AtMYB12 regulates flavonoids accumulation and abiotic stress tolerance in transgenic Arabidopsis thaliana

Integrative Analysis of the Transcriptome and Metabolome Reveals the Mechanism of Saline–Alkali Stress Tolerance in Astragalus membranaceus (Fisch) Bge. var. mongholicus (Bge.) Hsiao

Saline–alkali stress is a major abiotic stress affecting the quality and yield of crops. Astragalus membranaceus (Fisch) Bge. var. mongholicus (Bge.) Hsiao (A. mongholicus) is a well-known medicine food homology species with various pharmacological effects and health benefits that can grow well in saline–alkali soil. However, the molecular mechanisms underlying the adaptation of A. mongholicus plants to saline–alkali stress have not yet been clarified. Here, A. mongholicus plants were exposed to long-term saline–alkali stress (200 mmol·L -1 mixed saline–alkali solution), which limited the growth of A. mongholicus. The roots of A. mongholicus could resist long-term saline–alkali stress by increasing the activity of antioxidant enzymes and the content of osmolytes. Transcriptome analysis (via the Illumina platform) and metabolome analysis (via the Nexera UPLC Series QE Liquid Mass Coupling System) revealed that saline–alkali stress altered the activity of various metabolic pathways (e.g., amino acid metabolism, carbohydrate metabolism, lipid metabolism, and biosynthesis of other secondary metabolites). A total of 3,690 differentially expressed genes (DEGs) and 997 differentially accumulated metabolites (DAMs) were identified in A. mongholicus roots under saline–alkali stress, and flavonoid-related DEGs and DAMs were significantly up-regulated. Pearson correlation analysis revealed significant correlations between DEGs and DAMs related to flavonoid metabolism. MYB transcription factors might also contribute to the regulation of flavonoid biosynthesis. Overall, the results indicate that A. mongholicus plants adapt to saline–alkali stress by up-regulating the biosynthesis of flavonoids, which enhances the medicinal value of A. mongholicus.

Transcriptome Analysis Reveals Differentially Expressed Genes That Regulate Biosynthesis of the Active Compounds with Methyl Jasmonate in Rosemary Suspension Cells

To study the effects of Methyl jasmonates (MeJA) on rosemary suspension cells, the antioxidant enzymes’ change of activities under different concentrations of MeJA, including 0 (CK), 10 (M10), 50 (M50) and 100 μM MeJA (M100). The results demonstrated that MeJA treatments increased the activities of phenylalanine ammonla-lyase (PAL), superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and polyphenol oxidase (PPO) and reduced the contents of hydrogen peroxide (H₂O₂) and malondialdehyde (MDA), thus accelerating the ROS scavenging. Comparative transcriptome analysis of different concentrations of MeJA showed that a total of 7836, 6797 and 8310 genes were differentially expressed in the comparisons of CKvsM10, CKvsM50, CKvsM100, respectively. The analysis of differentially expressed genes (DEGs) showed phenylpropanoid biosynthesis, vitamin B6, ascorbate and aldarate metabolism-related genes were significantly enriched. The transcripts of flavonoid and terpenoid metabolism pathways and plant hormone signal transduction, especially the jasmonic acid (JA) signal-related genes, were differentially expressed in CKvsM50 and CKvsM100 comparisons. In addition, the transcription factors (TFs), e.g., MYC2, DELLA, MYB111 played a key role in rosemary suspension cells under MeJA treatments. qRT-PCR of eleven DEGs showed a high correlation between the RNA-seq and the qRT-PCR result. Taken together, MeJA alleviated peroxidative damage of the rosemary suspension cells in a wide concentration range via concentration-dependent differential expression patterns. This study provided a transcriptome sequence resource responding to MeJA and a valuable resource for the genetic and genomic studies of the active compounds engineering in rosemary.

Cross-Tolerance and Autoimmunity as Missing Links in Abiotic and Biotic Stress Responses in Plants: A Perspective toward Secondary Metabolic Engineering

Plants employ a diversified array of defense activities when they encounter stress. Continuous activation of defense pathways that were induced by mutation or altered expression of disease resistance genes and mRNA surveillance mechanisms develop abnormal phenotypes. These plants show continuous defense genes' expression, reduced growth, and also manifest tissue damage by apoptosis. These macroscopic abrasions appear even in the absence of the pathogen and can be attributed to a condition known as autoimmunity. The question is whether it is possible to develop an autoimmune mutant that does not fetch yield and growth penalty and provides enhanced protection against various biotic and abiotic stresses via secondary metabolic pathways' engineering. This review is a discussion about the common stress-fighting mechanisms, how the concept of cross-tolerance instigates propitious or protective autoimmunity, and how it can be achieved by engineering secondary metabolic pathways.

Epigenetic and transcriptional responses underlying mangrove adaptation to UV-B

Tropical plants have adapted to strong solar ultraviolet (UV) radiation. Here we compare molecular responses of two tropical mangroves Avecennia marina and Rhizophora apiculata to high-dose UV-B. Whole-genome bisulfate sequencing indicates that high UV-B induced comparable hyper- or hypo-methylation in three sequence contexts (CG, CHG, and CHH, where H refers to A, T, or C) in A. marina but mainly CHG hypomethylation in R. apiculata. RNA and small RNA sequencing reveals UV-B induced relaxation of transposable element (TE) silencing together with up-regulation of TE-adjacent genes in R. apiculata but not in A. marina. Despite conserved upregulation of flavonoid biosynthesis and downregulation of photosynthesis genes caused by high UV-B, A. marina specifically upregulated ABC transporter and ubiquinone biosynthesis genes that are known to be protective against UV-B-induced damage. Our results point to divergent responses underlying plant UV-B adaptation at both the epigenetic and transcriptional level.

Primary Bitter Taste of Citrus is Linked to a Functional Allele of the 1,2-Rhamnosyltransferase Gene Originating from Citrus grandis

1,2-Rhamnosyltransferase (1,2RhaT) catalyzes the final step of production of flavanone neohesperidoside (FNH) that is responsible for the primary bitter taste of citrus fruits. In this study, species-specific flavonoid profiles were determined in 87 Citrus accessions by identifying eight main flavanone glycosides (FGs). Accumulation of FNHs was completely correlated to the presence of the 1,2RhaT gene in 87 citrus accessions analyzed using a novel 1,2RhaT-specific DNA marker. Pummelo (Citrus grandis) was identified as the genetic origin for a function allele of 1,2RhaT that underpinned FNH-bitterness in modern citrus cultivars. In addition, genes encoding six MYB and five bHLH transcription factors were shown to coexpress with 1,2RhaT and other flavonoid pathway genes related to FNH accumulation, indicating that these transcription factors may affect the fruit taste of citrus. This study provides a better understanding of bitterness formation in Citrus varieties and a genetic marker for the early selection of nonbitterness lines in citrus breeding programs.

Integrated Metabolomic and Transcriptomic Analysis Reveals the Flavonoid Regulatory Network by Eutrema EsMYB90

Flavonoids are representative secondary metabolites with different metabolic functions in plants. Previous study found that ectopic expression of EsMYB90 from Eutremasalsugineum could strongly increase anthocyanin content in transgenic tobacco via regulating the expression of anthocyanin biosynthesis genes. In the present research, metabolome analysis showed that there existed 130 significantly differential metabolites, of which 23 metabolites enhanced more than 1000 times in EsMYB90 transgenic tobacco leaves relative to the control, and the top 10 of the increased metabolites included caffeic acid, cyanidin O-syringic acid, myricetin and naringin. A total of 50 markedly differential flavonoids including flavones (14), flavonols (13), flavone C-glycosides (9), flavanones (7), catechin derivatives (5), anthocyanins (1) and isoflavone (1) were identified, of which 46 metabolites were at a significantly enhanced level. Integrated analysis of metabolome and transcriptome revealed that ectopic expression of EsMYB90 in transgenic tobacco leaves is highly associated with the prominent up-regulation of 16 flavonoid metabolites and the corresponding 42 flavonoid biosynthesis structure genes in phenylpropanoid/flavonoid pathways. Dual luciferase assay documented that EsMYB90 strongly activated the transcription of NtANS and NtDFR genes via improving their promoter activity in transiently expressed tobacco leaves, suggesting that EsMYB90 functions as a key regulator on anthocyanin and flavonoid biosynthesis. Taken together, the crucial regulatory role of EsMYB90 on enhancing many flavonoid metabolite levels is clearly demonstrated via modulating flavonoid biosynthesis gene expression in the leaves of transgenic tobacco, which extends our understanding of the regulating mechanism of MYB transcription factor in the phenylpropanoid/flavonoid pathways and provides a new clue and tool for further investigation and genetic engineering of flavonoid metabolism in plants.

