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Phosphorus (P) is a major element required for plant growth and development. To cope with P shortage, plants activate local and long-distance signaling pathways, such as an increase in the production and exudation of strigolactones (SLs). The role of the latter in mitigating P deficiency is, however, still largely unknown. To shed light on this, we studied the transcriptional response to P starvation and replenishment in wild-type rice and a SL mutant, dwarf10 (d10), and upon exogenous application of the synthetic SL GR24. P starvation resulted in major transcriptional alterations, such as the upregulation of P TRANSPORTER, SYG1/PHO81/XPR1 (SPX) and VACUOLAR PHOSPHATE EFFLUX TRANSPORTER. Gene Ontology (GO) analysis of the genes induced by P starvation showed enrichment in phospholipid catabolic process and phosphatase activity. In d10, P deficiency induced upregulation of genes enriched for sesquiterpenoid production, secondary shoot formation and metabolic processes, including lactone biosynthesis. Furthermore, several genes induced by GR24 treatment shared the same GO terms with P starvation-induced genes, such as oxidation reduction, heme binding and oxidoreductase activity, hinting at the role that SLs play in the transcriptional reprogramming upon P starvation. Gene co-expression network analysis uncovered a METHYL TRANSFERASE that displayed co-regulation with known rice SL biosynthetic genes. Functional characterization showed that this gene encodes an enzyme catalyzing the conversion of carlactonoic acid to methyl carlactonoate. Our work provides a valuable resource to further studies on the response of crops to P deficiency and reveals a tool for the discovery of SL biosynthetic genes.

To establish persistent infections in host plants, herbivorous invaders, such as root-knot nematodes, must rely on effectors for suppressing damage-induced jasmonate-dependent host defenses. However, at present, the effector mechanisms targeting the biosynthesis of biologically active jasmonates to avoid adverse host responses are unknown.Using yeast-two-hybrid, in planta co-immunoprecipitation, and mutant analyses, we identified 12-oxophytodienoate reductase 2 (OPR2) as an important host target of the stylet-secreted effector MiMSP32 of the root-knot nematode Meloidogyne incognita. MiMSP32 has no informative sequence similarities with other functionally annotated genes but was selected for the discovery of novel effector mechanisms based on evidence of positive, diversifying selection.OPR2 catalyzes the conversion of a derivative of 12-oxophytodienoate to jasmonic acid (JA) and operates parallel to 12-oxophytodienoate reductase 3 (OPR3), which controls the main pathway in the biosynthesis of jasmonates. We show that MiMSP32 targets OPR2 to promote parasitism of M. incognita in host plants independent of OPR3-mediated JA biosynthesis.Artificially manipulating the conversion of the 12-oxophytodienoate by OPRs increases susceptibility to multiple unrelated plant invaders. Our study is the first to shed light on a novel effector mechanism targeting this process to regulate susceptibility of host plants

Thermomorphogenesis is, among other traits, characterized by enhanced hypocotyl elongation due to the induction of auxin biosynthesis genes like YUCCA8 by transcription factors, most notably PHYTOCHROME INTERACTING FACTOR 4 (PIF4). Efficient binding of PIF4 to the YUCCA8 locus under warmth depends on HISTONE DEACETYLASE 9 (HDA9) activity, which mediates histone H2A.Z depletion at the YUCCA8 locus. However, HDA9 lacks intrinsic DNA-binding capacity, and how HDA9 is recruited to YUCCA8, and possibly other PIF4-target sites, is currently not well understood. The Mediator complex functions as a bridge between transcription factors bound to specific promoter sequences and the basal transcription machinery containing RNA polymerase II. Mutants of Mediator component Mediator25 (MED25) exhibit reduced hypocotyl elongation and reduced expression of YUCCA8 at 27°C. In line with a proposed role for MED25 in thermomorphogenesis in Arabidopsis (Arabidopsis thaliana), we demonstrated an enhanced association of MED25 to the YUCCA8 locus under warmth and interaction of MED25 with both PIF4 and HDA9. Genetic analysis confirmed that MED25 and HDA9 operate in the same pathway. Intriguingly, we also showed that MED25 destabilizes HDA9 protein. Based on our findings, we propose that MED25 recruits HDA9 to the YUCCA8 locus by binding to both PIF4 and HDA9.

