Plant Hormonomics: Multiple Phytohormone Profiling by Targeted Metabolomics

Extraction and Quantification of Plant Hormones and RNA from Pea Axillary Buds

The quantification of plant hormones and related gene expression is essential to improve the understanding of the molecular regulation of plant growth and development. However, plant hormone quantification is still challenging due to extremely low endogenous levels and high chemical diversity. In this study, we present a convenient extraction protocol that enables the simultaneous extraction of both phytohormones and RNA from the same sample in a small quantity (approximately 10 mg). Using ultra-performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS/MS), this protocol provides a method to quantify 13 phytohormones and their derivatives from four classes (cytokinin, auxin, abscisic acid, and gibberellin) at the speed of 14 min per sample.

The RPN12a proteasome subunit is essential for the multiple hormonal homeostasis controlling the progression of leaf senescence

The 26S proteasome is a conserved multi-subunit machinery in eukaryotes. It selectively degrades ubiquitinated proteins, which in turn provides an efficient molecular mechanism to regulate numerous cellular functions and developmental processes. Here, we studied a new loss-of-function allele of RPN12a, a plant ortholog of the yeast and human structural component of the 19S proteasome RPN12. Combining a set of biochemical and molecular approaches, we confirmed that a rpn12a knock-out had exacerbated 20S and impaired 26S activities. The altered proteasomal activity led to a pleiotropic phenotype affecting both the vegetative growth and reproductive phase of the plant, including a striking repression of leaf senescence associate cell-death. Further investigation demonstrated that RPN12a is involved in the regulation of several conjugates associated with the auxin, cytokinin, ethylene and jasmonic acid homeostasis. Such enhanced aptitude of plant cells for survival in rpn12a contrasts with reports on animals, where 26S proteasome mutants generally show an accelerated cell death phenotype.

Auxin-regulated timing of transition from vegetative to reproductive growth in rapeseed (Brassica napus L.) under different nitrogen application rates

Accelerating the differentiation of floral meristem (FM) from shoot apical meristems (SAM) which determines the conversion from vegetative to reproductive growth is of great significance for the production of rapeseed (Brassica napus L.). In this research, the mechanisms of different nitrogen (N) application rates (low N, N1; normal N, N2; and high N, N3) on different FM development stages triggering the regulation of FM differentiation genes through the auxin biosynthetic and signal transduction were investigated. We found that the stage of FM differentiation, which was identified through a stereomicroscope and scanning electron microscope, came 4 and 7 days earlier under high N rate than under normal and low N levels, with the seed yield increased by 11.1 and 22.6%, respectively. Analysis of the auxin and its derivatives contents showed that the main biosynthesis way of auxin was the indole acetaldehyde oxime (IAOx) pathway, with 3-Indole acetonitrile dramatically accumulated during FM differentiation. At the same time, an obvious decrease of IAA contents at each FM differentiation stage was detected, and then gradually rose. Results of the expression of genes involved in auxin biosynthesis, auxin signaling transduction, and FM identification under five FM differentiation stages and three nitrogen application rates showed that genes involved in auxin biosynthesis were regulated before the FM differentiation stage, while the regulation of FM identity genes appeared mainly at the middle and later periods of the five stages, and the regulation level of genes varied under different N rates. Taken together, a high nitrogen rate could accelerate the initiation of FM differentiation, and auxin involved a lot in this regulation.

The mechanism of bud dehyperhydricity by the method of 'starvation drying combined with AgNO3' in Lycium ruthenicum

Micropropagation is very important for rapid clonal propagation and scientific research of woody plants. However, the micropropagated materials usually show hyperhydricity, which seriously hinders application of the micropropagation. Lycium ruthenicum is an important species of eco-economic forests. Herein, treatment of 'starvation and drying combined with 30 μM AgNO3' (SDCAg+) removed serious hyperhydricity of L. ruthenicum buds regenerated from its green-inflorescence-explants, and then gene expression, metabolites of various phytohormones, chloroplasts, chlorophyll (Chl) and total soluble proteins of the hyperhydric and dehyperhydric leaves were compared and analyzed. The results suggested that the SDCAg+ treatment might remove hyperhydricity of L. ruthenicum through: reducing water uptake; increasing water loss; up-regulating the expression of chloroplast-ribosomal-protein genes from nuclear genome; down-regulating the expression of cytoplasmic-ribosomal-protein genes; up-regulating the synthesis of the total soluble proteins; restoring the lamellar structure of chloroplast grana and matrix; improving Chl synthesis and reducing Chl metabolism; increasing expression of light-harvesting Chl protein complex genes and content of Chla and b; up-regulating both photosynthesis and starch and sucrose metabolism KEGG pathways; up-regulating abscisic acid, salicylic acid and their signaling; down-regulating cytokinin, jasmonic acid, jasmonoyl-l-isoleucine and their signaling. Also, the above events interact to form a regulatory network of dehyperhydricity by SDCAg+ treatment. Overall, the study indicated key genes/pathways and physiological/subcellular changes involved in dehyperhydricity and then established a dehyperhydric mechanism model of L. ruthenicum. This not only proposed clues for preventing or removing hyperhydricity but also laid foundations for molecular breeding of L. ruthenicum and other species.

Zaxinone synthase controls arbuscular mycorrhizal colonization level in rice

The Oryza sativa (rice) carotenoid cleavage dioxygenase OsZAS was described to produce zaxinone, a plant growth-promoting apocarotenoid. A zas mutant line showed reduced arbuscular mycorrhizal (AM) colonization, but the mechanisms underlying this behavior are unknown. Here, we investigated how OsZAS and exogenous zaxinone treatment regulate mycorrhization. Micromolar exogenous supply of zaxinone rescued root growth but not the mycorrhizal defects of the zas mutant, and even reduced mycorrhization in wild-type and zas genotypes. The zas line did not display the increase in the level of strigolactones (SLs) that was observed in wild-type plants at 7 days post-inoculation with AM fungus. Moreover, exogenous treatment with the synthetic SL analog GR24 rescued the zas mutant mycorrhizal phenotype, indicating that the lower AM colonization rate of zas is caused by a deficiency in SLs at the early stages of the interaction, and indicating that during this phase OsZAS activity is required to induce SL production, possibly mediated by the Dwarf14-Like (D14L) signaling pathway. OsZAS is expressed in arbuscule-containing cells, and OsPT11prom::OsZAS transgenic lines, where OsZAS expression is driven by the OsPT11 promoter active in arbusculated cells, exhibit increased mycorrhization compared with the wild type. Overall, our results show that the genetic manipulation of OsZAS activity in planta leads to a different effect on AM symbiosis from that of exogenous zaxinone treatment, and demonstrate that OsZAS influences the extent of AM colonization, acting as a component of a regulatory network that involves SLs.

Induced polyploidy deeply influences reproductive life cycles, related phytochemical features, and phytohormonal activities in blackberry species

In some cases, polyploidy is an important phenomenon in the evolution of fruit crops. Polyploidy can be used in fruit breeding programs to develop varieties with higher yields and better fruit quality, as well as better adaptation to adverse environmental conditions. In this study, three wild species of blackberry were subjected to different degrees of induced polyploidy, and the effects of which were evaluated on morphological, physiological, and phytohormonal traits. With the aim of gaining a deep insight into the generative phase of plant growth and development, different levels of induced polyploidy were evaluated on the three blackberry species, i.e., Rubus persicus Bioss. (2x, 4x, and 8x), R. caesius L. (2x and 4x), and R. hirtus Schreb. (2x and 4x). The results showed that the polyploid plants performed significantly better than their diploid counterparts in terms of morphological traits such as flower count per spike and berry weight, as well as biochemical traits such as total soluble solids in the leaves. Induced polyploidy increased berry weight and drupe count per fruit. Microscopic examinations revealed a smaller number of viable pollen in the polyploids, compared to the diploids. Electron microscopy showed that the octaploid R. persicus had larger conical cells on the flower surface, compared to the diploid R. persicus. Correlation analysis showed that the ratio of indoleacetic acid to jasmonic acid changed synergistically with the total soluble solids in the leaves during the fruit set. The ploidy level correlated significantly with the number of pistils, leaf green index, total soluble solids in the leaves, and glucose content in floral nectar. Overall, induced polyploidy allowed Rubus to develop advantageous traits that can benefit future breeding programs and expand reproductive research in blackberries.