Metabolome profiling and molecular docking analysis revealed the metabolic differences and potential pharmacological mechanisms of the inflorescence and succulent stem of Cistanche deserticola

Cistanche deserticola is an endangered plant used for medicine and food. Our purpose is to explore the differences in metabolism between inflorescences in non-medicinal parts and succulent stems in medicinal parts in order to strengthen the application and development of the non-medicinal parts of C. deserticola. We performed metabolomics analysis through LC-ESI-MS/MS on the inflorescences and succulent stems of three ecotypes (saline-alkali land, grassland and sandy land) of C. deserticola. A total of 391 common metabolites in six groups were identified, of which isorhamnetin O-hexoside (inflorescence) and rosinidin O-hexoside (succulent stems) can be used as chemical markers to distinguish succulent stems and inflorescences. Comparing the metabolic differences of three ecotypes, we found that most of the different metabolites related to salt-alkali stress were flavonoids. In particular, we mapped the biosynthetic pathway of phenylethanoid glycosides (PhGs) and showed the metabolic differences in the six groups. To better understand the pharmacodynamic mechanisms and targets of C. deserticola, we screened 88 chemical components and 15 potential disease targets through molecular docking. The active ingredients of C. deserticola have a remarkable docking effect on the targets of aging diseases such as osteoporosis, vascular disease and atherosclerosis. To explore the use value of inflorescence, we analyzed the molecular docking of the unique flavonoid metabolites in inflorescence with inflammation targets. The results showed that chrysoeriol and cynaroside had higher scores for inflammation targets. This study provides a scientific basis for the discovery and industrialization of the resource value of the non-medicinal parts of C. deserticola, and the realization of the sustainable development of C. deserticola. It also provides a novel strategy for exploring indications of Chinese herb.

Flow chart for exploring the metabolic and pharmacological characteristics of different parts of Cistanche deserticola.

EkFLS overexpression promotes flavonoid accumulation and abiotic stress tolerance in plant

Flavonoids with great medicinal value play an important role in plant individual growth and stress resistance. Flavonol synthetase (FLS) is one of the key enzymes to synthesize flavonoids. However, the role of the FLS gene in flavonoid accumulation and tolerance to abiotic stresses, as well as its mechanism has not yet been investigated systematically in plants. The aim of this research is to evaluate the effect of FLS overexpression on the accumulation of active ingredients and stress resistance in Euphorbia kansui Liou. The results showed that when the EkFLS gene was overexpressed in Arabidopsis thaliana, the accumulation of flavonoids was improved. In addition, when the wild-type and EkFLS overexpressed Arabidopsis plants were treated with ABA and MeJA, compared with WT Arabidopsis, EkFLS overexpressed Arabidopsis promoted stomatal aperture to influence photosynthesis of the plants, which in turn can promote stress resistance. Meanwhile, under MeJA, NaCl, and PEG treatment, EkFLS overexpressed in Arabidopsis induced higher accumulation of flavonoids, which significantly enhanced peroxidase (POD) and superoxide dismutase (SOD) activities that can scavenge reactive oxygen species in cells to protect the plant. These results indicated that EkFLS overexpression is strongly correlated to the increase of flavonoid synthesis and therefore the tolerance to abiotic stresses in plants, providing a theoretical basis for further improving the quality of medicinal plants and their resistance to abiotic stresses simultaneously.

Abiotic stress-induced anthocyanins in plants: Their role in tolerance to abiotic stresses

Abiotic stresses, such as heat, drought, salinity, low temperature, and heavy metals, inhibit plant growth and reduce crop productivity. Abiotic stresses are becoming increasingly extreme worldwide due to the ongoing deterioration of the global climate and the increase in agrochemical utilization and industrialization. Plants grown in fields are affected by one or more abiotic stresses. The consequent stress response of plants induces reactive oxygen species (ROS), which are then used as signaling molecules to activate stress-tolerance mechanism. However, under extreme stress conditions, ROS are overproduced and cause oxidative damage to plants. In such conditions, plants produce anthocyanins after ROS signaling via the transcription of anthocyanin biosynthesis genes. These anthocyanins are then utilized in antioxidant activities by scavenging excess ROS for their sustainability. In this review, we discuss the physiological, biochemical, and molecular mechanisms underlying abiotic stress-induced anthocyanins in plants and their role in abiotic stress tolerance. In addition, we highlight the current progress in the development of anthocyanin-enriched transgenic plants and their ability to increase abiotic stress tolerance. Overall, this review provides valuable information that increases our understanding of the mechanisms by which anthocyanins respond to abiotic stress and protect plants against it. This review also provides practical guidance for plant biologists who are engineering stress-tolerant crops using anthocyanin biosynthesis or regulatory genes.

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.

Comprehensive RNA-seq analysis revealed molecular pathways and genes associated with drought tolerance in wild soybean (Glycine soja Sieb. and Zucc.)

Drought stress at the germination stage is an important environmental stress limiting crop yield. Hence, our study investigated comparative root transcriptome profiles of four contrasting soybean genotypes viz., drought-tolerant (PI342618B/DTP and A214/DTL) and drought-sensitive (NN86-4/DSP and A195/DSL) under drought stress using RNA-Seq approach. A total of 4850 and 6272 differentially expressed genes (DEGs) were identified in tolerant (DTP and DTL) and sensitive (DSP and DSL) genotypes, respectively. Principle component analysis (PCA) and correlation analysis revealed higher correlation between DTP and DTL. Both gene ontology (GO) and MapMan analyses showed that the drought response was enriched in DEGs associated with water and auxin transport, cell wall/membrane, antioxidant activity, catalytic activity, secondary metabolism, signaling and transcription factor (TF) activities. Out of 981 DEGs screened from above terms, only 547 showed consistent opposite expression between contrasting genotypes. Twenty-eight DEGs of 547 were located on Chr.08 rich in QTLs and "Hotspot regions" associated with drought stress, and eight of them showed non-synonymous single nucleotide polymorphism. Hence, 10 genes (including above eight genes plus two hub genes) were predicated as possible candidates regulating drought tolerance, which needs further functional validation. Overall, the transcriptome profiling provided in-depth understanding about the genetic mechanism and candidate genes underlying drought tolerance in soybean.

Drought Resistance in Qingke Involves a Reprogramming of the Phenylpropanoid Pathway and UDP-Glucosyltransferase Regulation of Abiotic Stress Tolerance Targeting Flavonoid Biosynthesis

Tibetan hulless barley (qingke) is an important food crop in the Tibetan plateau. However, it often suffers from drought stress resulting in reduction of food production because of the extreme plateau environment. To elucidate the molecular mechanisms underlying the drought resistance of qingke, the transcriptomic and metabolomic responses of drought-sensitive (D) and drought-resistant (XL) accessions were characterized in experiments with a time course design. The phenylpropanoid pathway was reprogrammed by downregulating the lignin pathway and increasing the biosynthesis of flavonoids and anthocyanins, and this regulation improved plant tolerance for drought stress. Besides, flavonoid glycosides have induced accumulation of metabolites that participated in drought stress resistance. HVUL7H11410 exhibited the activity of wide-spectrum glucosyltransferase and mediated flavonoid glycosylation to enhance drought stress resistance. Overall, the findings provide insights into the regulatory mechanism underlying drought stress tolerance associated with metabolic reprogramming. Furthermore, the flavonoid-enriched qingke is more tolerant to drought stress and can be used as a functional food to benefit human health.

Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color

The cloning of agriculturally important genes is often complicated by haplotype variation across crop cultivars. Access to pan-genome information greatly facilitates the assessment of structural variations and rapid candidate gene identification. Here, we identified the red glume 1 (Rg-B1) gene using association genetics and haplotype analyses in ten reference grade wheat genomes. Glume color is an important trait to characterize wheat cultivars. Red glumes are frequent among Central European spelt, a dominant wheat subspecies in Europe before the 20th century. We used genotyping-by-sequencing to characterize a global diversity panel of 267 spelt accessions, which provided evidence for two independent introductions of spelt into Europe. A single region at the Rg-B1 locus on chromosome 1BS was associated with glume color in the diversity panel. Haplotype comparisons across ten high-quality wheat genomes revealed a MYB transcription factor as candidate gene. We found extensive haplotype variation across the ten cultivars, with a particular group of MYB alleles that was conserved in red glume wheat cultivars. Genetic mapping and transient infiltration experiments allowed us to validate this particular MYB transcription factor variants. Our study demonstrates the value of multiple high-quality genomes to rapidly resolve copy number and haplotype variations in regions controlling agriculturally important traits.