Many studies proposed the use of stable carbon isotope ratio (δ13C) as a predictor of abiotic stresses in plants, considering only drought and nitrogen deficiency without further investigating the impact of other nutrient deficiencies, that is, phosphorus (P) and/or iron (Fe) deficiencies. To fill this knowledge gap, we assessed the δ13C of barley (Hordeum vulgare L.), cucumber (Cucumis sativus L.), maize (Zea mays L.), and tomato (Solanum lycopersicon L.) plants suffering from P, Fe, and combined P/Fe deficiencies during a two-week period using an isotope-ratio mass spectrometer. Simultaneously, plant physiological status was monitored with an infra-red gas analyzer. Results show clear contrasting time-, treatment-, species-, and tissue-specific variations. Furthermore, physiological parameters showed limited correlation with δ13C shifts, highlighting that the plants' δ13C, does not depend solely on photosynthetic carbon isotope fractionation/discrimination (Δ). Hence, the use of δ13C as a predictor is highly discouraged due to its inability to detect and discern different nutrient stresses, especially when combined stresses are present.

Climate change necessitates increased stress resilience of food crops. We describe four potential solutions, with emphasis on a relatively novel approach aiming at true tolerance of drought rather than improved water-holding capacity of crops, which is a common approach in current breeding and genome editing efforts. Some Angiosperms are known to tolerate loss of 95% of their cellular water, without dying, not dissimilar to seeds. The molecular mechanisms and their regulation underlying this remarkable ability are potentially useful to design tolerant crops. Since most crops produce desiccation tolerant seeds, genomic information for this attribute is present but inactive in vegetative parts of the plant. Based on recent evidence from both seeds and desiccation tolerant Angiosperms we address possible routes to 'flipping the switch' to vegetative desiccation tolerance in major crops.

High-throughput (HTP) plant phenotyping approaches are developing rapidly and are already helping to bridge the genotype–phenotype gap. However, technologies should be developed beyond current physico-spectral evaluations to extend our analytical capacities to the subcellular level. Metabolites define and determine many key physiological and agronomic features in plants and an ability to integrate a metabolomics approach within current HTP phenotyping platforms has huge potential for added value. While key challenges remain on several fronts, novel technological innovations are upcoming yet under-exploited in a phenotyping context. In this review, we present an overview of the state of the art and how current limitations might be overcome to enable full integration of metabolomics approaches into a generic phenotyping pipeline in the near future.

We present unresolved questions in plant abiotic stress biology as posed by 15 research groups with expertise spanning eco-physiology to cell and molecular biology. We present unresolved questions in plant abiotic stress biology as posed by 15 research groups with expertise spanning eco-physiology to cell and molecular biology. Common themes of these questions include the need to better understand how plants detect water availability, temperature, salinity, and rising carbon dioxide (CO2) levels; how environmental signals interface with endogenous signaling and development (e.g. circadian clock and flowering time); and how this integrated signaling controls downstream responses (e.g. stomatal regulation, proline metabolism, and growth versus defense balance). The plasma membrane comes up frequently as a site of key signaling and transport events (e.g. mechanosensing and lipid-derived signaling, aquaporins). Adaptation to water extremes and rising CO2 affects hydraulic architecture and transpiration, as well as root and shoot growth and morphology, in ways not fully understood. Environmental adaptation involves tradeoffs that limit ecological distribution and crop resilience in the face of changing and increasingly unpredictable environments. Exploration of plant diversity within and among species can help us know which of these tradeoffs represent fundamental limits and which ones can be circumvented by bringing new trait combinations together. Better defining what constitutes beneficial stress resistance in different contexts and making connections between genes and phenotypes, and between laboratory and field observations, are overarching challenges.

Adaptor protein (AP) complexes are evolutionarily conserved vesicle transport regulators that recruit coat proteins, membrane cargoes and coated vesicle accessory proteins. As in plants endocytic and post-Golgi trafficking intersect at the trans-Golgi network, unique mechanisms for sorting cargoes of overlapping vesicular routes are anticipated. The plant AP complexes are part of the sorting machinery, but despite some functional information, their cargoes, accessory proteins and regulation remain largely unknown. Here, by means of various proteomics approaches, we generated the overall interactome of the five AP and the TPLATE complexes in Arabidopsis thaliana. The interactome converged on a number of hub proteins, including the thus far unknown adaptin binding-like protein, designated P34. P34 interacted with the clathrin-associated AP complexes, controlled their stability and, subsequently, influenced clathrin-mediated endocytosis and various post-Golgi trafficking routes. Altogether, the AP interactome network offers substantial resources for further discoveries of unknown endomembrane trafficking regulators in plant cells.

Seeds are essential for plant reproduction, survival, and dispersal. Germination ability and successful establishment of young seedlings strongly depend on seed quality and on environmental factors such as nutrient availability. In tomato (Solanum lycopersicum) and many other species, seed quality and seedling establishment characteristics are determined by genetic variation, as well as the maternal environment in which the seeds develop and mature. The genetic contribution to variation in seed and seedling quality traits and environmental responsiveness can be estimated at transcriptome level in the dry seed by mapping genomic loci that affect gene expression (expression QTLs) in contrasting maternal environments. In this study, we applied RNA-sequencing to construct a linkage map and measure gene expression of seeds of a tomato recombinant inbred line (RIL) population derived from a cross between S. lycopersicum (cv. Moneymaker) and S. pimpinellifolium (G1.1554). The seeds matured on plants cultivated under different nutritional environments, i.e., on high phosphorus or low nitrogen. The obtained single-nucleotide polymorphisms (SNPs) were subsequently used to construct a genetic map. We show how the genetic landscape of plasticity in gene regulation in dry seeds is affected by the maternal nutrient environment. The combined information on natural genetic variation mediating (variation in) responsiveness to the environment may contribute to knowledge-based breeding programs aiming to develop crop cultivars that are resilient to stressful environments.