Inactivation of the entire Arabidopsis group II GH3s confers tolerance to salinity and water deficit

Indole-3-acetic acid (IAA) controls a plethora of developmental processes. Thus, regulation of its concentration is of great relevance for plant performance. Cellular IAA concentration depends on its transport, biosynthesis and the various pathways for IAA inactivation, including oxidation and conjugation. Group II members of the GRETCHEN HAGEN 3 (GH3) gene family code for acyl acid amido synthetases catalysing the conjugation of IAA to amino acids. However, the high degree of functional redundancy among them has hampered thorough analysis of their roles in plant development. In this work, we generated an Arabidopsis gh3.1,2,3,4,5,6,9,17 (gh3oct) mutant to knock out the group II GH3 pathway. The gh3oct plants had an elaborated root architecture, showed an increased tolerance to different osmotic stresses, including an IAA-dependent tolerance to salinity, and were more tolerant to water deficit. Indole-3-acetic acid metabolite quantification in gh3oct plants suggested the existence of additional GH3-like enzymes in IAA metabolism. Moreover, our data suggested that 2-oxindole-3-acetic acid production depends, at least in part, on the GH3 pathway. Targeted stress-hormone analysis further suggested involvement of abscisic acid in the differential response to salinity of gh3oct plants. Taken together, our data provide new insights into the roles of group II GH3s in IAA metabolism and hormone-regulated plant development.

At the Crossroads of Salinity and Rhizobium-Legume Symbiosis

Legume roots interact with soil bacteria rhizobia to develop nodules, de novo symbiotic root organs that host these rhizobia and are mini factories of atmospheric nitrogen fixation. Nodulation is a sophisticated developmental process and is sensitive to several abiotic factors, salinity being one of them. While salinity influences both the free-living partners, symbiosis is more vulnerable than other aspects of plant and microbe physiology, and the symbiotic interaction is strongly impaired even under moderate salinity. In this review, we tease apart the various known components of rhizobium-legume symbiosis and how they interact with salt stress. We focus primarily on the initial stages of symbiosis since we have a greater mechanistic understanding of the interaction at these stages.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Cross-inoculation of rhizobiome from a congeneric ruderal plant imparts drought tolerance in maize (Zea mays) through changes in root morphology and proteome

Rhizobiome confer stress tolerance to ruderal plants, yet their ability to alleviate stress in crops is widely debated, and the associated mechanisms are poorly understood. We monitored the drought tolerance of maize (Zea mays) as influenced by the cross-inoculation of rhizobiota from a congeneric ruderal grass Andropogon virginicus (andropogon-inoculum), and rhizobiota from organic farm maintained under mesic condition (organic-inoculum). Across drought treatments (40% field capacity), maize that received andropogon-inoculum produced two-fold greater biomass. This drought tolerance translated to a similar leaf metabolomic composition as that of the well-watered control (80% field capacity) and reduced oxidative damage, despite a lower activity of antioxidant enzymes. At a morphological-level, drought tolerance was associated with an increase in specific root length and surface area facilitated by the homeostasis of phytohormones promoting root branching. At a proteome-level, the drought tolerance was associated with upregulation of proteins related to glutathione metabolism and endoplasmic reticulum-associated degradation process. Fungal taxa belonging to Ascomycota, Mortierellomycota, Archaeorhizomycetes, Dothideomycetes, and Agaricomycetes in andropogon-inoculum were identified as potential indicators of drought tolerance. Our study provides a mechanistic understanding of the rhizobiome-facilitated drought tolerance and demonstrates a better path to utilize plant-rhizobiome associations to enhance drought tolerance in crops.

Changes in the concentrations and transcripts for gibberellins and other hormones in a growing leaf and roots of wheat seedlings in response to water restriction

BACKGROUND

Bread wheat (Triticum aestivum) is a major source of nutrition globally, but yields can be seriously compromised by water limitation. Redistribution of growth between shoots and roots is a common response to drought, promoting plant survival, but reducing yield. Gibberellins (GAs) are necessary for shoot and root elongation, but roots maintain growth at lower GA concentrations compared with shoots, making GA a suitable hormone for mediating this growth redistribution. In this study, the effect of progressive drought on GA content was determined in the base of the 4th leaf and root tips of wheat seedlings, containing the growing regions, as well as in the remaining leaf and root tissues. In addition, the contents of other selected hormones known to be involved in stress responses were determined. Transcriptome analysis was performed on equivalent tissues and drought-associated differential expression was determined for hormone-related genes.

RESULTS

After 5 days of applying progressive drought to 10-day old seedlings, the length of leaf 4 was reduced by 31% compared with watered seedlings and this was associated with significant decreases in the concentrations of bioactive GA₁ and GA₄ in the leaf base, as well as of their catabolites and precursors. Root length was unaffected by drought, while GA concentrations were slightly, but significantly higher in the tips of droughted roots compared with watered plants. Transcripts for the GA-inactivating gene TaGA2ox4 were elevated in the droughted leaf, while those for several GA-biosynthesis genes were reduced by drought, but mainly in the non-growing region. In response to drought the concentrations of abscisic acid, cis-zeatin and its riboside increased in all tissues, indole-acetic acid was unchanged, while trans-zeatin and riboside, jasmonate and salicylic acid concentrations were reduced.

CONCLUSIONS

Reduced leaf elongation and maintained root growth in wheat seedlings subjected to progressive drought were associated with attenuated and increased GA content, respectively, in the growing regions. Despite increased TaGA2ox4 expression, lower GA levels in the leaf base of droughted plants were due to reduced biosynthesis rather than increased catabolism. In contrast to GA, the other hormones analysed responded to drought similarly in the leaf and roots, indicating organ-specific differential regulation of GA metabolism in response to drought.

Piperonylic acid alters growth, mineral content accumulation and reactive oxygen species-scavenging capacity in chia seedlings

p-Coumaric acid synthesis in plants involves the conversion of phenylalanine to trans-cinnamic acid via phenylalanine ammonia-lyase (PAL), which is then hydroxylated at the para-position under the action of trans-cinnamic acid 4-hydroxylase. Alternatively, some PAL enzymes accept tyrosine as an alternative substrate and convert tyrosine directly to p-coumaric acid without the intermediary of trans-cinnamic acid. In recent years, the contrasting roles of p-coumaric acid in regulating the growth and development of plants have been well-documented. To understand the contribution of trans-cinnamic acid 4-hydroxylase activity in p-coumaric acid-mediated plant growth, mineral content accumulation and the regulation of reactive oxygen species (ROS), we investigated the effect of piperonylic acid (a trans-cinnamic acid 4-hydroxylase inhibitor) on plant growth, essential macroelements, osmolyte content, ROS-induced oxidative damage, antioxidant enzyme activities and phytohormone levels in chia seedlings. Piperonylic acid restricted chia seedling growth by reducing shoot length, fresh weight, leaf area measurements and p-coumaric acid content. Apart from sodium, piperonylic acid significantly reduced the accumulation of other essential macroelements (such as K, P, Ca and Mg) relative to the untreated control. Enhanced proline, superoxide, hydrogen peroxide and malondialdehyde contents were observed. The inhibition of trans-cinnamic acid 4-hydroxylase activity significantly increased the enzymatic activities of ROS-scavenging enzymes such as superoxide dismutase, ascorbate peroxidase, catalase and guaiacol peroxidase. In addition, piperonylic acid caused a reduction in indole-3-acetic acid and salicylic acid content. In conclusion, the reduction in chia seedling growth in response to piperonylic acid may be attributed to a reduction in p-coumaric acid content coupled with elevated ROS-induced oxidative damage, and restricted mineral and phytohormone (indole-3-acetic acid and salicylic) levels.

An MYB Transcription Factor Modulates Panax notoginseng Resistance Against the Root Rot Pathogen Fusarium solani by Regulating the Jasmonate Acid Signaling Pathway and Photosynthesis

Root rot of Panax notoginseng, a precious Chinese medicinal plant, seriously impacts its sustainable production. However, the molecular regulatory mechanisms employed by P. notoginseng against root rot pathogens, including Fusarium solani, are still unclear. In this study, the PnMYB2 gene was isolated, and its expression was affected by independent treatments with four signaling molecules (methyl jasmonate, ethephon, salicylic acid, and hydrogen peroxide) as assessed by quantitative real-time PCR. Moreover, the PnMYB2 expression level was induced by F. solani infection. The PnMYB2 protein localized to the nucleus and may function as a transcription factor. When overexpressed in transgenic tobacco, the PnMYB2 gene conferred resistance to F. solani. Jasmonic acid (JA) metabolism and disease resistance-related genes were induced in the transgenic tobacco, and the JA content significantly increased compared with in the wild type. Additionally, transcriptome sequencing, Kyoto Encyclopedia of Genes and Genomes annotation enrichment, and metabolic pathway analyses of the differentially expressed genes in the transgenic tobacco revealed that JA metabolic, photosynthetic, and defense response-related pathways were activated. In summary, PnMYB2 is an important transcription factor in the defense responses of P. notoginseng against root rot pathogens that acts by regulating JA signaling, photosynthesis, and disease-resistance genes.