NtMYB12a acts downstream of sucrose to inhibit fatty acid accumulation by targeting lipoxygenase and SFAR genes in tobacco

MYB12 promotes flavonol biosynthesis in plants by targeting several early biosynthesis genes (EBGs) of this pathway. The transcriptions of these EBGs are also induced by sucrose signal. However, whether MYB12 is activated by sucrose signal and what the other roles MYB12 has in regulating plant metabolism are poorly understood. In this study, two NtMYB12 genes were cloned from Nicotiana tabacum. Both NtMYB12a and NtMYB12b are involved in regulating flavonoids biosynthesis in tobacco. NtMYB12a is further shown to inhibit the accumulation of fatty acid (FA) in tobacco leaves and seeds. Post-translational activation and chromatin immunoprecipitation assays demonstrate that NtMYB12a directly promotes the transcriptions of NtLOX6, NtLOX5, NtSFAR4 and NtGDSL2, which encode lipoxygenase (LOX) or SFAR enzymes catalyzing the degradation of FA. NtLOX6 and NtLOX5 are shown to prevent the accumulation of FA in the mature seeds and significantly reduced the percentage of polyunsaturated fatty acids (PUFAs) in tobacco. Sucrose stimulates the transcription of NtMYB12a, and loss function of NtMYB12a partially suppresses the decrease of FA content in tobacco seedlings caused by sucrose treatment. The regulation of sucrose on the expression of NtLOX6 and NtGDSL2 genes is mediated by NtMYB12a, whereas those of NtLOX5 and NtSFAR4 genes are independent of sucrose.

RNA-seq analysis reveals different drought tolerance mechanisms in two broadly adapted wheat cultivars 'TAM 111' and 'TAM 112'

Wheat cultivars 'TAM 111' and 'TAM 112' have been dominantly grown in the Southern U.S. Great Plains for many years due to their high yield and drought tolerance. To identify the molecular basis and genetic control of drought tolerance in these two landmark cultivars, RNA-seq analysis was conducted to compare gene expression difference in flag leaves under fully irrigated (wet) and water deficient (dry) conditions. A total of 2254 genes showed significantly altered expression patterns under dry and wet conditions in the two cultivars. TAM 111 had 593 and 1532 dry-wet differentially expressed genes (DEGs), and TAM 112 had 777 and 1670 at heading and grain-filling stages, respectively. The two cultivars have 1214 (53.9%) dry-wet DEGs in common, which agreed with their excellent adaption to drought, but 438 and 602 dry-wet DEGs were respectively shown only in TAM 111 and TAM 112 suggested that each has a specific mechanism to cope with drought. Annotations of all 2254 genes showed 1855 have functions related to biosynthesis, stress responses, defense responses, transcription factors and cellular components related to ion or protein transportation and signal transduction. Comparing hierarchical structure of biological processes, molecule functions and cellular components revealed the significant regulation differences between TAM 111 and TAM 112, particularly for genes of phosphorylation and adenyl ribonucleotide binding, and proteins located in nucleus and plasma membrane. TAM 112 showed more active than TAM 111 in response to drought and carried more specific genes with most of them were up-regulated in responses to stresses of water deprivation, heat and oxidative, ABA-induced signal pathway and transcription regulation. In addition, 258 genes encoding predicted uncharacterized proteins and 141 unannotated genes with no similar sequences identified in the databases may represent novel genes related to drought response in TAM 111 or TAM 112. This research thus revealed different drought-tolerance mechanisms in TAM 111 and TAM 112 and identified useful drought tolerance genes for wheat adaption. Data of gene sequence and expression regulation from this study also provided useful information of annotating novel genes associated with drought tolerance in the wheat genome.

Metabolomics Intervention Towards Better Understanding of Plant Traits

The majority of the most economically important plant and crop species are enriched with the availability of high-quality reference genome sequences forming the basis of gene discovery which control the important biochemical pathways. The transcriptomics and proteomics resources have also been made available for many of these plant species that intensify the understanding at expression levels. However, still we lack integrated studies spanning genomics–transcriptomics–proteomics, connected to metabolomics, the most complicated phase in phenotype expression. Nevertheless, for the past few decades, emphasis has been more on metabolome which plays a crucial role in defining the phenotype (trait) during crop improvement. The emergence of modern high throughput metabolome analyzing platforms have accelerated the discovery of a wide variety of biochemical types of metabolites and new pathways, also helped in improving the understanding of known existing pathways. Pinpointing the causal gene(s) and elucidation of metabolic pathways are very important for development of improved lines with high precision in crop breeding. Along with other-omics sciences, metabolomics studies have helped in characterization and annotation of a new gene(s) function. Hereby, we summarize several areas in the field of crop development where metabolomics studies have made its remarkable impact. We also assess the recent research on metabolomics, together with other omics, contributing toward genetic engineering to target traits and key pathway(s).

SlMYB14 promotes flavonoids accumulation and confers higher tolerance to 2,4,6-trichlorophenol in tomato

Flavonoids are small molecular secondary metabolites, which have a variety of biological functions. Transcriptional regulations of key enzyme genes play critical roles in the flavonoid biosynthesis. In this study, an R2R3-MYB transcription factor gene, SlMYB14, was isolated from tomato and characterized. The nucleus-localized SlMYB14 functions as a transcriptional activator in yeast. The expression of SlMYB14 could be induced by methyl jasmonic acid, wounding and ABA. SlMYB14 works downstream of SlMYC2 in the jasmonate signaling pathway. Overexpression of SlMYB14 under the control of CaMV35S promoter in tomato led to increased accumulation of flavonoids. RNA-sequencing analysis revealed that the transcript levels of several structural genes associated with flavonoid biosynthesis were up-regulated in transgenic tomato plants. Gel-shift assays confirmed that SlMYB14 protein could bind to the promoter regions of SlPAL genes. It was also found that overexpression of SlMYB14 improved the tolerance of transgenic plants to 2,4,6-trichlorophenol (2,4,6-TCP), an environmental organic pollutant which could cause serious oxidative damage to plant. These results suggest that SlMYB14 participates in the regulation of flavonoid biosynthesis and might play a role in maintaining reactive oxygen species homeostasis in plant. SlMYB14 gene also has the potential to contribute to the phytoremediation of 2,4,6-TCP-contaminated soils.

OsIAA18, an Aux/IAA Transcription Factor Gene, Is Involved in Salt and Drought Tolerance in Rice

Auxin/indoleacetic acid (Aux/IAA) proteins play an important regulatory role in the developmental process of plants and their responses to stresses. A previous study has shown that constitutive expression of OsIAA18, an Aux/IAA transcription factor gene of rice improved salt and osmotic tolerance in transgenic Arabidopsis plants. However, little work is known about the regulatory functions of the OsIAA18 gene in regulating the abiotic stress tolerance of rice. In this study, the OsIAA18 gene was introduced into the rice cultivar, Zhonghua 11 and the OsIAA18 overexpression in rice plants exhibited significantly enhanced salt and drought tolerance compared to the wild type (WT). Moreover, overexpression of OsIAA18 in rice increased endogenous levels of abscisic acid (ABA) and the overexpression of OsIAA18 in rice plants showed hypersensitivity to exogenous ABA treatment at both the germination and postgermination stages compared to WT. Overexpression of OsIAA18 upregulated the genes involved in ABA biosynthesis and signaling pathways, proline biosynthesis pathway, and reactive oxygen species (ROS)-scavenging system in the overexpression of OsIAA18 in rice plants under salt and drought stresses. Proline content, superoxide dismutase (SOD), and peroxidase (POD) activities were significantly increased, whereas malonaldehyde (MDA), hydrogen peroxide (H₂O₂), and superoxide anion radical (O₂ ^-) content were significantly decreased in the transgenic plants under salt and drought stresses. Taken together, we suggest that OsIAA18 plays a positive role in drought and salt tolerance by regulating stress-induced ABA signaling. The OsIAA18 gene has a potential application in genetically modified crops with enhanced tolerance to abiotic stresses.

