress response and memory in maize, especially focusing on several important pathways and signals in high temperature sensing, and the complex transcriptional regulation of ZmHSFs (Heat Shock Factors) in heat stress response. In addition, we highlighted interactions between ZmHSFs and several epigenetic regulation factors in coordinately regulating heat stress response and memory. Finally, we laid out strategies to systematically elucidate the regulatory network of maize heat stress response, and discussed approaches for breeding future heat-tolerance maize.

The multifaceted role of RNA-based regulation in plant stress memory

Plants have evolved interconnected regulatory pathways which enable them to respond and adapt to their environments. In plants, stress memory enhances stress tolerance through the molecular retention of prior stressful experiences, fostering rapid and robust responses to subsequent challenges. Mounting evidence suggests a close link between the formation of stress memories and effective future stress responses. However, the mechanism by which environmental stressors trigger stress memory formation is poorly understood. Here, we review the current state of knowledge regarding the RNA-based regulation on stress memory formation in plants and discuss research challenges and future directions. Specifically, we focus on the involvement of microRNAs (miRNAs), small interfering RNAs (siRNAs), long non-coding RNAs (lncRNAs), and alternative splicing (AS) in stress memory formation. miRNAs regulate target genes via post-transcriptional silencing, while siRNAs trigger stress memory formation through RNA-directed DNA methylation (RdDM). lncRNAs guide protein complexes for epigenetic regulation, and AS of pre-mRNAs is crucial to plant stress memory. Unraveling the mechanisms underpinning RNA-mediated stress memory formation not only advances our knowledge of plant biology but also aids in the development of improved stress tolerance in crops, enhancing crop performance and global food security.

Integrated analysis of transcriptome and miRNAome reveals the heat stress response of Pinellia ternata seedlings

Pinellia ternata (Thunb.) Briet., a valuable herb native to China, is susceptible to the "sprout tumble" phenomenon because of high temperatures, resulting in a significant yield reduction. However, the molecular regulatory mechanisms underlying the response of P. ternata to heat stress are not well understood. In this study, we integrated transcriptome and miRNAome sequencing to identify heat-response genes, microRNAs (miRNAs), and key miRNA-target pairs in P. ternata that differed between heat-stress and room-temperature conditions. Transcriptome analysis revealed extensive reprogramming of 4,960 genes across various categories, predominantly associated with cellular and metabolic processes, responses to stimuli, biological regulation, cell parts, organelles, membranes, and catalytic and binding activities. miRNAome sequencing identified 1,597 known/conserved miRNAs that were differentially expressed between the two test conditions. According to the analysis, genes and miRNAs associated with the regulation of transcription, DNA template, transcription factor activity, and sequence-specific DNA binding pathways may play a major role in the resistance to heat stress in P. ternata. Integrated analysis of the transcriptome and miRNAome expression data revealed 41 high-confidence miRNA-mRNA pairs, forming 25 modules. MYB-like proteins and calcium-responsive transcription coactivators may play an integral role in heat-stress resistance in P. ternata. Additionally, the candidate genes and miRNAs were subjected to quantitative real-time polymerase chain reaction to validate their expression patterns. These results offer a foundation for future studies exploring the mechanisms and critical genes involved in heat-stress resistance in P. ternata.

MicroRNA Profiling Revealed the Mechanism of Enhanced Cold Resistance by Grafting in Melon (Cucumis melo L.)

Grafting is widely used to improve the resistance to abiotic stresses in cucurbit plants, but the effect and molecular mechanism of grafting on cold stress are still unknown in melon. In this study, phenotypic characteristics, physiological indexes, small-RNA sequencing and expression analyses were performed on grafted plants with pumpkin rootstock (PG) and self-grafted plants (SG) to explore the mechanism of changed cold tolerance by grafting in melon. Compared with SG plants, the cold tolerance was obviously enhanced, the malondialdehyde (MDA) content was significantly decreased and the activities of antioxidant enzymes (superoxide dismutase, SOD; catalase, CAT; peroxidase, POD) were significantly increased in PG plants. Depend on differentially expressed miRNA (DEM) identification and expression pattern analyses, cme-miR156b, cme-miR156f and chr07_30026 were thought to play a key role in enhancing low-temperature resistance resulting from grafting. Subsequently, 24, 37 and 17 target genes of cme-miR156b, cme-miR156f and chr07_30026 were respectively predicted, and 21 target genes were co-regulated by cme-miR156b and cme-miR156f. Among these 57 unique target genes, the putative promoter of 13 target genes contained the low-temperature responsive (LTR) cis-acting element. The results of qRT-PCR indicated that six target genes (MELO3C002370, MELO3C009217, MELO3C018972, MELO3C016713, MELO3C012858 and MELO3C000732) displayed the opposite expression pattern to their corresponding miRNAs. Furthermore, MELO3C002370, MELO3C016713 and MELO3C012858 were significantly downregulated in cold-resistant cultivars and upregulated in cold-sensitive varieties after cold stimulus, and they acted as the key negative regulators of low-temperature response in melon. This study revealed three key miRNAs and three putative target genes involved in the cold tolerance of melon and provided a molecular basis underlying how grafting improved the low-temperature resistance of melon plants.

A Comprehensive Interaction Network Constructed Using miRNAs and mRNAs Provides New Insights into Potato Tuberization under High Temperatures

High temperatures delay tuberization and decrease potato (Solanum tuberosum L.) yields. However, the molecular mechanisms and regulatory networks underlying tuberization under high temperatures remain largely unknown. Here, we performed the mRNA and miRNA sequencing of leaves and stems to identify genes and regulatory networks involved in tuberization under high temperatures. A total of 2804 and 5001 differentially expressed genes (DEGs) under high-temperature stress were identified in leaves and stems, respectively. These genes were significantly enriched in gene ontology terms regarding meristem development, the sucrose biosynthetic process, and response to heat. Meanwhile, 101 and 75 differentially expressed miRNAs (DEmiRNAs) were identified in leaves and stems, respectively. We constructed an interaction network between DEmiRNAs and DEGs, identifying 118 and 150 DEmiRNA-DEG pairs in leaves and stems, respectively. We found three miRNA-mRNA candidate modules involved in tuberization under high temperatures, including stu-miR8030-5p/StCPY714, stu-miR7981f-p5/StAGL8a, and stu-miR10532A/StAGL8b. Our study constructed an interaction network between miRNAs and target genes and proposes candidate miRNA-gene modules that regulate tuber formation under high temperatures. Our study provides new insights for revealing the regulatory mechanism of the high-temperature inhibition of tuberization and also provides gene resources for improving the heat tolerance in potatoes.

Plant non-coding RNAs: The new frontier for the regulation of plant development and adaptation to stress

Most plant transcriptomes constitute functional non-coding RNAs (ncRNAs) that lack the ability to encode proteins. In recent years, more research has demonstrated that ncRNAs play important regulatory roles in almost all plant biological processes by modulating gene expression. Thus, it is important to study the biogenesis and function of ncRNAs, particularly in plant growth and development and stress tolerance. In this review, we systematically explore the process of formation and regulatory mechanisms of ncRNAs, particularly those of microRNAs (miRNAs), small interfering RNAs (siRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). Additionally, we provide a comprehensive overview of the recent advancements in ncRNAs research, including their regulation of plant growth and development (seed germination, root growth, leaf morphogenesis, floral development, and fruit and seed development) and responses to abiotic and biotic stress (drought, heat, cold, salinity, pathogens and insects). We also discuss research challenges and provide recommendations to advance the understanding of the roles of ncRNAs in agronomic applications.