Nitrogen represses haustoria formation through abscisic acid in the parasitic plant Phtheirospermum japonicum

Parasitic plants are globally prevalent pathogens that withdraw nutrients from their host plants using an organ known as the haustorium. The external environment including nutrient availability affects the extent of parasitism and to understand this phenomenon, we investigated the role of nutrients and found that nitrogen is sufficient to repress haustoria formation in the root parasite Phtheirospermum japonicum. Nitrogen increases levels of abscisic acid (ABA) in P. japonicum and prevents the activation of hundreds of genes including cell cycle and xylem development genes. Blocking ABA signaling overcomes nitrogen’s inhibitory effects indicating that nitrogen represses haustoria formation by increasing ABA. The effect of nitrogen appears more widespread since nitrogen also inhibits haustoria in the obligate root parasite Striga hermonthica. Together, our data show that nitrogen acts as a haustoria repressing factor and suggests a mechanism whereby parasitic plants use nitrogen availability in the external environment to regulate the extent of parasitism.

Parasitic plants obtain nutrients from their hosts. Here the authors show that nitrogen sufficiency suppresses parasitism in the root parasite Phtheirospermum japonicum by increasing levels of the phytohormone ABA suggesting that the degree of parasitism is regulated by nutrient availability.

Expression of a Chlorophyll b Reductase Gene from Zoysia japonica Causes Changes in Leaf Color and Chlorophyll Morphology in Agrostis stolonifera

The NYC-like (NOL) enzyme is considered as an essential enzyme for chlorophyll b degradation, which catalyzes the formation of 7-hydroxymethyl chlorophyll a from chlorophyll b. The ZjNOL gene was cloned from Zoysia japonica with a completed coding sequence of 981-bp in length, encoding 326 amino acids. ZjNOL was localized on the stroma side of the thylakoid membrane, and co-localized with ZjNYC in the chloroplasts. Multiple photoregulatory elements and hormone regulatory elements were identified in the promoter region of the ZjNOL gene, and the expression level of the ZjNOL gene was dramatically up-regulated in senescence leaves, which were regulated by a variety of plant hormones. ZjNOL's ectopic expression in creeping bentgrass produced yellow leaves, thicker cortex, and smaller vascular column cells. Additionally, transgenic plants exhibited morphological alterations in their chloroplast structure, and the number of grana and thylakoids per grana stack reduced dramatically. Transgenic plants also had a lower photosynthetic rate and Fm/Fv than the control. The transgenic plants displayed a decreased chlorophyll content and a greater rate of ion leakage. The properties and activities of ZjNOL will serve as a foundation for future research into gene functions and regulatory processes.

Physiological mechanisms of ABA-induced salinity tolerance in leaves and roots of rice

Abscisic acid (ABA) plays a crucial role in response to abiotic stress as important small molecules in regulating metabolism. This study aimed to evaluate the ability of foliar spraying ABA to regulate growth quality at rice seedling stage under salt stress. Results demonstrated that salt stress strongly reduced all the growth parameters of two rice seedlings ('Chaoyouqianhao' and 'Huanghuazhan'), caused prominent decrease in the levels of photosynthetic pigments (mainly in Huanghuazhan), photosynthesis and fluorescence parameters. Salinity treatment increased the concentration of malondialdehyde (MDA) and hydrogen peroxide (H2O2) in roots, whereas significant decreased H2O2 was found in leaves of Huanghuazhan. Additionally, salinity triggered high Na+ content particularly in leaves and enhanced catalase (CAT) activities, ascorbate peroxidase (APX) and peroxidase (POD) activities of the two rice seedlings. Nevertheless, salinity-induced increased root ascorbic acid (AsA) and glutathione (GSH) levels while decreased in leaves, which depended on treatment time. Conversely, ABA application partially or completely mitigated salinity toxicity on the seedlings. ABA could reverse most of the changed physiological parameters triggered by salt stress. Specially, ABA treatment improved antioxidant enzyme levels and significantly reduced the Na+ content of two varieties as well as increased the K+, Mg2+ and Ca2+ content in leaves and roots. ABA treatment increased the hormone contents of 1-aminocclopropane carboxylic acid (ACC), trans-zeatin (TZ), N6-isopentyladenosine (IPA), Indole-3-acetic acid (IAA), and ABA in leaves of two rice varieties under salt stress. It is suggested that ABA was beneficial to protect membrane lipid peroxidation, the modulation of antioxidant defense systems and endogenous hormonal balance with imposition to salt stress.

Molecular networking and collision cross section prediction for structural isomer and unknown compound identification in plant metabolomics: a case study applied to Zhanthoxylum heitzii extracts

Mass spectrometry-based plant metabolomics allow large-scale analysis of a wide range of compounds and the discovery of potential new active metabolites with minimal sample preparation. Despite recent tools for molecular networking, many metabolites remain unknown. Our objective is to show the complementarity of collision cross section (CCS) measurements and calculations for metabolite annotation in a real case study. Thus, a systematic and high-throughput investigation of root, bark, branch, and leaf of the Gabonese plant Zhanthoxylum heitzii was performed through ultra-high performance liquid chromatography high-resolution tandem mass spectrometry (UHPLC-QTOF/MS). A feature-based molecular network (FBMN) was employed to study the distribution of metabolites in the organs of the plants and discover potential new components. In total, 143 metabolites belonging to the family of alkaloids, lignans, polyphenols, fatty acids, and amino acids were detected and a semi-quantitative analysis in the different organs was performed. A large proportion of medical plant phytochemicals is often characterized by isomerism and, in the absence of reference compounds, an additional dimension of gas phase separation can result in improvements to both quantitation and compound annotation. The inclusion of ion mobility in the ultra-high performance liquid chromatography mass spectrometry workflow (UHPLC-IMS-MS) has been used to collect experimental CCS values in nitrogen and helium (CCS_N2 and CCS_He) of Zhanthoxylum heitzii features. Due to a lack of reference data, the investigation of predicted collision cross section has enabled comparison with the experimental values, helping in dereplication and isomer identification. Moreover, in combination with mass spectra interpretation, the comparison of experimental and theoretical CCS values allowed annotation of unknown features. The study represents a practical example of the potential of modern mass spectrometry strategies in the identification of medicinal plant phytochemical components.

Genetic variation in YIGE1 contributes to ear length and grain yield in maize

Ear length (EL), which is controlled by quantitative trait loci (QTLs), is an important component of grain yield and as such is a key target trait in maize breeding. However, very few EL QTLs have been cloned, and their molecular mechanisms are largely unknown. Here, using a genome wide association study (GWAS), we identified a QTL, YIGE1, which encodes an unknown protein that regulates EL by affecting pistillate floret number. Overexpression of YIGE1 increased female inflorescence meristem (IM) size, increased EL and kernel number per row (KNPR), and thus enhanced grain yield. By contrast, CRISPR/Cas9 knockout and Mutator insertion mutant lines of YIGE1 displayed decreased IM size and EL. A single-nucleotide polymorphism (SNP) located in the regulatory region of YIGE1 had a large effect on its promoter strength, which positively affected EL by increasing gene expression. Further analysis shows that YIGE1 may be involved in sugar and auxin signal pathways to regulate maize ear development, thus affecting IM activity and floret production in maize inflorescence morphogenesis. These findings provide new insights into ear development and will ultimately facilitate maize molecular breeding.

Plant Growth Regulators in Tree Rooting

Trees are long-lived organisms with complex life cycles that provide enormous benefits both in natural and cultivated stands [...]

Red Light and Glucose Enhance Cytokinin-Mediated Bud Initial Formation in Physcomitrium patens

Growth and development of Physcomitrium patens is endogenously regulated by phytohormones such as auxin and cytokinin. Auxin induces the transition of chloronema to caulonema. This transition is also regulated by additional factors such as quantity and quality of light, carbon supply, and other phytohormones such as strigolactones and precursors of gibberrelic acid. On the other hand, cytokinins induce the formation of bud initials following caulonema differentiation. However, the influence of external factors such as light or nutrient supply on cytokinin-mediated bud initial formation has not been demonstrated in Physcomitrium patens. This study deals with the effect of light quality and nutrient supply on cytokinin-mediated bud initial formation. Bud initial formation has been observed in wild type plants in different light conditions such as white, red, and blue light in response to exogenously supplied cytokinin as well as glucose. In addition, budding assay has been demonstrated in the cry1a mutant of Physcomitrium in different light conditions. The results indicate that carbon supply and red light enhance the cytokinin response, while blue light inhibits this process in Physcomitrium.