An R2R3-MYB Transcription Factor RmMYB108 Responds to Chilling Stress of Rosa multiflora and Conferred Cold Tolerance of Arabidopsis

A sudden cooling in the early spring or late autumn negatively impacts the plant growth and development. Although a number of studies have characterized the role of the transcription factors (TFs) of plant R2R3-myeloblastosis (R2R3-MYB) in response to biotic and abiotic stress, plant growth, and primary and specific metabolisms, much less is known about their role in Rosa multiflora under chilling stress. In the present study, RmMYB108, which encodes a nuclear-localized R2R3-MYB TF with a self-activation activity, was identified based on the earlier published RNA-seq data of R. multiflora plants exposed to short-term low-temperature stress and also on the results of prediction of the gene function referring Arabidopsis. The RmMYB108 gene was induced by stress due to chilling, salt, and drought and was expressed in higher levels in the roots than in the leaves. The heterologous expression of RmMYB108 in Arabidopsis thaliana significantly enhanced the tolerance of transgenic plants to freezing, water deficit, and high salinity, enabling higher survival and growth rates, earlier flowering and silique formation, and better seed quantity and quality compared with the wild-type (WT) plants. When exposed to a continuous low-temperature stress at 4°C, transgenic Arabidopsis lines-overexpressing RmMYB108 showed higher activities of superoxide dismutase and peroxidase, lower relative conductivity, and lower malondialdehyde content than the WT. Moreover, the initial fluorescence (F _o) and maximum photosynthetic efficiency of photosystem II (F _v/F _m) changed more dramatically in the WT than in transgenic plants. Furthermore, the expression levels of cold-related genes involved in the ICE1 (Inducer of CBF expression 1)-CBFs (C-repeat binding factors)-CORs (Cold regulated genes) cascade were higher in the overexpression lines than in the WT. These results suggest that RmMYB108 was positively involved in the tolerance responses when R. multiflora was exposed to challenges against cold, freeze, salt, or drought and improved the cold tolerance of transgenic Arabidopsis by reducing plant damage and promoting plant growth.

A R2R3-MYB Transcription Factor Gene, BpMYB123, Regulates BpLEA14 to Improve Drought Tolerance in Betula platyphylla

Drought stress causes various negative impacts on plant growth and crop production. R2R3-MYB transcription factors (TFs) play crucial roles in the response to abiotic stress. However, their functions in Betula platyphylla haven't been fully investigated. In this study, a R2R3 MYB transcription factor gene, BpMYB123, was identified from Betula platyphylla and reveals its significant role in drought stress. Overexpression of BpMYB123 enhances tolerance to drought stress in contrast to repression of BpMYB123 by RNA interference (RNAi) in transgenic experiment. The overexpression lines increased peroxidase (POD) and superoxide dismatase (SOD) activities, while decreased hydrogen peroxide (H₂O₂), superoxide radicals (O₂ ^-), electrolyte leakage (EL) and malondialdehyde (MDA) contents. Our study showed that overexpression of BpMYB123 increased BpLEA14 gene expression up to 20-fold due to BpMYB123 directly binding to the MYB1AT element of BpLEA14 promoter. These results indicate that BpMYB123 acts as a regulator via regulating BpLEA14 to improve drought tolerance in birch.

Integrative Analysis of the Metabolome and Transcriptome of Sorghum bicolor Reveals Dynamic Changes in Flavonoids Accumulation under Saline-Alkali Stress

With the perpetuation of soil salinization, it is imperative to improve the salt and alkaline tolerance of crops. Sorghum bicolor, a C4 crop, is often grown in semiarid areas due to its high tolerance of various abiotic stresses. Whether to improve the resistance of the sorghum itself or that of other crops, it is necessary to understand the response of sorghum under saline-alkali stress. An integrative analysis of the metabolome and transcriptome of sorghum under normal conditions and treatments of moderate and severe saline-alkali stress was performed. Among the different accumulated metabolites (DAMs) and differentially expressed genes (DEGs), flavonoid-related DAMs and DEGs were clearly changed. The level of flavonoids was increased under saline-alkali stress, and the change in flavonoids was dynamic as to whether total flavonoids or most flavonoid components accumulated more under moderate saline-alkali stress compared to severe stress. Some flavonoid metabolites were significantly correlated with the expression of flavonoid biosynthesis genes. MYB transcription factors may also contribute to the regulation of flavonoids levels. These findings present the dynamic changes and possible molecular mechanisms of flavonoids under different saline-alkali stresses and provide a foundation for future research and crop improvement.

Adaptability to abiotic stress regulated by γ-aminobutyric acid in relation to alterations of endogenous polyamines and organic metabolites in creeping bentgrass

The frequency and severity of global abiotic stresses such as heat, drought, and salt stress are increasing due to climate changes. Objectives of this study were to investigate effects of γ-aminobutyric acid (GABA) priming on inducing plants' acclimation to abiotic stress associated with alterations of endogenous polyamines (PAs), amino acids, and sugars in creeping bentgrass (Agrostis stolonifera). The pretreatment with GABA fertigation significantly alleviated heat-, drought-, and salt-induced declines in leaf relative water content, chlorophyll content, cell membrane stability, photochemical efficiency (Fv/Fm), and performance index on absorption basis (PIABS), and also further decreased stress-caused decline in osmotic potential in leaves. The GABA priming uniformly increased total PAs, spermidine, amino acids involved in GABA shunt (GABA, glutamic acid, and alanine), and other amino acids (phenylalanine, aspartic acid, and glycine) accumulation under heat, drought, and salt stress. The GABA priming also significantly improved methionine content under heat and drought stress, maltose, galactose, and talose content under heat and salt stress, or cysteine, serine, and threonine content under drought and salt stress. Interestingly, the GABA priming uniquely led to significant accumulation of spermine, fructose, and glucose under heat stress, putrescine, proline, and mannose under drought stress, or arginine, trehalose and xylose under salt stress, respectively. These particular PAs, sugars, and amino acids differentially or commonly regulated by GABA could play critical roles in osmotic adjustment, osmoprotection, antioxidant, energy source, and signal molecular for creeping bentgrass to acclimate diverse abiotic stresses.

The transcription factor WRKY22 is required during cryo-stress acclimation in Arabidopsis shoot tips

Storage of meristematic tissue at ultra-low temperatures offers a mean to maintain valuable genetic resources from vegetatively reproduced plants. To reveal the biology underlying cryo-stress, shoot tips of the model plant Arabidopsis thaliana were subjected to a standard preservation procedure. A transcriptomic approach was taken to describe the subsequent cellular events which occurred. The cryoprotectant treatment induced the changes in the transcript levels of genes associated with RNA processing and primary metabolism. Explants of a mutant lacking a functional copy of the transcription factor WRKY22 were compromised for recovery. A number of putative downstream targets of WRKY22 were identified, some related to phytohormone-mediated defense, to the osmotic stress response, and to development. There were also alterations in the abundance of transcript produced by genes encoding photosynthesis-related proteins. The wrky22 mutant plants developed an open stomata phenotype in response to their exposure to the cryoprotectant solution. WRKY22 probably regulates a transcriptional network during cryo-stress, linking the explant's defense and osmotic stress responses to changes in its primary metabolism. A model is proposed linking WRKY53 and WRKY70 downstream of the action of WRKY22.

De novo transcriptome sequencing and analysis of salt-, alkali-, and drought-responsive genes in Sophora alopecuroides

Background

Salinity, alkalinity, and drought stress are the main abiotic stress factors affecting plant growth and development. Sophora alopecuroides L., a perennial leguminous herb in the genus Sophora, is a highly salt-tolerant sand-fixing pioneer species distributed mostly in Western Asia and northwestern China. Few studies have assessed responses to abiotic stress in S. alopecuroides. The transcriptome of the genes that confer stress-tolerance in this species has not previously been sequenced. Our objective was to sequence and analyze this transcriptome.

Results

Twelve cDNA libraries were constructed in triplicate from mRNA obtained from Sophora alopecuroides for the control and salt, alkali, and drought treatments. Using de novo assembly, 902,812 assembled unigenes were generated, with an average length of 294 bp. Based on similarity searches, 545,615 (60.43%) had at least one significant match in the Nr, Nt, Pfam, KOG/COG, Swiss-Prot, and GO databases. In addition, 1673 differentially expressed genes (DEGs) were obtained from the salt treatment, 8142 from the alkali treatment, and 17,479 from the drought treatment. A total of 11,936 transcription factor genes from 82 transcription factor families were functionally annotated under salt, alkali, and drought stress, these include MYB, bZIP, NAC and WRKY family members. DEGs were involved in the hormone signal transduction pathway, biosynthesis of secondary metabolites and antioxidant enzymes; this suggests that these pathways or processes may be involved in tolerance towards salt, alkali, and drought stress in S. alopecuroides.