Genome-wide identification, stress- and hormone-responsive expression characteristics, and regulatory pattern analysis of Scutellaria baicalensis SbSPLs

SQUAMOSA PROMOTER BINDING PROTEIN-LIKEs (SPLs) encode plant-specific transcription factors that regulate plant growth and development, stress response, and metabolite accumulation. However, there is limited information on Scutellaria baicalensis SPLs. In this study, 14 SbSPLs were identified and divided into 8 groups based on phylogenetic relationships. SbSPLs in the same group had similar structures. Abscisic acid-responsive (ABRE) and MYB binding site (MBS) cis-acting elements were found in the promoters of 8 and 6 SbSPLs. Segmental duplications and transposable duplications were the main causes of SbSPL expansion. Expression analysis based on transcriptional profiling showed that SbSPL1, SbSPL10, and SbSPL13 were highly expressed in roots, stems, and flowers, respectively. Expression analysis based on quantitative real-time polymerase chain reaction (RT‒qPCR) showed that most SbSPLs responded to low temperature, drought, abscisic acid (ABA) and salicylic acid (SA), among which the expression levels of SbSPL7/9/10/12 were significantly upregulated in response to abiotic stress. These results indicate that SbSPLs are involved in the growth, development and stress response of S. baicalensis. In addition, 8 Sba-miR156/157 s were identified, and SbSPL1-5 was a potential target of Sba-miR156/157 s. The results of target gene prediction and coexpression analysis together indicated that SbSPLs may be involved in the regulation of L-phenylalanine (L-Phe), lignin and jasmonic acid (JA) biosynthesis. In summary, the identification and characterization of the SbSPL gene family lays the foundation for functional research and provides a reference for improved breeding of S. baicalensis stress resistance and quality traits.

microRNAs: Key Regulators in Plant Responses to Abiotic and Biotic Stresses via Endogenous and Cross-Kingdom Mechanisms

Dramatic shifts in global climate have intensified abiotic and biotic stress faced by plants. Plant microRNAs (miRNAs)-20-24 nucleotide non-coding RNA molecules-form a key regulatory system of plant gene expression; playing crucial roles in plant growth; development; and defense against abiotic and biotic stress. Moreover, they participate in cross-kingdom communication. This communication encompasses interactions with other plants, microorganisms, and insect species, collectively exerting a profound influence on the agronomic traits of crops. This article comprehensively reviews the biosynthesis of plant miRNAs and explores their impact on plant growth, development, and stress resistance through endogenous, non-transboundary mechanisms. Furthermore, this review delves into the cross-kingdom regulatory effects of plant miRNAs on plants, microorganisms, and pests. It proceeds to specifically discuss the design and modification strategies for artificial miRNAs (amiRNAs), as well as the protection and transport of miRNAs by exosome-like nanovesicles (ELNVs), expanding the potential applications of plant miRNAs in crop breeding. Finally, the current limitations associated with harnessing plant miRNAs are addressed, and the utilization of synthetic biology is proposed to facilitate the heterologous expression and large-scale production of miRNAs. This novel approach suggests a plant-based solution to address future biosafety concerns in agriculture.

The roles of miR156 in abiotic and biotic stresses in plants

MicroRNAs (miRNAs), known as a kind of non-coding RNA, can negatively regulate its target genes. To date, the roles of various miRNAs in plant development and resistance to abiotic and biotic stresses have been widely explored. The present review summarized and discussed the functions of miR156 or miR156-SPL module in abiotic and biotic stresses, such as drought, salt, heat, cold stress, UV-B radiation, heavy mental hazards, nutritional starvation, as well as plant viruses, plant diseases, etc. Based on this, the regulation of miR156-involved stress tolerance was better understood, thus, it would be much easier for plant biologists to carry out suitable strategies to help plants suffer from unfavorable living environments.

miRNA mediated regulation of nitrogen response and nitrogen use efficiency of plants: the case of wheat

Nitrogen (N) is needed for plant growth and development and is the major limiting nutrient due to its higher demand in agricultural production globally. The use of N fertilizers has increased considerably in recent years to achieve higher cereal yields. High N inputs coupled with declining N use efficiency (NUE) result in the degradation of the environment. Plants have developed multidimensional strategies in response to changes in N availability in soil. These strategies include N stress-induced responses such as changes in gene expression patterns. Several N stress-induced genes and other regulatory factors, such as microRNAs (miRNAs), have been identified in different plant species, opening a new avenue of research in plant biology. This review presents a general overview of miRNA-mediated regulation of N response and NUE. Further, the in-silico target predictions and the predicted miRNA-gene network for nutrient metabolism/homeostasis in wheat provide novel insights. The information on N-regulated miRNAs and the differentially expressed target transcripts are necessary resources for genetic improvement of NUE by genome editing.

Assessment of growing condition variables on alfalfa productivity

This study was conducted to assess the impact of growing condition variables on alfalfa (Medicago sativa L.) productivity. A total of 197 alfalfa yield results were acquired from the alfalfa field trials conducted by the South Korean National Agricultural Cooperative Federation or Rural Development Administration between 1983 and 2008. The corresponding climate and soil data were collected from the database of the Korean Meteorological Administration. Twenty-three growing condition variables were developed as explaining variables for alfalfa forage biomass production. Among them, twelve variables were chosen based on the significance of the partial-correlation coefficients or potential agricultural values. The selected partial correlation coefficients between the variables and alfalfa forage biomass ranged from -0.021 to 0.696. The influence of the selected twelve variables on yearly alfalfa production was summarized into three dominant factors through factor analysis. Along with the accumulated temperature variables, the loading scores of the daily mean temperature higher than 25°C were over 0.88 in factor 1. The sunshine duration at temperature between 0°C-25°C was 0.939 in factor 2. Precipitation days were 0.82, which was the greatest in factor 3. Stepwise regression applied with the three dominant factors resulted in the coefficients of factors 1, 2, and 3 for 0.633, 0.485, and 0.115, respectively, and the R-square of the model was 0.602. The environmental conditions limiting alfalfa growth, such as daily temperature higher than 25°C or daily mean temperature affected annual alfalfa production most substantially among the growing condition variables. Therefore, future cultivar selection should consider the capability of alfalfa to be tolerant to extreme summer weather along with biomass production potential.

Investigation of the expansin gene family in sugar beet (Beta vulgaris) by the genome-wide level and their expression responses under abiotic stresses

Sugar beet (Beta vulgaris ssp. vulgaris) is primarily used in sugar production worldwide. Expansins are a gene family of cell wall proteins effective in regulating cell wall structure. They also participate in developmental stages, including cell and leaf growth, root development, and fruit ripening. This study comprehensively characterizes the expansin gene family members found in the sugar beet genome. In addition, in silico expression analysis of sugar beet expansin genes under variable abiotic stress conditions and expression profiles of expansin genes under combined drought and heat stresses by the qRT-PCR method were evaluated in the study. A total of 31 sugar beet expansin genes were identified. BvuEXLA-02 and BvuEXLB-02 genes can have abiotic stress tolerance roles besides their roles in normal development. Determining the properties of sugar beet expansin, family members can help enable the cellulose hydrolysis mechanism and raise plant biomass. Elucidating expression profiles of the sugar beet expansin genes under variable stress conditions can support improving plant productivity. The results of the current study may also contribute to the deep understanding of sugar beet expansin genes in the future.

Noncoding RNAs and their roles in regulating the agronomic traits of crops

Molecular breeding is one of the most effective methods for improving the performance of crops. Understanding the genome features of crops, especially the physiological functions of individual genes, is of great importance to molecular breeding. Evidence has shown that genomes of both animals and plants transcribe numerous non-coding RNAs, which are involved in almost every aspect of development. In crops, an increasing number of studies have proven that non-coding RNAs are new genetic resources for regulating crop traits. In this review, we summarize the current knowledge of non-coding RNAs, which are potential crop trait regulators, and focus on the functions of long non-coding RNAs (lncRNAs) in determining crop grain yield, phased small-interfering RNAs (phasiRNAs) in regulating fertility, small interfering RNAs (siRNAs) and microRNAs (miRNAs) in facilitating plant immune response and disease resistance, and miRNAs mediating nutrient and metal stress. Finally, we also discuss the next-generation method for ncRNA application in crop domestication and breeding.