Spatiotemporal plant hormone analysis from cryosections using laser microdissection-liquid chromatography-mass spectrometry

Laser microdissection (LMD) is used for isolating specific regions or single cells from a wide variety of tissue samples under direct microscopic observation. The LMD method enables the harvest of the cells of interest in a region or specific cells for several analyses, such as DNA/RNA analysis, proteomics, metabolomics, and other molecular analyses. Currently, LMD is used to study various biological events at the tissue or cellular level; it has been used in a wide range of research fields. In this report, we describe techniques for isolating different tissues/specific cells from cryosections of incised Arabidopsis flowering stems by LMD for spatiotemporal quantitative plant hormone analysis. The endogenous indole-3-acetic acid levels in the epidermis/cortex, vascular bundles, and pith of Arabidopsis flowering stems were approximately 19.0 pg mm^-3, 33.5 pg mm^-3, and 3.32 pg mm^-3, respectively, and these endogenous levels were altered spatiotemporally after incision. We also analyzed jasmonic acid from LMD-isolated cells and showed that the endogenous levels increased in the range of approximately 200-3,500 pg mm^-3 depending on the tissue and region at 1 h after incision and then decreased to less than 100 pg mm^-3 or undetectable levels at 24 h after incision. Quantitative analyses of phytohormones, including jasmonic acid-related molecules, gibberellin, abscisic acid, and cytokinins, could also be performed using the same cell samples. These results showed that spatiotemporal changes in plant hormones could be quantitatively and simultaneously analyzed by LMD-isolated cells from cryosections with positional information. The combination of quantitative analysis by liquid chromatography-mass spectrometry (LC-MS) and sampling by the LMD method provides a comprehensive and quantitative understanding of spatiotemporal changes in plant hormones in a region- and tissue-specific manner. Therefore, LMD-LC-MS methods will contribute to our understanding of the physiological events that control the process of plant growth and development.

Comparative Transcriptomic Analysis Provides Insight into the Key Regulatory Pathways and Differentially Expressed Genes in Blueberry Flower Bud Endo- and Ecodormancy Release

Endodormancy is the stage that perennial plants must go through to prepare for the next seasonal cycle, and it is also an adaptation that allows plants to survive harsh winters. Blueberries (Vaccinium spp.) are known to have high nutritional and commercial value. To better understand the molecular mechanisms of bud dormancy release, the transcriptomes of flower buds from the southern highbush blueberry variety “O’Neal” were analyzed at seven time points of the endo- and ecodormancy release processes. Pairwise comparisons were conducted between adjacent time points; five kinds of phytohormone were identified via these processes. A total of 12,350 differentially expressed genes (DEGs) were obtained from six comparisons. Gene Ontology analysis indicated that these DEGs were significantly involved in metabolic processes and catalytic activity. KEGG pathway analysis showed that these DEGs were predominantly mapped to metabolic pathways and the biosynthesis of secondary metabolites in endodormancy release, but these DEGs were significantly enriched in RNA transport, plant hormone signal transduction, and circadian rhythm pathways in the process of ecodormancy release. The contents of abscisic acid (ABA), salicylic acid (SA), and 1-aminocyclopropane-1-carboxylate (ACC) decreased in endo- and ecodormancy release, and the jasmonic acid (JA) level first decreased in endodormancy release and then increased in ecodormancy release. Weighted correlation network analysis (WGCNA) of transcriptomic data associated with hormone contents generated 25 modules, 9 of which were significantly related to the change in hormone content. The results of this study have important reference value for elucidating the molecular mechanism of flower bud dormancy release.

Comprehensive Analysis of Long Non-coding RNA Modulates Axillary Bud Development in Tobacco (Nicotiana tabacum L.)

Long non-coding RNAs (lncRNAs) regulate gene expression and are crucial for plant growth and development. However, the mechanisms underlying the effects of activated lncRNAs on axillary bud development remain largely unknown. By lncRNA transcriptomes of axillary buds in topped and untopped tobacco plants, we identified a total of 13,694 lncRNAs. LncRNA analysis indicated that the promoted growth of axillary bud by topping might be partially ascribed to the genes related to hormone signal transduction and glycometabolism, trans-regulated by differentially expressed lncRNAs, such as MSTRG.52498.1, MSTRG.60026.1, MSTRG.17770.1, and MSTRG.32431.1. Metabolite profiling indicated that auxin, abscisic acid and gibberellin were decreased in axillary buds of topped tobacco lines, while cytokinin was increased, consistent with the expression levels of related lncRNAs. MSTRG.52498.1, MSTRG.60026.1, MSTRG.17770.1, and MSTRG.32431.1 were shown to be influenced by hormones and sucrose treatments, and were associated with changes of axillary bud growth in the overexpression of NtCCD8 plants (with reduced axillary buds) and RNA interference of NtTB1 plants (with increased axillary buds). Moreover, MSTRG.28151.1 was identified as the antisense lncRNA of NtTB1. Silencing of MSTRG.28151.1 in tobacco significantly attenuated the expression of NtTB1 and resulted in larger axillary buds, suggesting the vital function of MSTRG.28151.1 axillary bud developmen by NtTB1. Our findings shed light on lncRNA-mRNA interactions and their functional roles in axillary bud growth, which would improve our understanding of lncRNAs as important regulators of axillary bud development and plant architecture.

Genome-Wide Analysis and Characterization of the Proline-Rich Extensin-like Receptor Kinases (PERKs) Gene Family Reveals Their Role in Different Developmental Stages and Stress Conditions in Wheat (Triticum aestivum L.)

Proline-rich extensin-like receptor kinases (PERKs) are a class of receptor kinases implicated in multiple cellular processes in plants. However, there is a lack of information on the PERK gene family in wheat. Therefore, we identified 37 PERK genes in wheat to understand their role in various developmental processes and stress conditions. Phylogenetic analysis of PERK genes from Arabidopsis thaliana, Oryza sativa, Glycine max, and T. aestivum grouped them into eight well-defined classes. Furthermore, synteny analysis revealed 275 orthologous gene pairs in B. distachyon, Ae. tauschii, T. dicoccoides, O. sativa and A. thaliana. Ka/Ks values showed that most TaPERK genes, except TaPERK1, TaPERK2, TaPERK17, and TaPERK26, underwent strong purifying selection during evolutionary processes. Several cis-acting regulatory elements, essential for plant growth and development and the response to light, phytohormones, and diverse biotic and abiotic stresses, were predicted in the promoter regions of TaPERK genes. In addition, the expression profile of the TaPERK gene family revealed differential expression of TaPERK genes in various tissues and developmental stages. Furthermore, TaPERK gene expression was induced by various biotic and abiotic stresses. The RT-qPCR analysis also revealed similar results with slight variation. Therefore, this study's outcome provides valuable information for elucidating the precise functions of TaPERK in developmental processes and diverse stress conditions in wheat.

Arabidopsis inositol polyphosphate kinases IPK1 and ITPK1 modulate crosstalk between SA-dependent immunity and phosphate-starvation responses

KEY MESSAGE

Selective Arabidopsis thaliana inositol phosphate kinase functions modulate response amplitudes in innate immunity by balancing signalling adjustments with phosphate homeostasis networks. Pyrophosphorylation of InsP6 generates InsP7 and/or InsP8 containing high-energy phosphoanhydride bonds that are harnessed during energy requirements of a cell. As bona fide co-factors for several phytohormone networks, InsP7/InsP8 modulate key developmental processes. With requirements in transducing jasmonic acid (JA) and phosphate-starvation responses (PSR), InsP8 exemplifies a versatile metabolite for crosstalks between different cellular pathways during diverse stress exposures. Here we show that Arabidopsis thaliana INOSITOL PENTAKISPHOSPHATE 2-KINASE 1 (IPK1), INOSITOL 1,3,4-TRISPHOSPHATE 5/6-KINASE 1 (ITPK1), and DIPHOSPHOINOSITOL PENTAKISPHOSPHATE KINASE 2 (VIH2) implicated in InsP8 biosynthesis, suppress salicylic acid (SA)-dependent immunity. In ipk1, itpk1 or vih2 mutants, constitutive activation of defenses lead to enhanced resistance against the Pseudomonas syringae pv tomato DC3000 (PstDC3000) strain. Our data reveal that upregulated SA-signaling sectors potentiate increased expression of several phosphate-starvation inducible (PSI)-genes, previously known in these mutants. In reciprocation, upregulated PSI-genes moderate expression amplitudes of defense-associated markers. We demonstrate that SA is induced in phosphate-deprived plants, however its defense-promoting functions are likely diverted to PSR-supportive roles. Overall, our investigations reveal selective InsPs as crosstalk mediators in defense-phosphate homeostasis and in reprogramming stress-appropriate response intensities.