Conclusion

Our study first reported transcriptome reference sequence data in Sophora alopecuroides, a non-model plant without a reference genome. We determined digital expression profile and discovered a broad survey of unigenes associated with salt, alkali, and drought stress which provide genomic resources available for Sophora alopecuroides.

Pre-harvest climate and post-harvest acclimation to cold prevent from superficial scald development in Granny Smith apples

Superficial scald is one of the most serious postharvest physiological disorders that can affect apples after a prolonged cold storage period. This study investigated the impact of pre- and post-harvest climatic variations on superficial scald in a susceptible apple cultivar. Fruit batches with contrasting phenotypes for superficial scald incidence were identified among several years of "Granny Smith" fruit production. The "low scald" year pre-harvest climate was characterised by a warm period followed by a sudden decrease in temperature, playing the part of an in vivo acclimation to cold storage. This was associated with many abiotic stress responsive genes which were induced in fruit peel. In particular 48 Heat Shock Proteins (HSPs) and 5 Heat Shock transcription Factors (HSFs) were strongly induced at harvest when scald incidence was low. For "high scald" year, a post-harvest acclimation of 1 week was efficient in reducing scald incidence. Expression profiles of stress related genes were affected by the acclimation treatment and indicate fruit physiological adaptations to cold storage. The identified stress-responsive genes, and in particular HSPs, could be useful indicators of the fruit physiological status to predict the risk of scald occurrence as early as harvest.

Transcriptional Factors Regulate Plant Stress Responses through Mediating Secondary Metabolism

Plants are adapted to sense numerous stress stimuli and mount efficient defense responses by directing intricate signaling pathways. They respond to undesirable circumstances to produce stress-inducible phytochemicals that play indispensable roles in plant immunity. Extensive studies have been made to elucidate the underpinnings of defensive molecular mechanisms in various plant species. Transcriptional factors (TFs) are involved in plant defense regulations through acting as mediators by perceiving stress signals and directing downstream defense gene expression. The cross interactions of TFs and stress signaling crosstalk are decisive in determining accumulation of defense metabolites. Here, we collected the major TFs that are efficient in stress responses through regulating secondary metabolism for the direct cessation of stress factors. We focused on six major TF families including AP2/ERF, WRKY, bHLH, bZIP, MYB, and NAC. This review is the compilation of studies where researches were conducted to explore the roles of TFs in stress responses and the contribution of secondary metabolites in combating stress influences. Modulation of these TFs at transcriptional and post-transcriptional levels can facilitate molecular breeding and genetic improvement of crop plants regarding stress sensitivity and response through production of defensive compounds.

Metabolomics Analysis Reveals the Alkali Tolerance Mechanism in Puccinellia tenuiflora Plants Inoculated with Arbuscular Mycorrhizal Fungi

Soil alkalization is a major environmental threat that affects plant distribution and yield in northeastern China. Puccinellia tenuiflora is an alkali-tolerant grass species that is used for salt-alkali grassland restoration. However, little is known about the molecular mechanisms by which arbuscular mycorrhizal fungi (AMF) enhance P. tenuiflora responses to alkali stress. Here, metabolite profiling in P. tenuiflora seedlings with or without arbuscular mycorrhizal fungi (AMF) under alkali stress was conducted using liquid chromatography combined with time-of-flight mass spectrometry (LC/TOF-MS). The results showed that AMF colonization increased seedling biomass under alkali stress. In addition, principal component analysis (PCA) and orthogonal projections to latent structures discriminant analysis (OPLS-DA) demonstrated that non-AM and AM seedlings showed different responses under alkali stress. A heat map analysis showed that the levels of 88 metabolites were significantly changed in non-AM seedlings, but those of only 31 metabolites were significantly changed in AM seedlings. Moreover, the levels of a total of 62 metabolites were significantly changed in P. tenuiflora seedlings after AMF inoculation. The results suggested that AMF inoculation significantly increased amino acid, organic acid, flavonoid and sterol contents to improve osmotic adjustment and maintain cell membrane stability under alkali stress. P. tenuiflora seedlings after AMF inoculation produced more plant hormones (salicylic acid and abscisic acid) than the non-AM seedlings, probably to enhance the antioxidant system and facilitate ion balance under stress conditions. In conclusion, these findings provide new insights into the metabolic mechanisms of P. tenuiflora seedlings with arbuscular mycorrhizal fungi under alkali conditions and clarify the role of AM in the molecular regulation of this species under alkali stress.

Overexpression of Grapevine VvIAA18 Gene Enhanced Salt Tolerance in Tobacco

In plants, auxin/indoleacetic acid (Aux/IAA) proteins are transcriptional regulators that regulate developmental process and responses to phytohormones and stress treatments. However, the regulatory functions of the Vitis vinifera L. (grapevine) Aux/IAA transcription factor gene VvIAA18 have not been reported. In this study, the VvIAA18 gene was successfully cloned from grapevine. Subcellular localization analysis in onion epidermal cells indicated that VvIAA18 was localized to the nucleus. Expression analysis in yeast showed that the full length of VvIAA18 exhibited transcriptional activation. Salt tolerance in transgenic tobacco plants and Escherichia. coli was significantly enhanced by VvIAA18 overexpression. Real-time quantitative PCR analysis showed that overexpression of VvIAA18 up-regulated the salt stress-responsive genes, including pyrroline-5-carboxylate synthase (NtP5CS), late embryogenesis abundant protein (NtLEA5), superoxide dismutase (NtSOD), and peroxidase (NtPOD) genes, under salt stress. Enzymatic analyses found that the transgenic plants had higher SOD and POD activities under salt stress. Meanwhile, component analysis showed that the content of proline in transgenic plants increased significantly, while the content of hydrogen peroxide (H2O2) and malondialdehyde (MDA) decreased significantly. Based on the above results, the VvIAA18 gene is related to improving the salt tolerance of transgenic tobacco plants. The VvIAA18 gene has the potential to be applied to enhance plant tolerance to abiotic stress.

Genetic Analysis of the Transition from Wild to Domesticated Cotton (Gossypium hirsutum L.)

The evolution and domestication of cotton is of great interest from both economic and evolutionary standpoints. Although many genetic and genomic resources have been generated for cotton, the genetic underpinnings of the transition from wild to domesticated cotton remain poorly known. Here we generated an intraspecific QTL mapping population specifically targeting domesticated cotton phenotypes. We used 466 F₂ individuals derived from an intraspecific cross between the wild Gossypium hirsutum var. yucatanense (TX2094) and the elite cultivar G. hirsutum cv. Acala Maxxa, in two environments, to identify 120 QTL associated with phenotypic changes under domestication. While the number of QTL recovered in each subpopulation was similar, only 22 QTL were considered coincident (i.e., shared) between the two locations, eight of which shared peak markers. Although approximately half of QTL were located in the A-subgenome, many key fiber QTL were detected in the D-subgenome, which was derived from a species with unspinnable fiber. We found that many QTL are environment-specific, with few shared between the two environments, indicating that QTL associated with G. hirsutum domestication are genomically clustered but environmentally labile. Possible candidate genes were recovered and are discussed in the context of the phenotype. We conclude that the evolutionary forces that shape intraspecific divergence and domestication in cotton are complex, and that phenotypic transformations likely involved multiple interacting and environmentally responsive factors.

Transgenesis as a Tool for the Efficient Production of Selected Secondary Metabolites from in Vitro Plant Cultures

The plant kingdom abounds in countless species with potential medical uses. Many of them contain valuable secondary metabolites belonging to different classes and demonstrating anticancer, anti-inflammatory, antioxidant, antimicrobial or antidiabetic properties. Many of these metabolites, e.g., paclitaxel, vinblastine, betulinic acid, chlorogenic acid or ferrulic acid, have potential applications in medicine. Additionally, these compounds have many therapeutic and health-promoting properties. The growing demand for these plant secondary metabolites forces the use of new green biotechnology tools to create new, more productive in vitro transgenic plant cultures. These procedures have yielded many promising results, and transgenic cultures have been found to be safe, efficient and cost-effective sources of valuable secondary metabolites for medicine and industry. This review focuses on the use of various in vitro plant culture systems for the production of secondary metabolites.