Drying fruits and vegetables is a long-established preservation method, and for tomatoes, in most cases sun-drying is preferred. Semi-drying is relatively a new application aimed to preserve better the original tomato properties. We have assessed the effects of different drying methods on the phytochemical variation in tomato products using untargeted metabolomics and targeted analyses of key compounds. An LC-MS approach enabled the relative quantification of 890 mostly semi-polar secondary metabolites and GC–MS analysis in the relative quantification of 270 polar, mostly primary metabolites. Metabolite profiles of sun-dried and oven-dried samples were clearly distinct and temperature-dependent. Both treatments caused drastic changes in lycopene and vitamins with losses up to > 99% compared to freeze-dried controls. Semi-drying had less impact on these compounds. In vitro bioaccessibility analyses of total phenolic compounds and antioxidants in a gastrointestinal digestion protocol revealed the highest recovery rates in semi-dried fruits. Semi-drying is a better way of preserving tomato phytochemicals, based on both composition and bioaccessibility results. © 2022 Elsevier Ltd

Although plants are immobile, many of their organs are flexible to move in response to environmental cues. In dense vegetation, plants detect neighbors through far-red light perception with their leaf tip. They respond remotely, with asymmetrical growth between the abaxial and adaxial sides of the leafstalk, the petiole. This results in upward movement that brings the leaf blades into better lit zones of the canopy. The plant hormone auxin is required for this response, but it is not understood how non-differential leaf tip-derived auxin can remotely regulate movement. Here, we show that remote signaling of far-red light promotes auxin accumulation in the abaxial petiole. This local auxin accumulation is facilitated by reinforcing an intrinsic directionality of the auxin transport protein PIN3 on the petiole endodermis, as visualized with a PIN3-GFP line. Using an auxin biosensor, we show that auxin accumulates in all cell layers from endodermis to epidermis in the abaxial petiole, upon far-red light signaling in the remote leaf tip. In the petiole, auxin elicits a response to both auxin itself as well as a second growth promoter; gibberellin. We show that this dual regulation is necessary for hyponastic leaf movement in response to light. Our data indicate that gibberellin is required to permit cell growth, whereas differential auxin accumulation determines which cells can grow. Our results reveal how plants can spatially relay information about neighbor proximity from their sensory leaf tips to the petiole base, thus driving adaptive growth.

During salt stress, the root system architecture of a plant is important for survival. Different accessions ofArabidopsis thalianahave adopted different strategies in remodeling their root architecture during salt stress. Salt induces a multiphase growth response in roots, consisting of a stop phase, quiescent phase, recovery phase and eventually a new level of homeostasis. We explored natural variation in the length of and growth rate during these phases in both main and lateral roots and find that some accessions lack the quiescent phase. Using mathematical models and correlation-based network, allowed us to correlate dynamic traits to overall root architecture and discover that both the main root growth rate during homeostasis and lateral root appearance are the strongest determinants of overall root architecture. In addition, this approach revealed a trade-off between investing in main or lateral root length during salt stress. By studying natural variation in high-resolution temporal root growth using mathematical modeling, we gained new insights in the interactions between dynamic root growth traits and we identified key traits that modulate overall root architecture during salt stress.Summary statementBy studying natural variation in salt-induced root growth phases inArabidopsis, we show that main root growth rate during homeostasis and lateral root appearance contribute most to root architecture and we reveal a trade-off between investing in main and lateral root growth during salt stress.

Introduction The white asparagus season lasts 4 months while the harvest period per field is 8 weeks. Different varieties are better suited for harvesting early or late in the season. Little is known of the dynamics of secondary metabolites of white asparagus during the production season. Objective Characterization of the metabolome of white asparagus spears covering volatile and non-volatile composition in relation to quality aspects. Methods Eight varieties, harvested repeatedly during two consecutive seasons were analysed following an untargeted metabolomics workflow using SPME GC–MS and LC–MS. Linear regression, cluster and network analyses were used to explore the profile dynamics, unravel patterns and study the influence of genotype and environment. Results The metabolite profiles were influenced by the harvest moment and genetic background. Metabolites that significantly changed over time were distributed across seven clusters based on their temporal patterns. Two clusters including monoterpenes, benzenoids and saponins showed the most prominent seasonal changes. The changes depicted by the other five clusters were mainly ≤ 2-fold relative to the harvest start. Known asparagus aroma compounds were found to be relatively stable across the season/varieties. Heat-enhanced cultivation appeared to yield spears early in season with a similar metabolome to those harvested later. Conclusion The dynamics of the white asparagus metabolome is influenced by a complex relationship between the onset of spear development, the moment of harvest and the genetic background. The typical perceived asparagus flavour profile is unlikely to be significantly affected by these dynamics.