Biosynthesis-based spatial metabolome of Salvia miltiorrhiza Bunge by combining metabolomics approaches with mass spectrometry-imaging

Defining the spatial distributions of metabolites and their structures are the two key aspects for interpreting the complexities of biosynthesis pathways in plants. As a means of obtaining information on the spatial distribution of metabolites, a strategy is needed that has high sensitivity and allows visualization. Toward this goal, we carried an untargeted metabolomics to obtain detailed metabolic information on different plant parts of Salvia miltiorrhiza, the roots of which are widely used in traditional Chinese medicine. Systematic optimization of desorption electrospray ionization mass spectrometry imaging (DESI-MSI) including parameter selection and sample preparation were carried out to improve the sensitivity of the method for plant samples. Guided by the metabolomics data, the spatial distributions of diverse metabolites, including phenolic acids, flavonoids, tanshinones, carbohydrates, and lipids, were characterized and visualized for both the underground and aerial parts. To integrate the information pertaining to the spatial distribution of metabolites, the flavonoids and phenolic acids (phenylpropanoid metabolic pathway) were chosen as examples for in-depth study the biosynthesis pathways in S. miltiorrhiza. The complementary data obtained from the metabolomics study and mass spectrometry imaging enabled the identification of key reactions involved in flavonoid biosynthesis in flowers, which lead the changes in metabolite distribution. The analysis also identified the core precursor for phenolic acid biosynthesis in Salvia species. Therefore, the powerful combination of metabolomics and mass spectrometry imaging provides a basis for obtaining detailed information on spatial metabolome and constitutes a platform for deep understanding the biosynthesis of bioactive metabolites in plants.

Changing Temperature Conditions during Somatic Embryo Maturation Result in Pinus pinaster Plants with Altered Response to Heat Stress

Under the global warming scenario, obtaining plant material with improved tolerance to abiotic stresses is a challenge for afforestation programs. In this work, maritime pine (Pinus pinaster Aiton) plants were produced from somatic embryos matured at different temperatures (18, 23, or 28 °C, named after M18, M23, and M28, respectively) and after 2 years in the greenhouse a heat stress treatment (45 °C for 3 h/day for 10 days) was applied. Temperature variation during embryo development resulted in altered phenotypes (leaf histology, proline content, photosynthetic rates, and hormone profile) before and after stress. The thickness of chlorenchyma was initially larger in M28 plants, but was significantly reduced after heat stress, while increased in M18 plants. Irrespective of their origin, when these plants were subjected to a heat treatment, relative water content (RWC) and photosynthetic carbon assimilation rates were not significantly affected, although M18 plants increased net photosynthesis rate after 10 days recovery (tR). M18 plants showed proline contents that increased dramatically (2.4-fold) when subjected to heat stress, while proline contents remained unaffected in M23 and M28 plants. Heat stress significantly increased abscisic acid (ABA) content in the needles of maritime pine plants (1.4-, 3.6- and 1.9-fold in M18, M23, and M28 plants, respectively), while indole-3-acetic acid content only increased in needles from M23 plants. After the heat treatment, the total cytokinin contents of needles decreased significantly, particularly in M18 and M28 plants, although levels of active forms (cytokinin bases) did not change in M18 plants. In conclusion, our results suggest that maturation of maritime pine somatic embryos at lower temperature resulted in plants with better performance when subjected to subsequent high temperature stress, as demonstrated by faster and higher proline increase, lower increases in ABA levels, no reduction in active cytokinin, and a better net photosynthesis rate recovery.

A manipulation of carotenoid metabolism influence biomass partitioning and fitness in tomato

Improving yield, nutritional value and tolerance to abiotic stress are major targets of current breeding and biotechnological approaches that aim at increasing crop production and ensuring food security. Metabolic engineering of carotenoids, the precursor of vitamin-A and plant hormones that regulate plant growth and response to adverse growth conditions, has been mainly focusing on provitamin A biofortification or the production of high-value carotenoids. Here, we show that the introduction of a single gene of the carotenoid biosynthetic pathway in different tomato cultivars induced profound metabolic alterations in carotenoid, apocarotenoid and phytohormones pathways. Alterations in isoprenoid- (abscisic acid, gibberellins, cytokinins) and non-isoprenoid (auxin and jasmonic acid) derived hormones together with enhanced xanthophyll content influenced biomass partitioning and abiotic stress tolerance (high light, salt, and drought), and it caused an up to 77% fruit yield increase and enhanced fruit's provitamin A content. In addition, metabolic and hormonal changes led to accumulation of key primary metabolites (e.g. osmoprotectants and antiaging agents) contributing with enhanced abiotic stress tolerance and fruit shelf life. Our findings pave the way for developing a new generation of crops that combine high productivity and increased nutritional value with the capability to cope with climate change-related environmental challenges.

Metabolomic and transcriptomic analysis of Lycium chinese and L. ruthenicum under salinity stress

BACKGROUND

High soil salinity often adversely affects plant physiology and agricultural productivity of almost all crops worldwide, such as the crude drug known as wolfberry. However, the mechanism of this action in wolfberry is not fully understood yet.

RESULTS

Here in this study, we studied different mechanisms potentially in Chinese wolfberry (Lycium chinese, LC) and black wolfberry (L. ruthenicum, LR) under salinity stress, by analyzing their transcriptome, metabolome, and hormone changes. The hormone detection analysis revealed that the ABA content was significantly lower in LR than LC under normal condition, and increased sharply under salinity stress in LR but not in LC. The transcriptome analysis showed that the salinity-responsive genes in wolfberry were mainly enriched in MAPK signaling, amino sugar and nucleotide sugar metabolism, carbon metabolism, and plant hormone signal transduction pathways in LC, while mainly related to carbon metabolism and protein processing in endoplasmic reticulum in LR. Metabolome results indicated that LR harbored higher flavone and flavonoid contents than LC under normal condition. However, the flavone and flavonoid contents were hardly changed in LR, but increased substantially in LC when exposed to salinity stress.

CONCLUSIONS

Our results adds ABA and flavone to mechanism understanding of salinity tolerance in wolfberry. In addition, flavone plays a positive role in resistance to salinity stress in wolfberry.

The reliance of phytohormone biosynthesis on primary metabolite precursors

There is some debate as to whether phytohormone metabolites should be classified as primary or secondary metabolites. Phytohormones have profound effects on growth - a typical trait of primary metabolites - yet several of them are formed from secondary metabolite precursors. This is further exacerbated by the blurred distinction between primary and secondary metabolism. What is clearer, however, is that phytohormones display distinctive regulatory mechanisms from other metabolites. Moreover, by contrast to microbial and mammalian systems, the majority of plant metabolite receptors characterized to date are hormone receptors. Here, we provide an overview of the metabolic links between primary metabolism and phytohormone biosynthesis in an attempt to complement recent reviews covering the signaling crosstalk between elements of core metabolism and the phytohormones. In doing so, we cover the biosynthesis of both the classical metabolic phytohormones namely auxins, salicylic acid, jasmonate, ethylene, cytokinins, brassinosteroids, gibberellins and abscisic acid as well as recently described plant growth regulators which have been proposed as novel phytohormones namely strigolactones blumenols, zaxinone and β-cyclocitral as well as melatonin. For each hormone, we describe the primary metabolite precursors which fuel its synthesis, act as conjugates or in the case of 2-oxoglutarate act more directly as a co-substrate in the biosynthesis of gibberellin, auxin and salicylic acid. Furthermore, several amino acids operate as hormone conjugates, such as jasmonate-conjugates. In reviewing the biosynthesis of all the phytohormones simultaneously, the exceptional intricacy of the biochemical interplay that underpins their interaction emerges.

Liquid Chromatography-Tandem Mass Spectrometry-Based Profiling of Plant Hormones

Phytohormones plays crucial physiological functions in plants, where they are involved in plant development, reproduction, defense, and many other functions. Phytohormones production has been found to be regulated in response to abiotic and biotic factors affecting the plant metabolism, and therefore, biosynthesis of primary and secondary metabolites. Thus, the detection and quantification of phytohormones in different plant tissues are essential to be determined unraveling the various plant metabolic pathways and behavior. Yet phytohormones analysis is always problematic, since they are found in extremely low concentrations and have a wide range of chemical and physicochemical properties. As a result, the ideal method should start with an appropriate extraction procedure followed by quantification by highly sensitive instrumental techniques providing precise and robust results. The current chapter presents an improved extraction method based on liquid-liquid extraction from a 50-mg aliquot of plant tissue for analysis of the major classes of phytohormones. Then, mass spectrometry (MS) analysis is conducted using quadrupole/linear ion trap (QLIT) mass analyzer equipped with electrospray ionization (ESI) source after a liquid chromatographic separation step. The developed method demonstrates an appropriate feasibility addressing biological questions related to phytohormones production and regulation.