MicroRNA: A Dynamic Player from Signalling to Abiotic Tolerance in Plants

MicroRNAs (miRNAs) are a class of non-coding single-stranded RNA molecules composed of approximately 20-24 nucleotides in plants. They play an important regulatory role in plant growth and development and as a signal in abiotic tolerance. Some abiotic stresses include drought, salt, cold, high temperature, heavy metals and nutritional elements. miRNAs affect gene expression by manipulating the cleavage, translational expression or DNA methylation of target messenger RNAs (mRNAs). This review describes the current progress in the field considering two aspects: (i) the way miRNAs are produced and regulated and (ii) the way miRNA/target genes are used in plant responses to various abiotic stresses. Studying the molecular mechanism of action of miRNAs' downstream target genes could optimize the genetic manipulation of crop growth and development conditions to provide a more theoretically optimized basis for improving crop production. MicroRNA is a novel signalling mechanism in interplant communication relating to abiotic tolerance.

Arbuscular mycorrhizal fungus Rhizophagus irregularis alleviates drought stress in soybean with overexpressing the GmSPL9d gene by promoting photosynthetic apparatus and regulating the antioxidant system

Drought is the most destructive abiotic stress and negatively affects crop growth and productivity. Modern breeding efforts have produced numerous cultivars with distinct genetic traits that improve crop growth and drought stress tolerance. Arbuscular mycorrhizal fungi (AMF) can enhance drought tolerance in soybean plants by directly providing nutrients to plants, promoting photosynthesis, or influencing interspecific plant interactions in natural communities. However, the interactions between AMF and wild and transgenic soybean genotypes remain unclear. Therefore, in the present study, we evaluated the effect of arbuscular mycorrhizal fungi on the growth performance of drought-stressed transgenic soybean lines (ZXOE-11 and ZXOE-13) overexpressing GmSPL9d gene and their wild soybean Tianlong 1 (TL1) at the seedling stage (45 d after sowing). The results showed that colonization of wild and transgenic soybean with Rhizophagus irregularis significantly decreased the adverse effects of drought on plant growth. AMF inoculation significantly increased plant biomass, root activity, chlorophyll metabolism, photosynthesis, and chlorophyll fluorescence in wild-type and transgenic plants under both control and drought stress conditions. Drought causes the production of ROS, such as hydrogen peroxide, which enhances MDA, thereby decreasing the membrane stability index (MSI). However, AMF-inoculated plants exhibited decreased ROS accumulation and increased MSI. Moreover, AMF treatment significantly improved osmolyte, nitrogen, and nitrate reductase activity under control and drought conditions, which increased the relative water content. Furthermore, AMF treatment enhanced the antioxidant systems of drought-stressed plants by increasing the activities of peroxidase, superoxide dismutase, catalase, and ascorbate peroxidase. AMF improved the growth performance, photosynthesis, and antioxidant activity of transgenic plants under drought stress conditions. The present findings indicate that the AMF contribution to soybean seedling drought tolerance was more significant for the transgenic plants than for the wild plants under drought conditions. The current findings emphasize the possibility of growth and photosynthetic variation in the degree of AMF-associated drought resistance in soybean plants. Our findings suggest that future crop breeding challenges include developing cultivars for sustainable production and maximizing crop cultivar and fungal species (AMF) combinations in drought-stressed regions.

The miR156b-GmSPL2b module mediates male fertility regulation of cytoplasmic male sterility-based restorer line under high-temperature stress in soybean

High-temperature (HT) stress at flowering stage causes significant damage to soybean, including pollen abortion and fertilization failure, but few genes involved in male fertility regulation under HT stress in soybean have been characterized. Here, we demonstrated that miR156b-GmSPL2b module involved in male fertility regulation of soybean cytoplasmic male sterility (CMS)-based restorer line under HT stress. Overexpression of miR156b decreased male fertility in soybean CMS-based restorer line and its hybrid F₁ with CMS line under HT stress. RNA-seq analysis found that miR156b mediated male fertility regulation in soybean under HT stress by regulating the expression of pollen development and HT response related genes. Metabolomic analysis of miR156bOE revealed reduction in flavonoid content under HT stress. Integrated transcriptomic and metabolomic analysis showed that the overexpression of miR156b caused flavonoid metabolism disorder in soybean flower bud under HT stress. Knockout of GmSPL2b also decreased the thermotolerance of soybean CMS-based restorer line during flowering. Moreover, GmSPL2b turned out to be directly bounded to the promoter of GmHSFA6b. Further verification indicated that GmHSFA6b overexpression enhanced HT tolerance in Arabidopsis during flowering. Substance content and gene expression analysis revealed that miR156b-GmSPL2b may mediate reactive oxygen species clearance by regulating flavonoid metabolism, thus participating in the regulation of male fertility in soybean under HT stress. This study not only provided important progress for understanding the molecular mechanism of miR156b-GmSPL2b regulating the male fertility of soybean CMS-based restorer line under HT stress, but also provided genetic resources and theoretical basis for creating HT-tolerant strong restorer lines.

The MdmiR156n Regulates Drought Tolerance and Flavonoid Synthesis in Apple Calli and Arabidopsis

Drought is the major abiotic stress that limits apple productivity and quality. To date, many important and divergent regulatory functions of miR156/SBP genes in plant growth and development have been well understood. However, little is known about the role of apple miR156 in response to abiotic stress. To better understand the functions of MdmiR156 in abiotic stress tolerance, we constructed the overexpression (OE) and short tandem target mimic (STTM) vector of MdmiR156n and performed its functional analysis through the characterization of transgenic apple calli and Arabidopsis thaliana plants. In this study, MdmiR156n overexpression significantly increased the length of primary roots and the number of lateral roots in transgenic Arabidopsis plants under drought stress. In addition, MdmiR156n transgenic Arabidopsis and apple calli had a lower electrolyte leakage rate and less cell membrane damage than WT and STTM156 after drought stress. Further studies showed that MdmiR156n overexpression promoted the accumulation of flavonoids and scavenging of reactive oxygen species (ROS) under drought conditions in transgenic apple calli and A. thaliana plants. Taken together, overexpression MdmiR156n enhances drought tolerance by regulating flavonoid synthesis and ROS signaling cascades in apple calli and A. thaliana.

Deciphering the role of SPL12 and AGL6 from a genetic module that functions in nodulation and root regeneration in Medicago sativa

Our results show that SPL12 plays a crucial role in regulating nodule development in Medicago sativa L. (alfalfa), and that AGL6 is targeted and downregulated by SPL12. Root architecture in plants is critical because of its role in controlling nutrient cycling, water use efficiency and response to biotic and abiotic stress factors. The small RNA, microRNA156 (miR156), is highly conserved in plants, where it functions by silencing a group of SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors. We previously showed that transgenic Medicago sativa (alfalfa) plants overexpressing miR156 display increased nodulation, improved nitrogen fixation and enhanced root regenerative capacity during vegetative propagation. In alfalfa, transcripts of eleven SPLs, including SPL12, are targeted for cleavage by miR156. In this study, we characterized the role of SPL12 in root architecture and nodulation by investigating the transcriptomic and phenotypic changes associated with altered transcript levels of SPL12, and by determining SPL12 regulatory targets using SPL12-silencing and -overexpressing alfalfa plants. Phenotypic analyses showed that silencing of SPL12 in alfalfa caused an increase in root regeneration, nodulation, and nitrogen fixation. In addition, AGL6 which encodes AGAMOUS-like MADS box transcription factor, was identified as being directly targeted for silencing by SPL12, based on Next Generation Sequencing-mediated transcriptome analysis and chromatin immunoprecipitation assays. Taken together, our results suggest that SPL12 and AGL6 form a genetic module that regulates root development and nodulation in alfalfa.