New treatment steps are needed to better remove nutrients from WWTP effluents to prevent further eutrophication of the receiving waterbodies. Algae can be used to remove nutrients from effluent, but the subsequent removal of the algae biomass remains a challenge. Employing the high filtration capacity of dreissenid mussels may offer an efficient tool to remove effluent grown algae. The aim of the present study was therefore to evaluate if an algae-mussel trophic cascade allows an efficient removal of both nutrients and effluent-cultured algae. To this end, we inoculated WWTP effluent with the alga Tetradesmus obliquus in a batch system and monitored algal growth and nutrient concentrations for 11 days. Subsequently, we fed this algal-effluent solution to Dreissena bugensis for 3 days, after which we determined the amount of remaining algae and produced (pseudo)faeces. The algae-mussel set-up was able to remove 99% of P and 99% of N from the initial effluent, and the combination of algae settlement and mussel filtration resulted in a 94% removal of suspended algae after only 24 h. A total of 67% of the algae were consumed by the mussels after 3 days. Most filtered algae were deposited as pseudofaeces. An even higher efficiency may be achieved by selecting algae with a high nutrient removal capacity, but also with a high palatability for the mussels. Nonetheless, this is the first research that shows that an algae-mussel cascade could already offer an efficient solution to reduce nutrient concentrations in WWTP effluent. This may reduce costs, energy consumption and coagulants use at WWTPs, and could offer an alternative for high-tech treatment techniques, which may be more suitable in countries lacking the infrastructure to build these high-tech treatment steps.

We describe the dramatic shifts in translation that occur during seed maturation, germination, and seedling establishment. Using network analysis, we identify putative regulatory relationships and subsequently confirm some of them in vivo.Seed maturation is the developmental process that prepares the embryo for the desiccated waiting period before germination. It is associated with a series of physiological changes leading to the establishment of seed dormancy, seed longevity, and desiccation tolerance. We studied translational changes during seed maturation and observed a gradual reduction in global translation during seed maturation. Transcriptome and translatome profiling revealed specific reduction in the translation of thousands of genes. By including previously published data on germination and seedling establishment, a regulatory network based on polysome occupancy data was constructed: SeedTransNet. Network analysis predicted translational regulatory pathways involving hundreds of genes with distinct functions. The network identified specific transcript sequence features suggesting separate translational regulatory circuits. The network revealed several seed maturation-associated genes as central nodes, and this was confirmed by specific seed phenotypes of the respective mutants. One of the regulators identified, an AWPM19 family protein, PM19-Like1 (PM19L1), was shown to regulate seed dormancy and longevity. This putative RNA-binding protein also affects the translational regulation of its target mRNA, as identified by SeedTransNet. Our data show the usefulness of SeedTransNet in identifying regulatory pathways during seed phase transitions.

Trained sensory panels are regularly used to rate food products but do not allow for data-driven approaches to steer food product development. This study evaluated the potential of a molecular-based strategy by analyzing 27 tomato soups that were enhanced with yeast-derived flavor products using a sensory panel as well as LC-MS and GC-MS profiling. These data sets were used to build prediction models for 26 different sensory attributes using partial least squares analysis. We found driving separation factors between the tomato soups and metabolites predicting different flavors. Many metabolites were putatively identified as dipeptides and sulfur-containing modified amino acids, which are scientifically described as related to umami or having “garlic-like” and “onion-like” attributes. Proposed identities of high-impact sensory markers (methionyl-proline and asparagine-leucine) were verified using MS/MS. The overall results highlighted the strength of combining sensory data and metabolomics platforms to find new information related to flavor perception in a complex food matrix.