Molecular mechanisms and hormonal regulation underpinning morphological dormancy: a case study using Apium graveolens (Apiaceae)

Underdeveloped (small) embryos embedded in abundant endosperm tissue, and thus having morphological dormancy (MD) or morphophysiological dormancy (MPD), are considered to be the ancestral state in seed dormancy evolution. This trait is retained in the Apiaceae family, which provides excellent model systems for investigating the underpinning mechanisms. We investigated Apium graveolens (celery) MD by combined innovative imaging and embryo growth assays with the quantification of hormone metabolism, as well as the analysis of hormone and cell-wall related gene expression. The integrated experimental results demonstrated that embryo growth occurred inside imbibed celery fruits in association with endosperm degradation, and that a critical embryo size was required for radicle emergence. The regulation of these processes depends on gene expression leading to gibberellin and indole-3-acetic acid (IAA) production by the embryo and on crosstalk between the fruit compartments. ABA degradation associated with distinct spatiotemporal patterns in ABA sensitivity control embryo growth, endosperm breakdown and radicle emergence. This complex interaction between gibberellins, IAA and ABA metabolism, and changes in the tissue-specific sensitivities to these hormones is distinct from non-MD seeds. We conclude that the embryo growth to reach the critical size and the associated endosperm breakdown inside MD fruits constitute a unique germination programme.

Hormonome Dynamics During Microgametogenesis in Different Nicotiana Species

Plant microgametogenesis involves stages leading to the progressive development of unicellular microspores into mature pollen. Despite the active and continuing interest in the study of male reproductive development, little is still known about the hormonomics at each ontogenetic stage. In this work, we characterized the profiles and dynamics of phytohormones during the process of microgametogenesis in four Nicotiana species (Nicotiana tabacum, Nicotiana alata, Nicotiana langsdorffii, and Nicotiana mutabilis). Taking advantage of advanced HPLC-ESI-MS/MS, twenty to thirty endogenous hormone derivatives were identified throughout pollen ontogenesis, including cytokinins, auxins, ABA and its derivatives, jasmonates, and phenolic compounds. The spectra of endogenous phytohormones changed dynamically during tobacco pollen ontogeny, indicating their important role in pollen growth and development. The different dynamics in the accumulation of endogenous phytohormones during pollen ontogenesis between N. tabacum (section Nicotiana) and the other three species (section Alatae) reflects their different phylogenetic positions and origin within the genus Nicotiana. We demonstrated the involvement of certain phytohormone forms, such as cis-zeatin- and methylthiol-type CKs, some derivatives of abscisic acid, phenylacetic and benzoic acids, in pollen development for the first time here. Our results suggest that unequal levels of endogenous hormones and the presence of specific derivatives may be characteristic for pollen development in different phylogenetic plant groups. These results represent the currently most comprehensive study of plant hormones during the process of pollen development.

Auxin Treatment Enhances Anthocyanin Production in the Non-Climacteric Sweet Cherry (Prunus avium L.)

Abscisic acid (ABA) is a key signaling molecule promoting ripening of non-climacteric fruits such as sweet cherry (Prunus avium L.). To shed light on the role of other hormones on fruit development, ripening and anthocyanin production, the synthetic auxin 1-naphthaleneacetic acid (NAA) was applied to sweet cherry trees during the straw-color stage of fruit development. NAA-treated fruits exhibited higher concentrations of 1-aminocyclopropane-1-carboxylic acid (ACC) and ABA-glucose ester (ABA-GE), which are a precursor of ethylene and a primary storage form of ABA, respectively. Consistent with these observations, transcript levels of genes encoding ACC synthase and ACC oxidase, both involved in ethylene biosynthesis, were increased after 6 days of NAA treatment, and both ABA concentration and expression of the regulator gene of ABA biosynthesis (NCED1 encoding 9-cis-epoxycarotenoid dioxygenase) were highest during early fruit ripening. In addition, transcript levels of key anthocyanin regulatory, biosynthetic and transport genes were significantly upregulated upon fruit exposure to NAA. This was accompanied by an increased anthocyanin concentration and fruit weight whilst fruit firmness and cracking index decreased. Altogether our data suggest that NAA treatment alters ethylene production, which in turn induces ripening in sweet cherry and enhanced anthocyanin production, possibly through ABA metabolism. The results from our study highlight the potential to use a single NAA treatment for manipulation of cherry ripening.

Transcriptomic evaluation on methyl bromide-induced phytotoxicity in Arabidopsis thaliana and its mode of phytotoxic action via the occurrence of reactive oxygen species and uneven distribution of auxin hormones

The increase in worldwide trade has caused the quality maintenance of commercialized agriproducts to be crucial in keeping its economic value. In recent years, methyl bromide (MB) has been used dominantly during quarantine and pre-shipment, despite it being an environmental hazard with global repercussions. Through this study, it was shown that Arabidopsis thaliana's 2 h exposure to the MB treatment displayed no signs of phytotoxicity, whereas its 4 h exposure significantly interfered with growth. The transcriptomic analysis found the molecular modifications in A. thaliana after the MB fumigation with the up-regulation of genes specifically relative to the abiotic and oxidative stress, and the down-regulation of auxin transporter genes. Some important gene expressions were verified by RT-qPCR and their expression patterns were similar. Oxidative stresses via the reactive oxygen species (ROS) in relation to MB phytotoxicity were confirmed with the increased malondialdehyde in MB-4h-treated A. thaliana. Uneven distribution of auxins via lower expression of auxin transporter genes was also determined using UPLC-ESI-QqQ MS. Application of two ROS scavengers such as N-acetyl-cysteine and L-glutathione minimized MB phytotoxic effect in A. thaliana. Therefore, MB caused severe oxidative stress, and alternatives regarding the use of MB should be considered.

The Meloidogyne javanica effector Mj2G02 interferes with jasmonic acid signalling to suppress cell death and promote parasitism in Arabidopsis

Plant-parasitic nematodes can cause devastating damage to crops. These nematodes secrete effectors that suppress the host immune responses to enhance their survival. In this study, Mj2G02, an effector from Meloidogyne javanica, is described. In situ hybridization and transcriptional analysis showed that Mj2G02 was highly expressed in the early infection stages and exclusively expressed in the nematode subventral oesophageal gland cells. In planta RNA interference targeting Mj2G02 impaired M. javanica parasitism, and Mj2G02-transgenic Arabidopsis lines displayed more susceptibility to M. javanica. Using an Agrobacterium-mediated transient expression system and plant immune response assays, we demonstrated that Mj2G02 localized in the plant cell nuclei and could suppress Gpa2/RBP-1-induced cell death. Moreover, by RNA-Seq and quantitative reverse transcription PCR analyses, we showed that Mj2G02 was capable of interfering with the host jasmonic acid (JA) signalling pathway. Multiple jasmonate ZIM-domain (JAZ) genes were significantly upregulated, whereas the JAR1 gene and four JA-responsive genes, MYC3, UPI, THI2.1, and WRKY75, were significantly downregulated. In addition, HPLC analysis showed that the endogenous jasmonoyl-isoleucine (JA-Ile) level in Mj2G02-transgenic Arabidopsis lines was significantly decreased compared to that in wildtype plants. Our results indicate that the M. javanica effector Mj2G02 suppresses the plant immune response, therefore facilitating nematode parasitism. This process is probably mediated by a JA-Ile reduction and JAZ enhancement to repress JA-responsive genes.

Unravelling Plant Responses to Stress-The Importance of Targeted and Untargeted Metabolomics

Climate change and an increasing population, present a massive global challenge with respect to environmentally sustainable nutritious food production. Crop yield enhancements, through breeding, are decreasing, whilst agricultural intensification is constrained by emerging, re-emerging, and endemic pests and pathogens, accounting for ~30% of global crop losses, as well as mounting abiotic stress pressures, due to climate change. Metabolomics approaches have previously contributed to our knowledge within the fields of molecular plant pathology and plant-insect interactions. However, these remain incredibly challenging targets, due to the vast diversity in metabolite volatility and polarity, heterogeneous mixtures of pathogen and plant cells, as well as rapid rates of metabolite turn-over. Unravelling the systematic biochemical responses of plants to various individual and combined stresses, involves monitoring signaling compounds, secondary messengers, phytohormones, and defensive and protective chemicals. This demands both targeted and untargeted metabolomics approaches, as well as a range of enzymatic assays, protein assays, and proteomic and transcriptomic technologies. In this review, we focus upon the technical and biological challenges of measuring the metabolome associated with plant stress. We illustrate the challenges, with relevant examples from bacterial and fungal molecular pathologies, plant-insect interactions, and abiotic and combined stress in the environment. We also discuss future prospects from both the perspective of key innovative metabolomic technologies and their deployment in breeding for stress resistance.