Global scale transcriptome analysis reveals differentially expressed genes involve in early somatic embryogenesis in Dimocarpus longan Lour

BACKGROUND

Somatic embryogenesis (SE) is a process of somatic cells that dedifferentiate to totipotent embryonic stem cells and generate embryos in vitro. Longan SE has been established and wildly used as model system for studying embryogenesis in woody plants, SE-related genes had been characterized. In spite of that, a comprehensive overview of SE at a molecular level is still absent. To understand the molecular mechanisms during longan SE, we examined the transcriptome changes by using Illumina HiSeq from the four distinct developmental stages, including non-embryogenic callus (NEC), embryogenic callus (EC), incomplete compact pro-embryogenic cultures (ICpEC), globular embryos (GE).

RESULTS

RNA-seq of the four samples generated a total of 243.78 million high quality reads, approximately 81.5% of the data were mapped to longan genome. The cDNA libraries of NEC, EC, ICpEC and GE, generated 22,743, 19,745, 21,144, 21,102 expressed transcripts, 1935, 1710, 1816, 1732 novel transcripts, 2645, 366, 505, 588 unique genes, respectively. Comparative transcriptome analysis showed that a total of 10,642, 4180, 5846 and 1785 genes were differentially expressed in the pairwise comparisons of NEC_vs_EC, EC_vs_ICpEC, EC_vs_GE, ICpEC_vs_GE, respectively. Among them, plant hormones signalling related genes were significantly enriched, especially the auxin and cytokinin signalling components. The transcripts of flavonoid biosynthesis related genes were mainly expressed in NEC, while fatty acid biosynthesis related genes mainly accumulated in early SE. In addition, the extracelluar protein encoding genes LTP, CHI, GLP, AGP, EP1 were related to longan SE. Combined with the FPKM value of longan nine tissues transcription, 27 SE specific or preferential genes (LEC1, LEC1-like, PDF1.3, GH3.6, AGL80, PIN1, BBM, WOX9, WOX2, ABI3, et al.) and 28 NEC preferential genes (LEA5, CNOT3, DC2.15, PR1-1, NsLTP2, DIR1, PIP1, PIP2.1, TIP2-1, POD-P7 and POD5 et al.) were characterized as molecular markers for longan early SE. qRT-PCR validation of SE-related genes showed a high correlation between RNA-seq and qRT-PCR data.

CONCLUSION

This study provides new insights into the role of the transcriptome during early SE in longan. Differentially expressed genes reveal that plant hormones signalling, flavonoid and fatty acid biosynthesis, and extracelluar protein related genes were involved in longan early SE. It could serve as a valuable platform resource for further functional studies addressing embryogenesis in woody plants.

Functional characterization of a HD-ZIP IV transcription factor NtHDG2 in regulating flavonols biosynthesis in Nicotiana tabacum

The HD-ZIP Ⅳ transcription factors have been identified and functional characterized in many plant species. However, no tobacco HD-ZIP IV gene has been isolated, and it is not yet known whether HD-ZIP IV genes are involved in controlling flavonols accumulation in plants. Here, we cloned a HD ZIP gene named NtHDG2 from Nicotiana tabacum, which belongs to the class IV of HD-ZIP family, and the NtHDG2-GFP fusion protein is localized to the nucleus. We further observed that the flavonols contents in the NtHDG2 overexpression leaves increase to 1.9-4.5 folds of that in WT plants, but in the NtHDG2-RNAi plants the flavonols contents reduce to 20.9%-52.7% of that in WT plants. The transcriptions of one regulatory gene NtMYB12, and three structural genes (NtPAL, NtF3'H, NtF3GT), contributing to flavonols biosynthesis, were significantly induced by NtHDG2. However, the transcription level of NtNAC002, a flavonols biosynthesis repressor, was also significantly up-regulated in NtHDG2-overexpression lines, but significantly down-regulated in the RNAi lines, indicating that HDG2 regulates the synthesis of flavonols as a complex regulatory network. Moreover, ectopic expression of NtHDG2 gene promoted the transcription of several AP2/ERF genes, including NtERF1-5, NtERF109, NtDREB1, and NtCIPK11, which participate in regulating root development and resistance to abiotic stresses. Our findings reveal the new function of HD-ZIP IV transcription factors in flavonoids biosynthesis, and indicate that HD-ZIP IV members may play an important role in plant resistance to abiotic stress. The NtHDG2 gene provides a promising target for genetically manipulating to increase the amounts of flavonols in tobacco leaves.

Transcriptomic profiling revealed genes involved in response to cold stress in maize

Maize is an important food crop. Chilling stress can decrease maize production by affecting seed germination and seedling growth, especially in early spring. We analysed chlorophyll fluorescence, membrane lipids, secondary metabolites and the transcriptome of two maize inbred lines (chilling-tolerant M54 and chilling-sensitive 753F) after 0, 4 and 24 h cold stress. M54 showed better ability to protect PSII and accumulate secondary metabolites. From RNA sequencing data, we determined that the majority of cold-affected genes were involved in photosynthesis, secondary metabolism, and signal transduction. Genes important for maintaining photosystem structure and for regulating electron transport were less affected by cold stress in M54 than in 753F. Expression of genes related to secondary metabolism and unsaturated fatty acid synthesis were upregulated more strongly in M54 than in 753F and M54 accumulated more unsaturated fatty acids and secondary metabolites. As a result, M54 achieved relatively high cold tolerance by protecting the photosystems and maintaining the stability of cell membranes.

Identification of Two Novel R2R3-MYB Transcription factors, PsMYB114L and PsMYB12L, Related to Anthocyanin Biosynthesis in Paeonia suffruticosa

Flower color is a charming phenotype with very important ornamental and commercial values. Anthocyanins play a critical role in determining flower color pattern formation, and their biosynthesis is typically regulated by R2R3-MYB transcription factors (TFs). Paeonia suffruticosa is a famous ornamental plant with colorful flowers. However, little is known about the R2R3-MYB TFs that regulate anthocyanin accumulation in P. suffruticosa. In the present study, two R2R3-MYB TFs, namely, PsMYB114L and PsMYB12L, were isolated from the petals of P. suffruticosa 'Shima Nishiki' and functionally characterized. Sequence analysis suggested that PsMYB114L contained a bHLH-interaction motif, whereas PsMYB12L contained two flavonol-specific motifs (SG7 and SG7-2). Subsequently, the in vivo function of PsMYB114L and PsMYB12L was investigated by their heterologous expression in Arabidopsis thaliana and apple calli. In transgenic Arabidopsis plants, overexpression of PsMYB114L and of PsMYB12L caused a significantly higher accumulation of anthocyanins, resulting in purple-red leaves. Transgenic apple calli overexpressing PsMYB114L and PsMYB12L also significantly enhanced the anthocyanins content and resulted in a change in the callus color to red. Meanwhile, gene expression analysis in A. thaliana and apple calli suggested that the expression levels of the flavonol synthase (MdFLS) and anthocyanidin reductase (MdANR) genes were significantly downregulated and the dihydroflavonol 4-reductase (AtDFR) and anthocyanin synthase (AtANS) genes were significantly upregulated in transgenic lines of PsMYB114L. Moreover, the expression level of the FLS gene (MdFLS) was significantly downregulated and the DFR (AtDFR/MdDFR) and ANS (AtANS/MdANS) genes were all significantly upregulated in transgenic lines plants of PsMYB12L. These results indicate that PsMYB114L and PsMYB12L both enhance anthocyanin accumulation by specifically regulating the expression of some anthocyanin biosynthesis-related genes in different plant species. Together, these results provide a valuable resource with which to further study the regulatory mechanism of anthocyanin biosynthesis in P. suffruticosa and for the breeding of tree peony cultivars with novel and charming flower colors.

Identification of Potential Genes Responsible for Thermotolerance in Wheat under High Temperature Stress

Wheat, a major worldwide staple food crop, is relatively sensitive to a changing environment, including high temperature. The comprehensive mechanism of heat stress response at the molecular level and exploitation of candidate tolerant genes are far from enough. Using transcriptome data, we analyzed the gene expression profiles of wheat under heat stress. A total of 1705 and 17 commonly differential expressed genes (DEGs) were identified in wheat grain and flag leaf, respectively, through transcriptome analysis. Gene Ontology (GO) and pathway enrichment were also applied to illustrate the functions and metabolic pathways of DEGs involved in thermotolerance of wheat grain and flag leaf. Furthermore, our data suggest that there may be a more complex molecular mechanism or tighter regulatory network in flag leaf than in grain under heat stress over time, as less commonly DEGs, more discrete expression profiles of genes (principle component analysis) and less similar pathway response were observed in flag leaf. In addition, we found that transcriptional regulation of zeatin, brassinosteroid and flavonoid biosynthesis pathways may play an important role in wheat’s heat tolerance. The expression changes of some genes were validated using quantitative real-time polymerase chain reaction and three potential genes involved in the flavonoid biosynthesis process were identified.