Fusarium wilt, caused by Fusarium oxysporum f. sp. cucumerinum (Fo), is a severe soil-borne disease affecting cucumber production worldwide, particularly under monocropping in greenhouses. Silicon (Si) plays an important role in improving the resistance of crops to Fusarium wilt, but the underlying mechanism is largely unclear. Here, an in vitro study showed that 3 mmol·l-1 Si had the best inhibitory effect on the mycelial growth of F. oxysporum in potato dextrose agar (PDA) culture for 7 days. Subsequently, the occurrence of cucumber wilt disease and its mechanisms were investigated upon treatments with exogenous silicon under soil culture. The plant height, stem diameter, root length, and root activity under Si+Fo treatment increased significantly by 39.53%, 94.87%, 74.32%, and 95.11% compared with Fo only. Importantly, the control efficiency of Si+Fo was 69.31% compared with that of Fo treatment. Compared with Fo, the activities of peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) significantly increased by 148.92%, 26.47%, and 58.54%, while the contents of H2O2, O2·−, and malondialdehyde (MDA) notably decreased by 21.67%, 59.67%, and 38.701%, respectively, in roots of cucumber plants treated with Si + Fo. Compared with Fo treatment, the net photosynthesis rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), maximum RuBisCO carboxylation rates (Vcmax), maximum RuBP regeneration rates (Jmax), and activities of ribulose-1,5-bisphosphate carboxylase (RuBisCO), fructose-1,6-bisphosphatase (FBPase), and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and the expression of FBPA, TPI, SBPase, and FBPase in Si+Fo treatment increased significantly. Furthermore, Si alleviated stomatal closure and enhanced endogenous silicon content compared with only Fo inoculation. The study results suggest that exogenous silicon application improves cucumber resistance to Fusarium wilt by stimulating the antioxidant system, photosynthetic capacity, and stomatal movement in cucumber leaves. This study brings new insights into the potential of Si application in boosting cucumber resistance against Fusarium wilt with a bright prospect for Si use in cucumber production under greenhouse conditions.

Metabolomics is proving a useful approach for many of the main future goals in agronomy and food production such as sustainability/crop resilience, food quality, safety, storage, and nutrition. Targeted and/or untargeted small-molecule analysis, coupled to chemometric analysis, has already unveiled a great deal of the complexity of plant-based foods, but there is still 'dark matter' to be discovered. Moreover, state-of-the-art food metabolomics offers insights into the molecular mechanisms underlying sensorial and nutritional characteristics of foods and thus enables higher precision and speed. This review describes recent applications of food metabolomics from fork to farm and focuses on the opportunities these bring to continue food innovation and support the shift to plant-based foods.

Plants alter their morphology and cellular homeostasis to promote resilience under a variety of heat regimes. Molecular processes that underlie these responses have been intensively studied and found to encompass diverse mechanisms operating across a broad range of cellular components, timescales and temperatures. This review explores recent progress throughout this landscape with a particular focus on thermosensing in the model plant Arabidopsis. Direct temperature sensors include the photosensors phytochrome B and phototropin, the clock component ELF3 and an RNA switch. In addition, there are heat‐regulated processes mediated by ion channels, lipids and lipid‐modifying enzymes, taking place at the plasma membrane and the chloroplast. In some cases, the mechanism of temperature perception is well understood but in others, this remains an open question. Potential novel thermosensing mechanisms are based on lipid and liquid–liquid phase separation. Finally, future research directions of high temperature perception and signalling pathways are discussed., Knowledge of how plants sense elevated temperatures and initiate protective responses has greatly increased in recent years. Diverse mechanisms, involving changes in proteins, RNA and lipids, function in thermosensing across a range of timescales, locations and temperatures.

Mass spectrometry-based metabolomics approaches can enable detection and quantification of many thousands of metabolite features simultaneously. However, compound identification and reliable quantification are greatly complicated owing to the chemical complexity and dynamic range of the metabolome. Simultaneous quantification of many metabolites within complex mixtures can additionally be complicated by ion suppression, fragmentation and the presence of isomers. Here we present guidelines covering sample preparation, replication and randomization, quantification, recovery and recombination, ion suppression and peak misidentification, as a means to enable high-quality reporting of liquid chromatography– and gas chromatography–mass spectrometry-based metabolomics-derived data.

Expression quantitative trait locus mapping has been widely used to study the genetic regulation of gene expression in Arabidopsis thaliana. As a result, a large amount of expression quantitative trait locus data has been generated for this model plant; however, only a few causal expression quantitative trait locus genes have been identified, and experimental validation is costly and laborious. A prioritization method could help speed up the identification of causal expression quantitative trait locus genes. This study extends the machine-learning-based QTG-Finder2 method for prioritizing candidate causal genes in phenotype quantitative trait loci to be used for expression quantitative trait loci by adding gene structure, protein interaction, and gene expression. Independent validation shows that the new algorithm can prioritize 16 out of 25 potential expression quantitative trait locus causal genes within the top 20% rank. Several new features are important in prioritizing causal expression quantitative trait locus genes, including the number of protein–protein interactions, unique domains, and introns. Overall, this study provides a foundation for developing computational methods to prioritize candidate expression quantitative trait locus causal genes. The prediction of all genes is available in the AraQTL workbench (https://www.bioinformatics.nl/AraQTL/) to support the identification of gene expression regulators in Arabidopsis.