SPL12 Regulates AGL6 and AGL21 to Modulate Nodulation and Root Regeneration under Osmotic Stress and Nitrate Sufficiency Conditions in Medicago sativa

The highly conserved plant microRNA, miR156, affects root architecture, nodulation, symbiotic nitrogen fixation, and stress response. In Medicago sativa, transcripts of eleven SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE, SPLs, including SPL12, are targeted for cleavage by miR156. Our previous research revealed the role of SPL12 and its target gene, AGL6, in nodulation in alfalfa. Here, we investigated the involvement of SPL12, AGL6 and AGL21 in nodulation under osmotic stress and different nitrate availability conditions. Characterization of phenotypic and molecular parameters revealed that the SPL12/AGL6 module plays a negative role in maintaining nodulation under osmotic stress. While there was a decrease in the nodule numbers in WT plants under osmotic stress, the SPL12-RNAi and AGL6-RNAi genotypes maintained nodulation under osmotic stress. Moreover, the results showed that SPL12 regulates nodulation under a high concentration of nitrate by silencing AGL21. AGL21 transcript levels were increased under nitrate treatment in WT plants, but SPL12 was not affected throughout the treatment period. Given that AGL21 was significantly upregulated in SPL12-RNAi plants, we conclude that SPL12 may be involved in regulating nitrate inhibition of nodulation in alfalfa by targeting AGL21. Taken together, our results suggest that SPL12, AGL6, and AGL21 form a genetic module that regulates nodulation in alfalfa under osmotic stress and in response to nitrate.

Regulation of Na+/H+ exchangers, Na+/K+ transporters, and lignin biosynthesis genes, along with lignin accumulation, sodium extrusion, and antioxidant defense, confers salt tolerance in alfalfa

Accumulation of high sodium (Na⁺) leads to disruption of metabolic processes and decline in plant growth and productivity. Therefore, this study was undertaken to clarify how Na⁺/H⁺ exchangers and Na⁺/K⁺ transporter genes contribute to Na⁺ homeostasis and the substantial involvement of lignin biosynthesis genes in salt tolerance in alfalfa (Medicago sativa L.), which is poorly understood. In this study, high Na⁺ exhibited a substantial reduction of morphophysiological indices and induced oxidative stress indicators in Xingjiang Daye (XJD; sensitive genotype), while Zhongmu (ZM; tolerant genotype) remained unaffected. The higher accumulation of Na⁺ and the lower accumulation of K⁺ and K⁺/(Na⁺ + K⁺) ratio were found in roots and shoots of XJD compared with ZM under salt stress. The ZM genotype showed a high expression of SOS1 (salt overly sensitive 1), NHX1 (sodium/hydrogen exchanger 1), and HKT1 (high-affinity potassium transporter 1), which were involved in K⁺ accumulation and excess Na⁺ extrusion from the cells compared with XJD. The lignin accumulation was higher in the salt-adapted ZM genotype than the sensitive XJD genotype. Consequently, several lignin biosynthesis-related genes including 4CL2, CCoAOMT, COMT, CCR, C4H, PAL1, and PRX1 exhibited higher mRNA expression in salt-tolerant ZM compared with XJD. Moreover, antioxidant enzyme (catalase, superoxide dismutase, ascorbate peroxidase, and glutathione reductase) activity was higher in ZM relative to XJD. This result suggests that high antioxidant provided the defense against oxidative damages in ZM, whereas low enzyme activity with high Na⁺ triggered the oxidative damage in XJD. These findings together illustrate the ion exchanger, antiporter, and lignin biosysthetic genes involving mechanistic insights into differential salt tolerance in alfalfa.

Molecular insights into mechanisms underlying thermo-tolerance in tomato

Plant productivity is being seriously compromised by climate-change-induced temperature extremities. Agriculture and food safety are threatened due to global warming, and in many cases the negative impacts have already begun. Heat stress leads to significant losses in yield due to changes in growth pattern, plant phonologies, sensitivity to pests, flowering, grain filling, maturity period shrinkage, and senescence. Tomato is the second most important vegetable crop. It is very sensitive to heat stress and thus, yield losses in tomato due to heat stress could affect food and nutritional security. Tomato plants respond to heat stress with a variety of cellular, physiological, and molecular responses, beginning with the early heat sensing, followed by signal transduction, antioxidant defense, osmolyte synthesis and regulated gene expression. Recent findings suggest that specific plant organs are extremely sensitive to heat compared to the entire plant, redirecting the research more towards generative tissues. This is because, during sexual reproduction, developing pollens are the most sensitive to heat. Often, just a few degrees of temperature elevation during pollen development can have a negative effect on crop production. Furthermore, recent research has discovered certain genetic and epigenetic mechanisms playing key role in thermo-tolerance and have defined new directions for tomato heat stress response (HSR). Present challenges are to increase the understanding of molecular mechanisms underlying HS, and to identify superior genotypes with more tolerance to extreme temperatures. Several metabolites, genes, heat shock factors (HSFs) and microRNAs work together to regulate the plant HSR. The present review provides an insight into molecular mechanisms of heat tolerance and current knowledge of genetic and epigenetic control of heat-tolerance in tomato for sustainable agriculture in the future. The information will significantly contribute to improve breeding programs for development of heat tolerant cultivars.

Beat the heat: plant- and microbe-mediated strategies for crop thermotolerance

Heat stress (HS) affects plant growth and development, and reduces crop yield. To combat HS, plants have evolved several sophisticated strategies. The primary HS response in plants involves the activation of heat-shock transcription factors and heat-shock proteins (HSPs). Plants also deploy more advanced epigenetic mechanisms in response to recurring HS conditions. In addition, beneficial microbes can reprogram the plant epitranscriptome to induce thermotolerance, and have the potential to improve crop yield productivity by mitigating HS-induced inhibition of growth and development. We summarize the latest advances in plant epigenetic regulation and highlight microbe-mediated thermotolerance in plants.

Regulatory role of microRNAs (miRNAs) in the recent development of abiotic stress tolerance of plants

MicroRNAs (miRNAs) are a distinct groups of single-stranded non-coding, tiny regulatory RNAs approximately 20-24 nucleotides in length. miRNAs negatively influence gene expression at the post-transcriptional level and have evolved considerably in the development of abiotic stress tolerance in a number of model plants and economically important crop species. The present review aims to deliver the information on miRNA-mediated regulation of the expression of major genes or Transcription Factors (TFs), as well as genetic and regulatory pathways. Also, the information on adaptive mechanisms involved in plant abiotic stress responses, prediction, and validation of targets, computational tools, and databases available for plant miRNAs, specifically focus on their exploration for engineering abiotic stress tolerance in plants. The regulatory function of miRNAs in plant growth, development, and abiotic stresses consider in this review, which uses high-throughput sequencing (HTS) technologies to generate large-scale libraries of small RNAs (sRNAs) for conventional screening of known and novel abiotic stress-responsive miRNAs adds complexity to regulatory networks in plants. The discoveries of miRNA-mediated tolerance to multiple abiotic stresses, including salinity, drought, cold, heat stress, nutritional deficiency, UV-radiation, oxidative stress, hypoxia, and heavy metal toxicity, are highlighted and discussed in this review.

Combined Analysis of the Metabolome and Transcriptome to Explore Heat Stress Responses and Adaptation Mechanisms in Celery (Apium graveolens L.)