NtMYB4 and NtCHS1 Are Critical Factors in the Regulation of Flavonoid Biosynthesis and Are Involved in Salinity Responsiveness

High levels of salinity induce serious oxidative damage in plants. Flavonoids, as antioxidants, have important roles in reactive oxygen species (ROS) scavenging. In the present study, the tobacco R2R3 MYB type repressor, NtMYB4, was isolated and characterized. The expression of NtMYB4 was suppressed by salinity. Overexpression of NtMYB4 reduced the salt tolerance in transgenic tobacco plants. NtMYB4 repressed the promoter activity of NtCHS1 and negatively regulated its expression. Rutin accumulation was significantly decreased in NtMYB4 overexpressing transgenic plants and NtCHS1 RNAi silenced transgenic plants. Moreover, high H2O2 andO 2 - contents were detected in both types of rutin-reduced transgenic plants under high salt stress. In addition, exogenous rutin supplementation effectively scavenged ROS (H2O2 andO 2 - ) and improved the salt tolerance of the rutin-reduced transgenic plants. In contrast, NtCHS1 overexpressing plants had increased rutin accumulation, lower H2O2 andO 2 - contents, and higher tolerance to salinity. These results suggested that tobacco NtMYB4 acts as a salinity response repressor and negatively regulates NtCHS1 expression, which results in the reduced flavonoid accumulation and weakened ROS-scavenging ability under salt stress.

Quercetin potentiates the concurrent hyper-accumulation of cellular biomass and lipids in Chlorella vulgaris

Provision of chemical modulators has emerged as an effective strategy to govern cell growth and development. Here, the impact of flavonoid quercetin on algal growth, lipid accumulation and transcriptional patterns was investigated in the green microalga Chlorella vulgaris. These results demonstrated that quercetin (15 μg/l) significantly enhanced the cellular biomass and photosynthetic efficiency, with up to 2.5-fold in the biomass in the stationary phase. Lipidomic analyses revealed that lipid content was increased by 1.8-fold. Furthermore, the functional mechanism of quercetin on the molecular level was dissected by transcriptomic analysis. Results revealed that quercetin upregulated the expression pattern of key genes involved in cellular signaling mechanisms such as phosphatidylinositol 4-kinase α, thus consequently enhanced cell growth. Altogether, the data present in this study demonstrate the dramatic role of quercetin on enhancing microalgal biomass and lipid accumulation by unprecedented regulation, of key metabolic nodes, for the first time and provide a novel insight into microalgal metabolism and regulation.

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

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

RNA-Seq analysis revealed genes associated with drought stress response in kabuli chickpea (Cicer arietinum L.)

Drought is the most important constraint that effects chickpea production globally. RNA-Seq has great potential to dissect the molecular mechanisms of tolerance to environmental stresses. Transcriptome profiles in roots and shoots of two contrasting Iranian kabuli chickpea genotypes (Bivanij and Hashem) were investigated under water-limited conditions at early flowering stage using RNA-Seq approach. A total of 4,572 differentially expressed genes (DEGs) were identified. Of these, 261 and 169 drought stress responsive genes were identified in the shoots and the roots, respectively, and 17 genes were common in the shoots and the roots. Gene Ontology (GO) analysis revealed several sub-categories related to the stress, including response to stress, defense response and response to stimulus in the tolerant genotype Bivanij as compared to the sensitive genotype Hashem under drought stress. In addition, several Transcription factors (TFs) were identified in major metabolic pathways such as, ABA, proline and flavonoid biosynthesis. Furthermore, a number of the DEGs were observed in "QTL-hotspot" regions which were reported earlier in chickpea. Drought tolerance dissection in the genotypes revealed that the genes and the pathways involved in shoots of Bivanij were the most important factor to make a difference between the genotypes for drought tolerance. The identified TFs in the experiment, particularly those which were up-regulated in shoots of Bivanij during drought stress, were potential candidates for enhancing tolerance to drought.

An Overview of the Genetics of Plant Response to Salt Stress: Present Status and the Way Forward

Salinity is one of the major threats faced by the modern agriculture today. It causes multidimensional effects on plants. These effects depend upon the plant growth stage, intensity, and duration of the stress. All these lead to stunted growth and reduced yield, ultimately inducing economic loss to the farming community in particular and to the country in general. The soil conditions of agricultural land are deteriorating at an alarming rate. Plants assess the stress conditions, transmit the specific stress signals, and then initiate the response against that stress. A more complete understanding of plant response mechanisms and their practical incorporation in crop improvement is an essential step towards achieving the goal of sustainable agricultural development. Literature survey shows that investigations of plant stresses response mechanism are the focus area of research for plant scientists. Although these efforts lead to reveal different plant response mechanisms against salt stress, yet many questions still need to be answered to get a clear picture of plant strategy to cope with salt stress. Moreover, these studies have indicated the presence of a complicated network of different integrated pathways. In order to work in a progressive way, a review of current knowledge is critical. Therefore, this review aims to provide an overview of our understanding of plant response to salt stress and to indicate some important yet unexplored dynamics to improve our knowledge that could ultimately lead towards crop improvement.

BPH1, a novel substrate receptor of CRL3, plays a repressive role in ABA signal transduction

BPH1 acts as a substrate receptor of CRL3 complex and negatively regulates ABA-mediated cellular responses. The study on its function provides information that helps further understand the relationship between ABA signaling and UPS. Abscisic acid (ABA) plays a crucial role in a variety of cellular processes, including seed dormancy, inhibition of seedling growth, and drought resistance in plants. Cullin3-RING E3 ligase (CRL3) complex is a type of multi-subunit E3 ligase, and BTB/POZ protein, a component of CRL3 complex, functions as a receptor to determine a specific substrate. To elucidate the CRL3 complex that participates in ABA-mediated cellular processes, we first investigated ABA-inducible BTB/POZ genes based on data from the AtGenExpress Visualization Tool (AVT). We then isolated an ABA-inducible gene encoding a potential CRL3 substrate receptor in Arabidopsis, BPH1 (BTB/POZ protein hypersensitive to ABA 1). The isolate gene has a BTB/POZ domain and a NPH3 domain within its N-terminal and C-terminal region, respectively. Yeast two-hybrid and co-immunoprecipitation assays showed that BPH1 physically interacted with cullin3a, a scaffold protein of CRL3, suggesting that it functions as an Arabidopsis CRL3 substrate receptor. The functional mutation of BPH1 caused delayed seed germination in response to ABA and enhanced sensitivity by NaCl and mannitol treatments as ABA-related stresses. Moreover, bph1 mutants exhibited enhanced stomatal closure under ABA application and reduced water loss when compared with wild-type, implying their enhanced tolerance to drought stress. Based on the information from microarray/AVT data and expression analysis of various ABA-inducible genes between wild-type and bph1 plants following ABA treatments, we concluded loss of BPH1 resulted in hyper-induction of a large portion of ABA-inducible genes in response to ABA. Taken together, these results show that BPH1 is negatively involved in ABA-mediated cellular events.

Transcriptome analysis of embryonic domains in Norway spruce reveals potential regulators of suspensor cell death

The terminal differentiation and elimination of the embryo-suspensor is the earliest manifestation of programmed cell death (PCD) during plant ontogenesis. Molecular regulation of suspensor PCD remains poorly understood. Norway spruce (Picea abies) embryos provide a powerful model for studying embryo development because of their large size, sequenced genome, and the possibility to obtain a large number of embryos at a specific developmental stage through somatic embryogenesis. Here, we have carried out global gene expression analysis of the Norway spruce embryo-suspensor versus embryonal mass (a gymnosperm analogue of embryo proper) using RNA sequencing. We have identified that suspensors have enhanced expression of the NAC domain-containing transcription factors, XND1 and ANAC075, previously shown to be involved in the initiation of developmental PCD in Arabidiopsis. The analysis has also revealed enhanced expression of Norway spruce homologues of the known executioners of both developmental and stress-induced cell deaths, such as metacaspase 9 (MC9), cysteine endopeptidase-1 (CEP1) and ribonuclease 3 (RNS3). Interestingly, a spruce homologue of bax inhibitor-1 (PaBI-1, for Picea abies BI-1), an evolutionarily conserved cell death suppressor, was likewise up-regulated in the embryo-suspensor. Since Arabidopsis BI-1 so far has been implicated only in the endoplasmic reticulum (ER)-stress induced cell death, we investigated its role in embryogenesis and suspensor PCD using RNA interference (RNAi). We have found that PaBI-1-deficient lines formed a large number of abnormal embryos with suppressed suspensor elongation and disturbed polarity. Cytochemical staining of suspensor cells has revealed that PaBI-1 deficiency suppresses vacuolar cell death and induces necrotic type of cell death previously shown to compromise embryo development. This study demonstrates that a large number of cell-death components are conserved between angiosperms and gymnosperms and establishes a new role for BI-1 in the progression of vacuolar cell death.