Soil salinity is an increasing worldwide problem for agriculture, affecting plant growth and yield. To understand the molecular mechanisms activated in response to salt in plants, we investigated the Catharanthus roseus Receptor like Kinase 1 Like (CrRLK1L) family, which contains well described sensors previously shown to be involved in maintaining and sensing the structural integrity of the cell walls. We found that herk1the1-4 double mutants, lacking the function of the Arabidopsis thaliana Receptor like Kinase HERKULES1 combined with a gain-of-function allele of THESEUS1, phenocopied the phenotypes previously reported in plants lacking FERONIA (FER) function. We report that both fer-4 and herk1the1-4 mutants respond strongly to salt application, resulting in a more intense activation of early and late stress responses. We also show that salt triggers de-methyl esterification of loosely bound pectins, responsible for the activation of several salt response signaling pathways. Addition of calcium chloride or chemically inhibiting pectin methyl esterase (PME) activity reduced activation of the early signaling protein Mitogen Activated Protein Kinase 6 (MPK6) as well as amplitude of salt-induced marker gene induction. MPK6 is required for the full induction of the salt-induced gene expression markers we tested. The sodium specific root halotropism response on the other hand, appears independent of MPK6 or calcium application, and is only mildly influenced by the cell wall sensors FER/HERK1/THE1-4 or alteration of PME activity. We hypothesize a model where salt-triggered modification of pectin requires the functionality of FER alone or the HERK1/THE1 combination to attenuate salt responses. Collectively, our results show the complexity of salt stress responses and salt sensing mechanisms and their connection to cell wall modifications, responsible for several salt response pathways and ultimately plant resilience to salinity.

Geranylgeranyl diphosphate (GGPP) produced by GGPP synthase (GGPPS) serves as a precursor for many plastidial isoprenoids, including carotenoids. Phytoene synthase (PSY) converts GGPP into phytoene, the first committed intermediate of the carotenoid pathway., Here we used biochemical, molecular, and genetic tools to characterise the plastidial members of the GGPPS family in tomato (Solanum lycopersicum) and their interaction with PSY isoforms., The three tomato GGPPS isoforms found to localise in plastids (SlG1, 2 and 3) exhibit similar kinetic parameters. Gene expression analyses showed a preferential association of individual GGPPS and PSY isoforms when carotenoid biosynthesis was induced during root mycorrhization, seedling de-etiolation and fruit ripening. SlG2, but not SlG3, physically interacts with PSY proteins. By contrast, CRISPR-Cas9 mutants defective in SlG3 showed a stronger impact on carotenoid levels and derived metabolic, physiological and developmental phenotypes compared with those impaired in SlG2. Double mutants defective in both genes could not be rescued., Our work demonstrates that the bulk of GGPP production in tomato chloroplasts and chromoplasts relies on two cooperating GGPPS paralogues, unlike other plant species such as Arabidopsis thaliana, rice or pepper, which produce their essential plastidial isoprenoids using a single GGPPS isoform., This work was funded by the European Regional Development Fund (FEDER) and the Spanish Agencia Estatal de Investigación (grants BIO2017-84041-P and BIO2017-90877-REDT) and Generalitat de Catalunya (2017SGR-710) to MRC. Support by the collaborative European Union’s Horizon 2020 (EU-H2020) ERA-IB-2 (Industrial Biotechnology) BioProMo project to MRC (PCIN-2015-103), RK and JB (053-80-725) is also acknowledged. CRAG is financially supported by the Severo Ochoa Programme for Centres of Excellence in R&D 2016–2019 (SEV-2015-0533) and the Generalitat de Catalunya CERCA Programme. MVB was funded with a Spanish Ministry of Education, Culture and Sports PhD fellowship (FPU14/05142) and a EU-H2020 COST Action CA15136 (EuroCaroten) short-stay fellowship. ME is supported by a Spanish Agencia Estatal de Investigación (BES-2017-080652) PhD fellowship. IFS is supported by the EU-H2020 Marie S. Curie Action 753301 (Arcatom).

Split-stream processing of asparagus waste stream is a novel approach to produce spray-dried powder and fibre. Asparagus ingredients processed by this method and a commercial asparagus powder were compared by evaluating their flavour profile in a soup formulation. Professional sensory panel and untargeted metabolomics approaches using GC–MS and LC–MS were carried out. Unsupervised and supervised statistical analyses were performed to highlight discriminatory metabolites and correlate these to sensory attributes. The spray-dried powder scored higher on asparagus flavour compared to the commercial powder. The fibre negatively impacted the taste and mouthfeel of the soups. GC-O-MS confirmed the role of dimethyl sulphide, 2-methoxy-3-isopropyl pyrazine and 2-methoxy-3-isobutyl pyrazine in asparagus odour. Seven new volatile compounds are also proposed to contribute to asparagus flavour notes, most of which were more abundant in the spray-dried powder. This research demonstrates the feasibility of upcycling asparagus waste streams into flavour-rich ingredients with good sensorial properties.