Celery is an important leafy vegetable that can grow during the cool season and does not tolerate high temperatures. Heat stress is widely acknowledged as one of the main abiotic stresses affecting the growth and yield of celery. The morphological and physiological indices of celery were investigated in the present study to explore the physiological mechanisms in response to high temperatures. Results showed that the antioxidant enzyme activity, proline, relative conductivity, and malondialdehyde were increased, while chlorophyll and the water content of leaves decreased under high-temperature conditions. Short-term heat treatment increased the stomatal conductance to cool off the leaves by transpiration; however, long-term heat treatment led to stomatal closure to prevent leaf dehydration. In addition, high temperature caused a disordered arrangement of palisade tissue and a loose arrangement of spongy tissue in celery leaves. Combined metabolomic and transcriptomic analyses were further used to reveal the regulatory mechanisms in response to heat stress at the molecular level in celery. A total of 1003 differential metabolites were identified and significantly enriched in amino acid metabolism and the tricarboxilic acid (TCA) cycle. Transcriptome sequencing detected 24,264 different genes, including multiple transcription factor families such as HSF, WRKY, MYB, AP2, bZIP, and bHLH family members that were significantly upregulated in response to heat stress, suggesting that these genes were involved in the response to heat stress. In addition, transcriptional and metabolic pathway analyses showed that heat stress inhibited the glycolysis pathway and delayed the TCA cycle but increased the expression of most amino acid synthesis pathways such as proline, arginine, and serine, consistent with the results of physiological indicators. qRT-PCR further showed that the expression pattern was similar to the expression abundance in the transcriptome. The important metabolites and genes in celery that significantly contributed to the response to high temperatures were identified in the present study, which provided the theoretical basis for breeding heat-resistant celery.

Alfalfa transcriptome profiling provides insight into miR156-mediated molecular mechanisms of heat stress tolerance

Heat is one of the major environmental stressors that negatively affects alfalfa production. Previously, we reported the role of microRNA156 (miR156) in heat tolerance, however, mechanisms and downstream genes involved in this process were not fully studied. To provide further insight, we compared an empty vector control and miR156 overexpressing alfalfa plants (miR156+) after exposing them to heat stress (40 °C) for 24h. We collected leaf samples for transcriptome analysis to illustrate the miR156-regualted molecular mechanisms underlying the heat stress response. A total of 3579 differentially expressed genes (DEG) were detected exclusively in miR156+ plants under heat stress using the Medicago sativa genome as reference. GO and KEGG analysis indicated that these DEGs were mainly involved in "polysaccharide metabolism", "response to chemical", "secondary metabolism", "carbon metabolism" and "cell cycle". Transcription factors predicted in miR156+ plants belonged to TCP family, MYB, ABA response element-binding factor, WRKY and heat shock transcription factor. We also identified two new SPL family gene member (SPL8a and SPL12a), putatively regulated by miR156. The present study provides comprehensive transcriptome profile of alfalfa, identifies a number of genes and pathways, and reveals a miR156-regulated network of mechanisms at the gene expression level to modulate heat responses in alfalfa.

Regulation of small RNA-mediated high temperature stress responses in crop plants

Small RNAs have emerged as key players of gene expression regulation. Several lines of evidences highlight their role in modulating high temperature stress responsiveness in plants. Throughout their life cycle, plants have to regulate their gene expression at various developmental phases, physiological changes, and in response to biotic or environmental stress. High temperature is one the most common abiotic stress for crop plants, that results in impaired morphology, physiology, and yield. However, plants have certain mechanisms that enable them to withstand such conditions by modulating the expression of stress-related genes. Small RNA (sRNA)-regulated gene expression is one such mechanism which is ubiquitous in all eukaryotes. The sRNAs mainly include micro RNAs (miRNAs) and small interfering RNAs (siRNAs). They are primarily associated with the gene silencing either through translation inhibition, mRNA degradation, or DNA methylation. During high temperature stress the increased or decreased level of miRNAs altered the protein accumulation of target transcripts and, therefore, regulate stress responses. Several reports are available in plants which are genetically engineered through expressing artificial miRNAs resulted in thermotolerance. sRNAs have also been reported to bring the epigenetic changes on chromatin region through RNA-dependent DNA methylation (RdDM). The present article draws a brief illustration of sRNA origin, their functional mechanisms, role in high temperature stress, and possible application for developing stress tolerant crop plants.

Molecular Characterization of the miR156/MsSPL Model in Regulating the Compound Leaf Development and Abiotic Stress Response in Alfalfa

Plant leaf patterns and shapes are spectacularly diverse. Changing the complexity of leaflet numbers is a valuable approach to increase its nutrition and photosynthesis. Alfalfa (Medicago sativa) is the most important forage legume species and has diversified compound leaf patterns, which makes it a model species for studying compound leaf development. However, transcriptomic information from alfalfa remains limited. In this study, RNA-Seq technology was used to identify 3746 differentially expressed genes (DEGs) between multifoliate and trifoliate alfalfa. Through an analysis of annotation information and expression data, SPL, one of the key regulators in modifiable plant development and abiotic stress response, was further analyzed. Here, thirty MsSPL genes were obtained from the alfalfa genome, of which 16 had the putative miR156 binding site. A tissue expression pattern analysis showed that the miR156-targeted MsSPLs were divided into two classes, namely, either tissue-specific or widely expressed in all tissues. All miR156-targeted SPLs strongly showed diversification and positive roles under drought and salt conditions. Importantly, miR156/MsSPL08 was significantly suppressed in multifoliate alfalfa. Furthermore, in the paralogous mutant of MsSPL08 isolated from Medicago truncatula, the phenotypes of mutant plants reveal that miR156/MsSPL08 is involved not only involved the branches but also especially regulates the number of leaflets. The legume is a typical compound leaf plant; the ratio of the leaflet often affects the quality of the forage. This study sheds light on new functions of SPL genes that regulate leaflet number development.

The CRISPR/Cas9-Mediated Modulation of SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE 8 in Alfalfa Leads to Distinct Phenotypic Outcomes

Alfalfa (Medicago sativa L.) is the most widely grown perennial leguminous forage and is an essential component of the livestock industry. Previously, the RNAi-mediated down-regulation of alfalfa SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE 8 (MsSPL8) was found to lead to increased branching, regrowth and biomass, as well as enhanced drought tolerance. In this study, we aimed to further characterize the function of MsSPL8 in alfalfa using CRISPR/Cas9-induced mutations in this gene. We successfully generated alfalfa genotypes with small insertions/deletions (indels) at the target site in up to three of four MsSPL8 alleles in the first generation. The efficiency of editing appeared to be tightly linked to the particular gRNA used. The resulting genotypes displayed consistent morphological alterations, even with the presence of up to two wild-type MsSPL8 alleles, including reduced leaf size and early flowering. Other phenotypic effects appeared to be dependent upon mutational dosage, with those plants with the highest number of mutated MsSPL8 alleles also exhibiting significant decreases in internode length, plant height, shoot and root biomass, and root length. Furthermore, MsSPL8 mutants displayed improvements in their ability to withstand water-deficit compared to empty vector control genotypes. Taken together, our findings suggest that allelic mutational dosage can elicit phenotypic gradients in alfalfa, and discrepancies may exist in terms of MsSPL8 function between alfalfa genotypes, growth conditions, or specific alleles. In addition, our results provide the foundation for further research exploring drought tolerance mechanisms in a forage crop.