KIX domain of AtMed15a, a Mediator subunit of Arabidopsis, is required for its interaction with different proteins

Med15 is an important subunit of Mediator Tail module and is characterized by a KIX domain present towards amino terminal. In yeast and metazoans, Med15 KIX domain has been found to interact with various transcription factors regulating several processes including carbohydrate metabolism, lipogenesis, stress response and multidrug resistance. Mechanism of Med15 functioning in Arabidopsis is largely unknown. In this study, interactome of KIX domain of Arabidopsis Med15, AtMed15a, was characterized. We found 45 proteins that interact with AtMed15a KIX domain, including 11 transcription factors, 3 single strand nucleic acid-binding proteins and 1 splicing factor. The third helix of the KIX domain was found to be involved in most of the interactions. Mapping of the regions participating in the interactions revealed that the activation domain of a transcription factor, UKTF1 interacted with AtMed15a KIX domain. Thus, our results suggest that in Arabidopsis, activation domain of transcription factors target KIX domain of AtMed15a for their transcriptional responses.

A Functional Genomic Perspective on Drought Signalling and its Crosstalk with Phytohormone-mediated Signalling Pathways in Plants

INTRODUCTION

Drought stress is one of the most important abiotic stresses that negatively influence crop performance and productivity. Plants acclimatize to drought stress conditions through altered molecular, biochemical and physiological responses. Gene and/or protein expression and regulation are thought to be modulated upon stress perception and signal transduction for providing requisite endurance to plants.Plant growth regulators or phytohormones are important molecules required for various biological processes in plants and are also central to stress signalling pathways. Among various phytohormones, Abscisic Acid (ABA) and Ethylene (ET) are considered to be the most vital growth regulators implicated in drought stress signalling and tolerance. Besides the above two known classical phytohormones, Salicylic Acid (SA) and Jasmonic Acid (JA) have also been found to potentially enhance abiotic stress tolerance particularly that of drought, salinity, and heat stress tolerance in plants. Apart from these several other growth regulators such as Cytokinins (CKs), Auxin (AUX), Gibberellic Acid (GA), Brassinosteroids (BRs) and Strigolactones (SLs) have also been reported to actively participate in abiotic stress responses and tolerance in plants. The abiotic stress signalling in plants regulated by these hormones further depends upon the nature, intensity, and duration of exposure to various environmental stresses. It has been reported that all these phytohormones are also involved in extensive crosstalk and signal transduction among themselves and/or with other factors.

CONCLUSION

This review thus summarizes the molecular mechanism of drought signalling and its crosstalk with various phytohormone signalling pathways implicated in abiotic stress response and tolerance.

Genome-wide sequential, evolutionary, organizational and expression analyses of phenylpropanoid biosynthesis associated MYB domain transcription factors in Arabidopsis

The MYB gene family represents one of the largest groups of transcription factors in plants. Recent evidences have also demonstrated key role of MYB transcription factors in regulating the expression of major genes involved in the biosynthesis of phenylpropanoid compounds which confer biotic and abiotic stress tolerance in plant species. However, no comprehensive genome-wide analysis of the phenylpropanoid pathway-associated MYB transcription factors has been reported thus far. In this study, 11 Arabidopsis MYB proteins, such as MYB3, MYB4, MYB7, MYB11, MYB12, MYB32, MYB75, MYB90, MYB111, MYB113, and MYB114 were initially identified considering their reported regulatory function in phenylpropanoid biosynthesis pathway. Subsequent genome-wide analysis have identified the corresponding homologues from Glycine max, Vigna radiata, Oryza sativa, and Zea mays, while homologous of Arabidopsis MYB75, MYB90, MYB113, and MYB114 were not detected in rice and maize genomes. The identified MYB proteins were classified into three groups (I-III) based on phylogeny. Sequence and domain analysis revealed presence of two conserved DNA binding MYB domains in the selected MYB proteins. Promoter analysis indicated presence of cis-regulatory elements related to light signaling, development, and stress response. Expression analysis of selected Arabidopsis MYB genes revealed their function in plant development and abiotic stress response, consistent with gene ontology annotations. Together, these results provide a useful framework for further experimental studies for the functional characterization of the target MYB genes in the context of regulation of phenylpropanoid biosynthesis and plant stress response.

Transcriptomics Analyses Reveal Wheat Responses to Drought Stress during Reproductive Stages under Field Conditions

Drought is a major abiotic stress that limits wheat production worldwide. To ensure food security for the rapidly increasing world population, improving wheat yield under drought stress is urgent and relevant. In this study, an RNA-seq analysis was conducted to study the effect of drought on wheat transcriptome changes during reproductive stages under field conditions. Our results indicated that drought stress during early reproductive periods had a more severe impact on wheat development, gene expression and yield than drought stress during flowering. In total, 115,656 wheat genes were detected, including 309 differentially expressed genes (DEGs) which responded to drought at various developmental stages. These DEGs were involved in many critical processes including floral development, photosynthetic activity and stomatal movement. At early developmental stages, the proteins of drought-responsive DEGs were mainly located in the nucleus, peroxisome, mitochondria, plasma membrane and chloroplast, indicating that these organelles play critical roles in drought tolerance in wheat. Furthermore, the validation of five DEGs confirmed their responsiveness to drought under different genetic backgrounds. Functional verification of DEGs of interest will occur in our subsequent research. Collectively, the results of this study not only advanced our understanding of wheat transcriptome changes under drought stress during early reproductive stages but also provided useful targets to manipulate drought tolerance in wheat at different development stages.

Overexpression of a Tartary Buckwheat Gene, FtbHLH3, Enhances Drought/Oxidative Stress Tolerance in Transgenic Arabidopsis

bHLH (basic helix-loop-helix) transcription factors play important roles in the abiotic stress response in plants, but their characteristics and functions in tartary buckwheat (Fagopyrum tataricum), a flavonoid-rich cereal crop with a strong stress tolerance, have not been fully investigated. Here, a novel bHLH gene, designated FtbHLH3, was isolated and characterized. Expression analysis in tartary buckwheat revealed that FtbHLH3 was mainly induced by polyethylene glycol 6000 (PEG6000) and abscisic acid (ABA) treatments. Subcellular localization and a yeast one-hybrid assay indicated that FtbHLH3 has transcriptional activation activities. Overexpression of FtbHLH3 in Arabidopsis resulted in increased drought/oxidative tolerance, which was attributed to not only lower malondialdehyde (MDA), ion leakage (IL), and reactive oxygen species (ROS) but also higher proline (Pro) content, activities of antioxidant enzymes, and photosynthetic efficiency in transgenic lines compared to wild type (WT). Moreover, qRT-PCR analysis indicated that the expression of multiple stress-responsive genes in the transgenic lines was significantly higher than in WT under drought stress. In particular, the expression of AtNCED, a rate-limiting enzyme gene in ABA biosynthesis, was increased significantly under both normal and stress conditions. Additionally, an ABA-response-element (ABRE) was also found in the promoter regions. Furthermore, the transgenic Arabidopsis lines of the FtbHLH3 promoter had higher GUS activity after drought stress. In summary, our results indicated that FtbHLH3 may function as a positive regulator of drought/oxidative stress tolerance in transgenic Arabidopsis through an ABA-dependent pathway.

Hormone signaling pathways under stress combinations

As sessile organisms, plants are continuously exposed to various environmental stresses. In contrast to the controlled conditions employed in many researches, more than one or more abiotic and/or biotic stresses simultaneously occur and highly impact growth of plants and crops in the field environments. Therefore, an urgent need to generate crops with enhanced tolerance to stress combinations exists. Researchers, however, focused on the mechanisms underlying acclimation of plants to combined stresses only in recent studies. Plant hormones might be a key regulator of the tailored responses of plants to different stress combinations. Co-ordination between different hormone signaling, or hormone signaling and other pathways such as ROS regulatory mechanisms could be flexible, being altered by timing and types of stresses, and could be different depending on plant species under the stress combinations. In this review, update on recent studies focusing on complex-mode of hormone signaling under stress combinations will be provided.