Evaluation of genetic diversity and identification of superior genotypes is a fundamental step in walnut breeding programs. In addition, information on biochemical properties of superior genotypes can help walnut breeders to release commercial varieties with high kernel quality. To gain more information on superior genotypes, a walnut population located in southwest of Iran was morphologically evaluated from 2010 to 2016. Based on important walnut breeding traits, nine superior walnut genotypes were selected from a total of 612 tested genotypes. These genotypes were characterized by high yield, moderate to late-leafing, lateral bearing, thin shell and large nuts with light and extra-light kernel color. Biochemical traits of the selected superior genotypes were evaluated for two consecutive years (2017 and 2018) and a high variation was observed among genotypes in respect of oil, protein and total phenol contents. Oil, protein and phenol contents of walnut kernels ranged between 57.9 to 69.6%, 13.0 to18.1% and 46.6 to 61.5 mg GAE g-1, respectively. Polyunsaturated fatty acids (PUFA), monounsaturated fatty acids (MUFA) and saturated fatty acids (SFA) constituted on average 63.8%, 26.7% and 9.7% of fatty acid content, respectively. There was a negative correlation between some phenological traits and oil and protein contents. Lateral bearing genotypes had darker kernels with higher amounts of saturated fatty acids. In general, the selected walnut genotypes not only are superior in various aspects of phenotypic characteristics, but also have high kernel quality and nutritional value which can be used as a source of desirable genes for future walnut breeding programs.

Recognition at the plasma membrane of danger signals (elicitors) belonging to the classes of the microbe/pathogen- and damage-associated molecular patterns is a key event in pathogen sensing by plants and is associated with a rapid activation of immune responses. Different cellular compartments, including plasma membrane, chloroplasts, nuclei and mitochondria, are involved in the immune cellular program. However, how pathogen sensing is transmitted throughout the cell remains largely to be uncovered. Arabidopsis NPK1-related Proteins (ANPs) are mitogen-activated protein kinase kinase kinases previously shown to have a role in immunity. In this paper, we studied the in vivo intracellular dynamics of ANP1- and ANP3-GFP fusions and found that under basal physiological conditions both proteins are present in the cytosol, while ANP3 is also localized in mitochondria. After elicitor perception, both proteins are present also in the plastids and nuclei, revealing a localization pattern that is so far unique. The N-terminal region of the protein kinases is responsible for their localization in mitochondria and plastids. Moreover, we found that the localization of ANPs coincides with the sites of elicitor-induced ROS accumulation and that plants lacking ANP function do not accumulate intracellular ROS. This article is protected by copyright. All rights reserved.

Plants transitioned from an aquatic to a terrestrial lifestyle during their evolution. On land, fluctuations on water availability in the environment became one of the major problems they encountered. The appearance of morpho‐physiological adaptations to cope with and tolerate water loss from the cells was undeniably useful to survive on dry land. Some of these adaptations, such as carbon concentrating mechanisms (CCMs), desiccation tolerance (DT) and root impermeabilization, appeared in multiple plant lineages. Despite being crucial for evolution on land, it has been unclear how these adaptations convergently evolved in the various plant lineages. Recent advances on whole genome and transcriptome sequencing are revealing that co‐option of genes and gene regulatory networks (GRNs) is a common feature underlying the convergent evolution of these adaptations. In this review, we address how the study of CCMs and DT has provided insight into convergent evolution of GRNs underlying plant adaptation to dry environments, and how these insights could be applied to currently emerging understanding of evolution of root impermeabilization through different barrier cell types. We discuss examples of co‐option, conservation and innovation of genes and GRNs at the cell, tissue and organ levels revealed by recent phylogenomic (comparative genomic) and comparative transcriptomic studies., In this review, the authors highlight recent research on signatures of convergent evolution of regulatory networks underlying carbon concentrating mechanisms such as C4 and CAM photosynthesis, desiccation tolerance in seeds and resurrection plants and impermeabilization of root exodermis.