Combined Stress Conditions in Melon Induce Non-additive Effects in the Core miRNA Regulatory Network

Climate change has been associated with a higher incidence of combined adverse environmental conditions that can promote a significant decrease in crop productivity. However, knowledge on how a combination of stresses might affect plant development is still scarce. MicroRNAs (miRNAs) have been proposed as potential targets for improving crop productivity. Here, we have combined deep-sequencing, computational characterization of responsive miRNAs and validation of their regulatory role in a comprehensive analysis of response of melon to several combinations of four stresses (cold, salinity, short day, and infection with a fungus). Twenty-two miRNA families responding to double and/or triple stresses were identified. The regulatory role of the differentially expressed miRNAs was validated by quantitative measurements of the expression of the corresponding target genes. A high proportion (ca. 60%) of these families (mainly highly conserved miRNAs targeting transcription factors) showed a non-additive response to multiple stresses in comparison with that observed under each one of the stresses individually. Among those miRNAs showing non-additive response to stress combinations, most interactions were negative, suggesting the existence of functional convergence in the miRNA-mediated response to combined stresses. Taken together, our results provide compelling pieces of evidence that the response to combined stresses cannot be easily predicted from the study individual stresses.

Genome-Wide Characterization of SPL Gene Family in Codonopsis pilosula Reveals the Functions of CpSPL2 and CpSPL10 in Promoting the Accumulation of Secondary Metabolites and Growth of C. pilosula Hairy Root

SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors play critical roles in regulating diverse aspects of plant growth and development, including vegetative phase change, plant architecture, anthocyanin accumulation, lateral root growth, etc. In the present study, 15 SPL genes were identified based on the genome data of Codonopsis pilosula, a well-known medicinal plant. Phylogenetic analysis clustered CpSPLs into eight groups (G1-G8) along with SPLs from Arabidopsis thaliana, Solanum lycopersicum, Oryza sativa and Physcomitrella patens. CpSPLs in the same group share similar gene structure and conserved motif composition. Cis-acting elements responding to light, stress and phytohormone widely exist in their promoter regions. Our qRT-PCR results indicated that 15 CpSPLs were differentially expressed in different tissues (root, stem, leaf, flower and calyx), different developmental periods (1, 2 and 3 months after germination) and various conditions (NaCl, MeJA and ABA treatment). Compared with the control, overexpression of CpSPL2 or CpSPL10 significantly promoted not only the growth of hairy roots, but also the accumulation of total saponins and lobetyolin. Our results established a foundation for further investigation of CpSPLs and provided novel insights into their biological functions. As far as we know, this is the first experimental research on gene function in C. pilosula.

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.

Comparative analysis of alfalfa (Medicago sativa L.) seedling transcriptomes reveals genotype-specific drought tolerance mechanisms

Drought is one of the main abiotic factors that affect alfalfa yield. The identification of genes that control this complex trait can provide important insights for alfalfa breeding. However, little is known about how alfalfa responds and adapts to drought stress, particularly in cultivars of differing drought tolerance. In this study, the drought-tolerant cultivar Dryland 'DT' and the drought-sensitive cultivar WL343HQ 'DS' were used to characterize leaf and root physiological responses and transcriptional changes in response to water deficit. Under drought stress, Dryland roots (DTR) showed more differentially expressed genes than WL343HQ roots (DSR), whereas WL343HQ leaves (DSL) showed more differentially expressed genes than Dryland leaves (DTL). Many of these genes were involved in stress-related pathways, carbohydrate metabolism, and lignin and wax biosynthesis, which may have improved the drought tolerance of alfalfa. We also observed that several genes related to ABA metabolism, root elongation, peroxidase activity, cell membrane stability, ubiquitination, and genetic processing responded to drought stress in alfalfa. We highlighted several candidate genes, including sucrose synthase, xylan 1,4-beta-xylosidase, primary-amine oxidase, and alcohol-forming fatty acyl-CoA reductase, for future studies on drought stress resistance in alfalfa and other plant species. In summary, our results reveal the unique drought adaptation and resistance characteristics of two alfalfa genotypes. These findings, which may be valuable for drought resistance breeding, warrant further gene functional analysis to augment currently available information and to clarify the drought stress regulatory mechanisms of alfalfa and other plants.

Genome-Wide Characterization and Expression Analysis of the SBP-Box Gene Family in Sweet Orange (Citrus sinensis)

SBP-box is an important plant-specific transcription factor family and is involved in diverse biological processes. Here, we identified a total of 15 SBP-BOX genes in the important fruit crop sweet orange (Citrus sinensis) and characterized their gene structures, conserved domain and motif, chromosomal location, and cis-acting regulatory elements. SBP genes were classified into four subfamilies based on the amino acid sequence homology, and the classification is equally strongly supported by the gene and protein structures. Our analysis revealed that segmental duplication events were the main driving force in the evolution of CsSBP genes, and gene pairs might undergo extensive purifying selection. Further synteny analysis of the SBP members among sweet orange and other plant species provides valuable information for clarifying the CsSBP family evolutionary relationship. According to publicly available RNA-seq data and qRT-PCR analysis from various sweet orange tissues, CsSBP genes may be expressed in different tissues and developmental stages. Gene expression analysis showed variable expression profiles of CsSBP genes under various abiotic stresses, such as high and low-temperature, salt, and wound treatments, demonstrating the potential role of SBP members in sweet orange response to abiotic stress. Noticeably, all CsSBP genes were also downregulated in sweet orange upon the infection of an important fungal pathogen Diaporthe citri. Our results provide valuable information for exploring the role of SBP-Box in sweet orange.

Genome-wide analysis of the Universal stress protein A gene family in Vitis and expression in response to abiotic stress

Universal Stress Protein A (USPA) plays critical roles in the regulation of growth, development and response to abiotic stress in plants. To date, most research related to the role of USPA in plants has been carried out in herbaceous models such as Arabidopsis, rice and soybean. Here, we used bioinformatics approaches to identify 21 USPA genes in the genome of Vitis vinifera L. Phylogenetic analysis revealed that VvUSPAs could be divided into eight clades. Based on predicted chromosomal locations, we identified 16 pairs of syntenic, orthologous genes between A. thaliana and V. vinifera. Further promoter cis-elements analysis, together with identification of potential microRNA (miRNA) binding sites, suggested that at least some of the VvUSPAs participate in response to phytohormones and abiotic stress. To add support for this, we analyzed the developmental and stress-responsive expression patterns of the homologous USPA genes in the drought-resistant wild Vitis yeshanensis accession 'Yanshan-1' and the drought-sensitive Vitis riparia accession 'He'an'. Most of the USPA genes were upregulated in different degrees in the two genotypes after drought stress and exposure to ethephon (ETH), abscisic acid (ABA) and methyl jasmonate (MeJA). Individual USPA genes showed various tissue-specific expression patterns. Heterologous expression of five selected genes (VvUSPA2, VvUSPA3, VvUSPA11, VvUSPA13 and VvUSPA16) in Escherichia coli (E. coli) enhanced resistance to drought stress. Our study provides a model for mapping gene function in response to abiotic stress and identified three candidate genes, VvUSPA3, VvUSPA11 and VvUSPA16, as regulators of drought response in V. vinifera.

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.