Genome-Wide Identification and Characterization of the Brassinazole-resistant (BZR) Gene Family and Its Expression in the Various Developmental Stage and Stress Conditions in Wheat (Triticum aestivum L.)

Brassinosteroids (BRs) play crucial roles in various biological processes, including plant developmental processes and response to diverse biotic and abiotic stresses. However, no information is currently available about this gene family in wheat (Triticum aestivum L.). In the present investigation, we identified the BZR gene family in wheat to understand the evolution and their role in diverse developmental processes and under different stress conditions. In this study, we performed the genome-wide analysis of the BZR gene family in the bread wheat and identified 20 TaBZR genes through a homology search and further characterized them to understand their structure, function, and distribution across various tissues. Phylogenetic analyses lead to the classification of TaBZR genes into five different groups or subfamilies, providing evidence of evolutionary relationship with Arabidopsis thaliana, Zea mays, Glycine max, and Oryza sativa. A gene exon/intron structure analysis showed a distinct evolutionary path and predicted the possible gene duplication events. Further, the physical and biochemical properties, conserved motifs, chromosomal, subcellular localization, and cis-acting regulatory elements were also examined using various computational approaches. In addition, an analysis of public RNA-seq data also shows that TaBZR genes may be involved in diverse developmental processes and stress tolerance mechanisms. Moreover, qRT-PCR results also showed similar expression with slight variation. Collectively, these results suggest that TaBZR genes might play an important role in plant developmental processes and various stress conditions. Therefore, this work provides valuable information for further elucidate the precise role of BZR family members in wheat.

Salt Stress Enhances Early Symbiotic Gene Expression in Medicago truncatula and Induces a Stress-Specific Set of Rhizobium-Responsive Genes

Salt stress is a major agricultural concern inhibiting not only plant growth but also the symbiotic association between legume roots and the soil bacteria rhizobia. This symbiotic association is initiated by a molecular dialogue between the two partners, leading to the activation of a signaling cascade in the legume host and, ultimately, the formation of nitrogen-fixing root nodules. Here, we show that a moderate salt stress increases the responsiveness of early symbiotic genes in Medicago truncatula to its symbiotic partner, Sinorhizobium meliloti while, conversely, inoculation with S. meliloti counteracts salt-regulated gene expression, restoring one-third to control levels. Our analysis of early nodulin 11 (ENOD11) shows that salt-induced expression is dynamic, Nod-factor dependent, and requires the ionic but not the osmotic component of salt. We demonstrate that salt stimulation of rhizobium-induced gene expression requires NSP2, which functions as a node to integrate the abiotic and biotic signals. In addition, our work reveals that inoculation with S. meliloti succinoglycan mutants also hyperinduces ENOD11 expression in the presence or absence of salt, suggesting a possible link between rhizobial exopolysaccharide and the plant response to salt stress. Finally, we identify an accessory set of genes that are induced by rhizobium only under conditions of salt stress and have not been previously identified as being nodulation-related genes. Our data suggest that interplay of core nodulation genes with different accessory sets, specific for different abiotic conditions, functions to establish the symbiosis. Together, our findings reveal a complex and dynamic interaction between plant, microbe, and environment.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Uncovering the multi-level response of Glycine max L. to the application of allelopathic biostimulant from Levisticum officinale Koch

The interest expressed by the agriculture in the category of innovative biostimulants is due to the intensive search for natural preparations. Our study is the first ever to report a complex approach to the use of allelopathic extracts from Levisticum officinale Koch. roots in soybean cultivation, includes analyses of morphological observations, and analyses of biochemical indicators. Hot method of aqueous extraction was applied. The extracts were administered via foliar application and soil treatment. Lovage extracts had high contents of polyphenolic compounds and rich micro- and macroelemental composition. The infusions did not contain gibberellic acid and indole-3-acetic acid but the abscisic acid and saccharose, glucose, and fructose were found. The extracts modified soybean plant physiology, as manifested by changes in biometric traits. Plants responded positively by increased yield. Seeds from the treated plants had higher contents of micro- and macroelements, as well as total concentrations of lipids (with a slight decrease in protein content). In addition, they featured changes in their amino acid profile and fatty acid composition. The application of allelopathic biostimulant caused increased concentrations of isoflavones and saponins. The natural biostimulants from Levisticum officinale may become a valuable tool in the sustainable agriculture.

Altered Root Growth, Auxin Metabolism and Distribution in Arabidopsis thaliana Exposed to Salt and Osmotic Stress

Salt and osmotic stress are the main abiotic stress factors affecting plant root growth and architecture. We investigated the effect of salt (100 mM NaCl) and osmotic (200 mM mannitol) stress on the auxin metabolome by UHPLC-MS/MS, auxin distribution by confocal microscopy, and transcript levels of selected genes by qRT-PCR in Arabidopsis thaliana ecotype Columbia-0 (Col-0) and DR5rev::GFP (DR5) line. During long-term stress (13 days), a stability of the auxin metabolome and a tendency to increase indole-3-acetic acid (IAA) were observed, especially during salt stress. Short-term stress (3 h) caused significant changes in the auxin metabolome, especially NaCl treatment resulted in a significant reduction of IAA. The data derived from auxin profiling were consistent with gene expressions showing the most striking changes in the transcripts of YUC, GH3, and UGT transcripts, suggesting disruption of auxin biosynthesis, but especially in the processes of amide and ester conjugation. These data were consistent with the auxin distribution observed in the DR5 line. Moreover, NaCl treatment caused a redistribution of auxin signals from the quiescent center and the inner layers of the root cap to the epidermal and cortical cells of the root elongation zone. The distribution of PIN proteins was also disrupted by salt stress; in particular, PIN2 was suppressed, even after 5 min of treatment. Based on our results, the DR5 line was more sensitive to the applied stresses than Col-0, although both lines showed similar trends in root morphology, as well as transcriptome and metabolome parameters under stress conditions.

Full-length transcriptome analysis provides new insights into the early bolting occurrence in medicinal Angelica sinensis

Angelica sinensis (Oliv.) Diels root part is an integral component of traditional Chinese medicine, widely prescribed to improve blood circulation and blood stasis. However, early bolting of A. sinensis compromises the quality of the roots and hence is a major limitation for yield of medicinal materials. To date, little information about the molecular mechanisms underlying bolting is available for this important medicinal plant. To identify genes putatively involved in early bolting, we have conducted the transcriptome analysis of the shoot tips of the early-bolting plants and non-bolting (normal) plants of A. sinensis, respectively, using a combination of third-generation sequencing and next-generation sequencing. A total of 43,438 non-redundant transcripts were collected and 475 unique differentially expressed genes (DEGs) were identified. Gene annotation and functional analyses revealed that DEGs were highly involved in plant hormone signaling and biosynthesis pathways, three main flowering pathways, pollen formation, and very-long-chain fatty acids biosynthesis pathways. The levels of endogenous hormones were also changed significantly in the early bolting stage of A. sinensis. This study provided new insights into the transcriptomic control of early bolting in A. sinensis, which could be further applied to enhance the yield of medicinally important raw materials.

Discovery and modulation of diterpenoid metabolism improves glandular trichome formation, artemisinin production and stress resilience in Artemisia annua

Plants synthesize diverse diterpenoids with numerous functions in organ development and stress resistance. However, the role of diterpenoids in glandular trichome (GT) development and GT-localized biosynthesis in plants remains unknown. Here, the identification of 10 diterpene synthases (diTPSs) revealed the diversity of diterpenoid biosynthesis in Artemisia annua. Protein-protein interactions (PPIs) between AaKSL1 and AaCPS2 in the plastids highlighted their potential functions in modulating metabolic flux to gibberellins (GAs) or ent-isopimara-7,15-diene-derived metabolites (IDMs) through metabolic engineering. A phenotypic analysis of transgenic plants suggested a complex repertoire of diterpenoids in Artemisia annua with important roles in GT formation, artemisinin accumulation and stress resilience. Metabolic engineering of diterpenoids simultaneously increased the artemisinin yield and stress resistance. Transcriptome and metabolic profiling suggested that bioactive GA₄ /GA₁ promote GT formation. Collectively, these results expand our knowledge of diterpenoids and show the potential of diterpenoids to simultaneously improve both the GT-localized metabolite yield and stress resistance, in planta.