Heat-Responsive miRNAs Participate in the Regulation of Male Fertility Stability in Soybean CMS-Based F1 under High Temperature Stress

MicroRNAs (miRNAs), a class of noncoding small RNAs (sRNAs), are widely involved in the response to high temperature (HT) stress at both the seedling and flowering stages. To dissect the roles of miRNAs in regulating male fertility in soybean cytoplasmic male sterility (CMS)-based F1 under HT, sRNA sequencing was performed using flower buds from HT-tolerant and HT-sensitive CMS-based F1 combinations (NF1 and YF1, respectively). A total of 554 known miRNAs, 59 new members of known miRNAs, 712 novel miRNAs, and 1145 target genes of 580 differentially expressed miRNAs (DEMs) were identified under normal temperature and HT conditions. Further integrated analysis of sRNA and transcriptome sequencing found that 21 DEMs and 15 differentially expressed target genes, such as gma-miR397a/Laccase 2, gma-miR399a/Inorganic phosphate transporter 1-4, and gma-miR4413a/PPR proteins, mitochondrial-like, were negatively regulated under HT stress. Furthermore, all members of the gma-miR156 family were suppressed by HT stress in both NF1 and YF1, but were highly expressed in YF1 under HT condition. The negative correlation between gma-miR156b and its target gene squamosa promoter-binding protein-like 2b was confirmed by expression analysis, and overexpression of gma-miR156b in Arabidopsis led to male sterility under HT stress. With these results, we proposed that miRNAs play an important role in the regulation of male fertility stability in soybean CMS-based F1 under HT stress.

Involvement of the miR156/SPL module in flooding response in Medicago sativa

The highly conserved plant microRNA, miR156, affects plant development, metabolite composition, and stress response. Our previous research revealed the role of miR156 in abiotic stress response in Medicago sativa exerted by downregulating SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE transcription factors. Here we investigated the involvement and possible mechanism of action of the miR156/SPL module in flooding tolerance in alfalfa. For that, we used miR156 overexpressing, SPL13RNAi, flood-tolerant (AAC-Trueman) and -sensitive (AC-Caribou) alfalfa cultivars exposed to flooding. We also used Arabidopsis ABA insensitive (abi1-2, abi5-8) mutants and transgenic lines with either overexpressed (KIN10-OX1, KIN10-OX2) or silenced (KIN10RNAi-1, KIN10RNAi-2) catalytic subunit of SnRK1 to investigate a possible role of ABA and SnRK1 in regulating miR156 expression under flooding. Physiological analysis, hormone profiling and global transcriptome changes revealed a role for miR156/SPL module in flooding tolerance. We also identified nine novel alfalfa SPLs (SPL1, SPL1a, SPL2a, SPL7, SPL7a, SPL8, SPL13a, SPL14, SPL16) responsive to flooding. Our results also showed a possible ABA-dependent SnRK1 upregulation to enhance miR156 expression, resulting in downregulation of SPL4, SPL7a, SPL8, SPL9, SPL13, and SPL13a. We conclude that these effects induce flooding adaptive responses in alfalfa and modulate stress physiology by affecting the transcriptome, ABA metabolites and secondary metabolism.

The miR156/SPL module regulates apple salt stress tolerance by activating MdWRKY100 expression

Salt stress dramatically impedes plant growth and development as well as crop yield. The apple production regions are reduced every year, because of the secondary salt damage by improper fertilization and irrigation. To expand the cultivation area of apple (Malus domestica) and select salt-resistant varieties, the mechanism of salt tolerance in apple is necessary to be clarified. The miR156/SPL regulatory module plays key roles in embryogenesis, morphogenesis, life cycle stage transformation, flower formation and other processes. However, its roles in the mechanisms of salt tolerance are unknown. In order to elucidate the mechanism of 156/SPL regulating salt stress in apple, we performed RLM-5' RACE and stable genetic transformation technology to verify that both mdm-MIR156a and MdSPL13 responded to salt stress in apple and that the latter was the target of the former. MIR156a overexpression weakened salt resistance in apple whereas MdSPL13 overexpression strengthened it. A total of 6094 differentially expressed genes relative to nontransgenic apple plants were found by RNA-Seq analysis of MdSPL13OE. Further verification indicated that MdSPL13 targeted the MdWRKY100 gene promoter. Moreover, MdWRKY100 overexpression enhanced salt tolerance in apple. Our results revealed that the miR156/SPL module regulates salt tolerance by up-regulating MdWRKY100 in apple. This study is the first to elucidate the mechanism underlying the miRNA network response to salt stress in apple and provides theoretical and empirical bases and genetic resources for the molecular breeding of salt tolerance in apple.

Label-free quantitative proteomic analysis of alfalfa in response to microRNA156 under high temperature

BACKGROUND

Abiotic stress, including heat, is one of the major factors that affect alfalfa growth and forage yield. The small RNA, microRNA156 (miR156), regulates multiple traits in alfalfa during abiotic stress. The aim of this study was to explore the role of miR156 in regulating heat response in alfalfa at the protein level.

RESULTS

In this study, we compared an empty vector control and miR156 overexpressing (miR156OE) alfalfa plants after exposing them to heat stress (40 °C) for 24 h. We measured physiological parameters of control and miR156OE plants under heat stress, and collected leaf samples for protein analysis. A higher proline and antioxidant contents were detected in miR156OE plants than in controls under heat stress. Protein samples were analyzed by label-free quantification proteomics. Across all samples, a total of 1878 protein groups were detected. Under heat stress, 45 protein groups in the empty vector plants were significantly altered (P < 0.05; |log2FC| > 2). Conversely, 105 protein groups were significantly altered when miR156OE alfalfa was subjected to heat stress, of which 91 were unique to miR156OE plants. The identified protein groups unique to miR156OE plants were related to diverse functions including metabolism, photosynthesis, stress-response and plant defenses. Furthermore, we identified transcription factors in miR156OE plants, which belonged to squamosa promoter binding-like protein, MYB, ethylene responsive factors, AP2 domain, ABA response element binding factor and bZIP families of transcription factors.

CONCLUSIONS

These results suggest a positive role for miR156 in heat stress response in alfalfa. They reveal a miR156-regulated network of mechanisms at the protein level to modulate heat responses in alfalfa.

Transcriptome-IPMS analysis reveals a tissue-dependent miR156/SPL13 regulatory mechanism in alfalfa drought tolerance

Background

We previously reported on the interplay between miR156/SPL13 and WD40–1/DFR to improve response to drought stress in alfalfa (Medicago sativa L.). Here we aimed to investigate whether the role of miR156/SPL13 module in drought response is tissue-specific, and to identify SPL13-interacting proteins. We analyzed the global transcript profiles of leaf, stem, and root tissues of one-month old RNAi-silenced SPL13 (SPL13RNAi) alfalfa plants exposed to drought stress and conducted protein-protein interaction analysis to identify SPL13 interacting partners.

Result

Transcript analysis combined with weighted gene co-expression network analysis showed tissue and genotype-specific gene expression patterns. Moreover, pathway analysis of stem-derived differentially expressed genes (DEG) revealed upregulation of genes associated with stress mitigating primary and specialized metabolites, whereas genes associated with photosynthesis light reactions were silenced in SPL13RNAi plants. Leaf-derived DEG were attributed to enhanced light reactions, largely photosystem I, II, and electron transport chains, while roots of SPL13RNAi plants upregulated transcripts associated with metal ion transport, carbohydrate, and primary metabolism. Using immunoprecipitation combined with mass spectrometry (IPMS) we showed that SPL13 interacts with proteins involved in photosynthesis, specialized metabolite biosynthesis, and stress tolerance.

Conclusions

We conclude that the miR156/SPL13 module mitigates drought stress in alfalfa by regulating molecular and physiological processes in a tissue-dependent manner.

Tobacco NtabSPL6-2 can enhance local and systemic resistances of Arabidopsis thaliana to bacterial and fungal pathogens

NtabSPL6-2 of Nicotiana tabacum was introduced into Arabidopsis by Agrobacterium-mediated floral-dip method. Compared to wild-type Col-0 plants, the arrangement of cauline leaves in NtabSPL6-2 transgenic plants was converted into opposite from simple and alternate, and the margin of rosette leaves was serrated. NtabSPL6-2 transgenic plants possessed a significantly greater fresh weight. Subcellular localization by fusion with GFP confirmed that the encoded product of NtabSPL6-2 existed in the nucleus. The leaves of NtabSPL6-2 transgenic plants exhibited an enhanced capacity to restrain the bacterial reproduction after infection by Pseudomonas syringae, accompanied by higher expression of the pathogenesis-related gene PR1 in the infiltrated leaves, indicating NtabSPL6-2 could improve the defense response of Arabidopsis to P. syringae at the local sites. Similarly, it was confirmed that NtabSPL6-2 could enhance the systemic acquired resistance of Arabidopsis in response to P. syringae. In addition, the area of necrotic plaque appearing on the transgenic leaves inoculated with Botrytis cinerea was smaller and accompanied by an upregulation of PR1 and PR5, indicating NtabSPL6-2 transgenic leaves were less susceptible to the fungal pathogen. Moreover, there was less accumulation of reactive oxygen species (H2O2 and O2-) and malondialdehyde in the local infected sites of transgenic plants, whereas the wild-type Col-0 plants were more oxidatively injured after infestation by B. cinerea.

Characterization of the Role of SPL9 in Drought Stress Tolerance in Medicago sativa

Extreme environmental conditions, such as drought, are expected to increase in frequency and severity due to climate change, leading to substantial deficiencies in crop yield and quality. Medicago sativa (alfalfa) is an important crop that is relied upon as a staple source of forage in ruminant feed. Despite its economic importance, alfalfa production is constrained by abiotic stress, including drought. In this report, we investigate the role of Squamosa Promoter Binding Protein-Like 9 (SPL9), a target of miR156, in drought tolerance. Transgenic alfalfa plants with RNAi-silenced MsSPL9 (SPL9-RNAi) were compared to wild-type (WT) alfalfa for phenotypic changes and drought tolerance indicators. In SPL9-RNAi plants, both stem thickness and plant height were reduced in two- and six-month-old alfalfa, respectively; however, yield was unaffected. SPL9-RNAi plants showed less leaf senescence and had augmented relative water content under drought conditions, indicating that SPL9-RNAi plants had greater drought tolerance potential than WT plants. Interestingly, SPL9-RNAi plants accumulated more stress-alleviating anthocyanin compared to WT under both drought and well-watered control conditions, suggesting that MsSPL9 may contribute to drought tolerance in alfalfa, at least in part, by regulating anthocyanin biosynthesis. The results suggest that targeting MsSPL9 is a suitable means for improving alfalfa resilience towards drought conditions.

Biotechnological Perspectives of Omics and Genetic Engineering Methods in Alfalfa

For several decades, researchers are working to develop improved major crops with better adaptability and tolerance to environmental stresses. Forage legumes have been widely spread in the world due to their great ecological and economic values. Abiotic and biotic stresses are main factors limiting legume production, however, alfalfa (Medicago sativa L.) shows relatively high level of tolerance to drought and salt stress. Efforts focused on alfalfa improvements have led to the release of cultivars with new traits of agronomic importance such as high yield, better stress tolerance or forage quality. Alfalfa has very high nutritional value due to its efficient symbiotic association with nitrogen-fixing bacteria, while deep root system can help to prevent soil water loss in dry lands. The use of modern biotechnology tools is challenging in alfalfa since full genome, unlike to its close relative barrel medic (Medicago truncatula Gaertn.), was not released yet. Identification, isolation, and improvement of genes involved in abiotic or biotic stress response significantly contributed to the progress of our understanding how crop plants cope with these environmental challenges. In this review, we provide an overview of the progress that has been made in high-throughput sequencing, characterization of genes for abiotic or biotic stress tolerance, gene editing, as well as proteomic and metabolomics techniques bearing biotechnological potential for alfalfa improvement.

Dynamic architecture and regulatory implications of the miRNA network underlying the response to stress in melon

miRNAs are small RNAs that regulate mRNAs at both transcriptional and posttranscriptional level. In plants, miRNAs are involved in the regulation of different processes including development and stress-response. Elucidating how stress-responsive miRNAs are regulated is key to understand the global response to stress but also to develop efficient biotechnological tools that could help to cope with stress. Here, we describe a computational approach based on sRNA sequencing, transcript quantification and degradome data to analyse the accumulation, function and structural organization of melon miRNAs reactivated under seven biotic and abiotic stress conditions at two and four days post-treatment. Our pipeline allowed us to identify fourteen stress-responsive miRNAs (including evolutionary conserved such as miR156, miR166, miR172, miR319, miR398, miR399, miR894 and miR408) at both analysed times. According to our analysis miRNAs were categorized in three groups showing a broad-, intermediate- or narrow- response range. miRNAs reactive to a broad range of environmental cues appear as central components in the stress-response network. The strictly coordinated response of miR398 and miR408 (broad response-range) to the seven stress treatments during the period analysed here reinforces this notion. Although both, the amplitude and diversity of the miRNA-related response to stress changes during the exposition time, the architecture of the miRNA-network is conserved. This organization of miRNA response to stress is also conserved in rice and soybean supporting the conservation of miRNA-network organization in other crops. Overall, our work sheds light into how miRNA networks in plants organize and function during stress.

The interplay between miR156/SPL13 and DFR/WD40-1 regulate drought tolerance in alfalfa

BACKGROUND

Developing Medicago sativa L. (alfalfa) cultivars tolerant to drought is critical for the crop's sustainable production. miR156 regulates various plant biological functions by silencing SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors.

RESULTS

To understand the mechanism of miR156-modulated drought stress tolerance in alfalfa we used genotypes with altered expression levels of miR156, miR156-regulated SPL13, and DIHYDROFLAVONOL-4-REDUCTASE (DFR) regulating WD40-1. Previously we reported the involvement of miR156 in drought tolerance, but the mechanism and downstream genes involved in this process were not fully studied. Here we illustrate the interplay between miR156/SPL13 and WD40-1/DFR to regulate drought stress by coordinating gene expression with metabolite and physiological strategies. Low to moderate levels of miR156 overexpression suppressed SPL13 and increased WD40-1 to fine-tune DFR expression for enhanced anthocyanin biosynthesis. This, in combination with other accumulated stress mitigating metabolites and physiological responses, improved drought tolerance. We also demonstrated that SPL13 binds in vivo to the DFR promoter to regulate its expression.

CONCLUSIONS

Taken together, our results reveal that moderate relative miR156 transcript levels are sufficient to enhance drought resilience in alfalfa by silencing SPL13 and increasing WD40-1 expression, whereas higher miR156 overexpression results in drought susceptibility.

Harnessing the Potential of Forage Legumes, Alfalfa, Soybean, and Cowpea for Sustainable Agriculture and Global Food Security

Substantial improvements in access to food and increased purchasing power are driving many people toward consuming nutrition-rich foods causing an unprecedented demand for protein food worldwide, which is expected to rise further. Forage legumes form an important source of feed for livestock and have potential to provide a sustainable solution for food and protein security. Currently, alfalfa is a commercially grown source of forage and feed in many countries. However, soybean and cowpea also have the potential to provide quality forage and fodder for animal use. The cultivation of forage legumes is under threat from changing climatic conditions, indicating the need for breeding cultivars that can sustain and acclimatize to the negative effects of climate change. Recent progress in genetic and genomic tools have facilitated the identification of quantitative trait loci and genes/alleles that can aid in developing forage cultivars through genomics-assisted breeding. Furthermore, transgenic technology can be utilized to manipulate the genetic makeup of plants to improve forage digestibility for better animal performance. In this article, we assess the genetic potential of three important legume crops, alfalfa, soybean, and cowpea in supplying quality fodder and feed for livestock. In addition, we examine the impact of climate change on forage quality and discuss efforts made in enhancing the adaptation of the plant to the abiotic stress conditions. Subsequently, we suggest the application of integrative approaches to achieve adequate forage production amid the unpredictable climatic conditions.