Elevated CO2 modulates the effect of heat stress responses in Triticum aestivum by differential expression of isoflavone reductase-like (IRL) gene

Two wheat genotypes forming high and low biomass (HB and LB), exhibiting differential expression of an isoflavone reductase-like (IRL) gene, and resulting in contrasting grain yield under heat stress field conditions, were analyzed in detail for their responses under controlled heat and elevated CO2 conditions. Significant differences in IRL expression between the two lines were hypothesized to be the basis of their differential performance under the tested conditions and their stress tolerance potential. By a holistic approach integrating advanced cell physiological phenotyping of the antioxidative and phytohormone system in spikes and leaves with measurements of ecophysiological and agronomic traits, the genetic differences of the genotypes in IRL expression were assessed. In response to heat and elevated CO2, the two genotypes showed opposite regulation of IRL expression, which was associated with cytokinin concentration, total flavonoid contents, activity of superoxide dismutase, antioxidant capacity and photosynthetic rate in leaves and cytokinin concentration and ascorbate peroxidase activity in spikes. Our study showed that IRL expression is associated with wheat yield performance under heat stress at anthesis, mediated by diverse physiological mechanisms. Hence, based on our results, the IRL gene is a promising candidate for developing genetic markers for breeding heat-tolerant wheat.

Elevated Temperature Induced Adaptive Responses of Two Lupine Species at Early Seedling Phase

This study aimed to investigate the impact of climate warming on hormonal traits of invasive and non-invasive plants at the early developmental stage. Two different lupine species—invasive Lupinus polyphyllus Lindl. and non-invasive Lupinus luteus L.—were used in this study. Plants were grown in climate chambers under optimal (25 °C) and simulated climate warming conditions (30 °C). The content of phytohormone indole-3-acetic acid (IAA), ethylene production and the adaptive growth of both species were studied in four-day-old seedlings. A higher content of total IAA, especially of IAA-amides and transportable IAA, as well as higher ethylene emission, was determined to be characteristic for invasive lupine both under optimal and simulated warming conditions. It should be noted that IAA-L-alanine was detected entirely in the invasive plants under both growth temperatures. Further, the ethylene emission values increased significantly in invasive lupine hypocotyls under 30 °C. Invasive plants showed plasticity in their response by reducing growth in a timely manner and adapting to the rise in temperature. Based on the data of the current study, it can be suggested that the invasiveness of both species may be altered under climate warming conditions.

Dynamics of Auxin and Cytokinin Metabolism during Early Root and Hypocotyl Growth in Theobroma cacao

The spatial location and timing of plant developmental events are largely regulated by the well balanced effects of auxin and cytokinin phytohormone interplay. Together with transport, localized metabolism regulates the concentration gradients of their bioactive forms, ultimately eliciting growth responses. In order to explore the dynamics of auxin and cytokinin metabolism during early seedling growth in Theobroma cacao (cacao), we have performed auxin and cytokinin metabolite profiling in hypocotyls and root developmental sections at different times by using ultra-high-performance liquid chromatography-electrospray tandem mass spectrometry (UHPLC-MS/MS). Our work provides quantitative characterization of auxin and cytokinin metabolites throughout early root and hypocotyl development and identifies common and distinctive features of auxin and cytokinin metabolism during cacao seedling development.

Natural allelic variation in a modulator of auxin homeostasis improves grain yield and nitrogen use efficiency in rice

The external application of nitrogen (N) fertilizers is an important practice for increasing crop production. However, the excessive use of fertilizers significantly increases production costs and causes environmental problems, making the improvement of crop N-use efficiency (NUE) crucial for sustainable agriculture in the future. Here we show that the rice (Oryza sativa) NUE quantitative trait locus DULL NITROGEN RESPONSE1 (qDNR1), which is involved in auxin homeostasis, reflects the differences in nitrate (NO3-) uptake, N assimilation, and yield enhancement between indica and japonica rice varieties. Rice plants carrying the DNR1indica allele exhibit reduced N-responsive transcription and protein abundance of DNR1. This, in turn, promotes auxin biosynthesis, thereby inducing AUXIN RESPONSE FACTOR-mediated activation of NO3- transporter and N-metabolism genes, resulting in improved NUE and grain yield. We also show that a loss-of-function mutation at the DNR1 locus is associated with increased N uptake and assimilation, resulting in improved rice yield under moderate levels of N fertilizer input. Therefore, modulating the DNR1-mediated auxin response represents a promising strategy for achieving environmentally sustainable improvements in rice yield.

Boronic Acid-Functionalized Scholl-Coupling Mesoporous Polymers for Online Solid-Phase Extraction of Brassinosteroids from Plant-Derived Foodstuffs

Brassinosteroids (BRs) are natural, nontoxic, non-hazardous, biosafe, and eco-friendly plant hormones, possessing diverse pharmacological activities. However, little is known about the type and content of BRs in frequently consumed plant-derived foodstuffs because of their low abundance and high abundance of interference. In this study, a selective, accurate, and sensitive method based on the online solid-phase extraction using the boronic acid-functionalized Scholl-coupling microporous polymer was developed for the analysis of BRs in plant-derived foodstuffs. Under optimum conditions, an excellent linearity (R² ≥ 0.9970) and lower limits of detection (0.010-0.070 pg mL^-1) were obtained. The high relative recoveries were in the range of 90.33-109.34% with relative standard deviations less than 9.73%. The method was successfully used for the determination of BRs in fifteen plant-derived foodstuffs. The present work offers a valuable tool for exploring BRs from the plant-derived foodstuffs and can provide useful information for developing functional foods.

Regulation of 2,4-D Isooctyl Ester on Triticum aestivum and Aegilops tauschii Tillering and Endogenous Phytohormonal Responses

Tillering is an important agronomic trait essential for the yield of Triticum aestivum and the propagation of Aegilops tauschii. However, the effect of phytohormones on T. aestivum and Ae. tauschii tillering and the underlying regulatory mechanisms remain poorly understood. In the study, we found that T. aestivum and Ae. tauschii exhibited different tillering sensitivities to the auxin herbicide 2,4-D isooctyl ester. At 3 days post-application, tiller bud growth was inhibited by 77.50% in T. aestivum, corresponding to 2.0-fold greater inhibition than that in Ae. tauschii (38.71%). Transcriptome analysis showed that differentially expressed genes (DEGs) in the T. aestivum response to 2,4-D isooctyl ester were mainly enriched in plant hormone metabolism and signal transduction pathways, but similar changes were not observed in Ae. tauschii. Among that, the auxin biosynthesis and signaling induced by 2,4-D isooctyl ester was quite different between the two species. A total of nine candidate genes involved in varied tillering responses were selected from the DEGs and validated by quantitative real-time PCR. Endogenous hormone levels were assayed to further verify the RNA-seq results. After 2,4-D isooctyl ester treatment, a significant increase in abscisic acid (ABA) levels was observed in T. aestivum, whereas ABA levels were relatively stable in Ae. tauschii. The herbicide induced more cytokinin (CTK) accumulation in Ae. tauschii than in T. aestivum. External ABA clearly restricted tiller bud growth in both T. aestivum and Ae. tauschii, while 6-benzyl aminopurine had no significant effect. These results indicate that ABA and CTK may be related with 2,4-D isooctyl ester-regulated tillering differences between the two species, which will help to further understand the mechanism of the auxin-mediated regulation of tillering.

Coordinating the morphogenesis-differentiation balance by tweaking the cytokinin-gibberellin equilibrium

Morphogenesis and differentiation are important stages in organ development and shape determination. However, how they are balanced and tuned during development is not fully understood. In the compound leaved tomato, an extended morphogenesis phase allows for the initiation of leaflets, resulting in the compound form. Maintaining a prolonged morphogenetic phase in early stages of compound-leaf development in tomato is dependent on delayed activity of several factors that promote differentiation, including the CIN-TCP transcription factor (TF) LA, the MYB TF CLAU and the plant hormone Gibberellin (GA), as well as on the morphogenesis-promoting activity of the plant hormone cytokinin (CK). Here, we investigated the genetic regulation of the morphogenesis-differentiation balance by studying the relationship between LA, CLAU, TKN2, CK and GA. Our genetic and molecular examination suggest that LA is expressed earlier and more broadly than CLAU and determines the developmental context of CLAU activity. Genetic interaction analysis indicates that LA and CLAU likely promote differentiation in parallel genetic pathways. These pathways converge downstream on tuning the balance between CK and GA. Comprehensive transcriptomic analyses support the genetic data and provide insights into the broader molecular basis of differentiation and morphogenesis processes in plants.

Morphogenesis and differentiation are crucial steps in the formation and shaping of organs in both plants and animals. A wide array of transcription factors and hormones were shown to act together to support morphogenesis or promote differentiation. However, a comprehensive molecular and genetic understating of how morphogenesis and differentiation are coordinated during development is still missing. We addressed these questions in the context of the development of the tomato compound leaf, for which many regulators have been described. Investigating the coordination among these different actors, we show that several discrete genetic pathways promote differentiation. Downstream of these separate pathways, two important plant hormones, cytokinin and gibberellin, act antagonistically to tweak the morphogenesis-differentiation balance.