Most land plants entertain a mutualistic symbiosis known as arbuscular mycorrhiza with fungi (Glomeromycota) that provide them with essential mineral nutrients, in particular phosphate (Pi), and protect them from biotic and abiotic stress. Arbuscular mycorrhizal (AM) symbiosis increases plant productivity and biodiversity and is therefore relevant for both natural plant communities and crop production. However, AM fungal populations suffer from intense farming practices in agricultural soils, in particular Pi fertilization. The dilemma between natural fertilization from AM symbiosis and chemical fertilization has raised major concern and emphasizes the need to better understand the mechanisms by which Pi suppresses AM symbiosis. Here, we test the hypothesis that Pi may interfere with AM symbiosis via the phytohormone gibberellic acid (GA) in the Solanaceous model systems Petunia hybrida and Nicotiana tabacum. Indeed, we find that GA is inhibitory to AM symbiosis and that Pi may cause GA levels to increase in mycorrhizal roots. Consistent with a role of endogenous GA as an inhibitor of AM development, GA-defective N. tabacum lines expressing a GA-metabolizing enzyme (GA methyltransferase—GAMT) are colonized more quickly by the AM fungus Rhizoglomus irregulare, and exogenous Pi is less effective in inhibiting AM colonization in these lines. Systematic gene expression analysis of GA-related genes reveals a complex picture, in which GA degradation by GA2 oxidase plays a prominent role. These findings reveal potential targets for crop breeding that could reduce Pi suppression of AM symbiosis, thereby reconciling the advantages of Pi fertilization with the diverse benefits of AM symbiosis.

Light spectral composition influences plant growth and metabolism, and has important consequences for interactions with plant-feeding arthropods and their natural enemies. In greenhouse horticulture, light spectral composition can be precisely manipulated by light-emitting diodes (LEDs), and LEDs are already used to optimize crop production and quality. However, because light quality also modulates plant secondary metabolism and defense, it is important to understand the underlying mechanisms in the context of the growth-defense trade-off. We review the effects of the spectral composition of supplemental light currently used, or potentially used, in greenhouse horticulture on the mechanisms underlying plant growth and defense. This information is important for exploring opportunities to optimize crop performance and pest management, and thus for developing resilient crop-production systems.

Key message: Loss of viability of recalcitrant seeds upon dehydration is associated with changes in expression levels of genes associated with seed development, the antioxidant defense system and stress responses. Abstract: Araucaria angustifolia is a Brazilian conifer species that produces desiccation-sensitive seeds. Conservation of recalcitrant seeds by conventional seed banking has severe limitations as the underlying mechanisms of quick viability loss upon drying remain unclear. The aim of this study was to shed light on these underlying mechanisms in A. angustifolia by analyzing the transcript levels of genes related to seed development, antioxidant systems and stress responses in seeds subjected to dehydration. To be able to perform these expression analyses, an additional aim was to identify candidate reference genes suitable for gene expression analyses in A. angustifolia. Using GeNorm software we analyzed 10 selected candidate reference genes for RT-qPCR analysis of gene expression in embryonic axis and cotyledon tissues of dehydrated seeds. The most stable candidate reference genes for normalization of gene expression data in heterogeneous samples (inter-tissues) were ACT, GAPDH and SAR1. Slight drying (35% water content) had a positive effect on seed viability since radicle protrusion values (84%) did not differ significantly from undried seeds (94%). Seed viability, however, decreased dramatically when seeds were dried down to a water content of 28%. Transcript levels of ABI3, LEC1, SMP, APX, MIPS and XERO1 decreased in embryonic axis and cotyledons during dehydration, whereas transcript levels of CAT and NAC increased. Our study provides information on reference genes that are adequate for gene expression studies in A. angustifolia seeds and shows that loss of seed viability during dehydration appears to be associated with a decrease in transcript levels of genes related to desiccation tolerance.

Seeds show incredible variation in their attributes, such as dormancy, longevity and, hence, quality. It is of eminent importance to study this variation across and within species and higher taxa in order to ensure successful agricultural production and preservation of biodiversity, not least in times of a changing climate.

Summary Advances in synthetic biology and metabolic engineering have proven the potential of introducing metabolic by‐passes within cell factories. These pathways can provide a more efficient alternative to endogenous counterparts due to their insensitivity to host's regulatory mechanisms. In this work, we replaced the endogenous essential 2‐C‐methyl‐D‐erythritol 4‐phosphate (MEP) pathway for isoprenoid biosynthesis in the industrially relevant bacterium Rhodobacter sphaeroides by an orthogonal metabolic route. The native 2‐C‐methyl‐D‐erythritol 4‐phosphate (MEP) pathway was successfully replaced by a heterologous mevalonate (MVA) pathway from a related bacterium. The functional replacement was confirmed by analysis of the reporter molecule amorpha‐4,11‐diene after cultivation with [4‐13C]glucose. The engineered R. sphaeroides strain relying exclusively on the MVA pathway was completely functional in conditions for sesquiterpene production and, upon increased expression of the MVA enzymes, it reached even higher sesquiterpene yields than the control strain coexpressing both MEP and MVA modules. This work represents an example where substitution of an essential biochemical pathway by an alternative, heterologous pathway leads to enhanced biosynthetic performance., This work describes the design and implementation of pathway replacement in isoprenoid metabolism in the bacterium Rhodobacter sphaeroides. Integration of a heterologous mevalonate pathway was followed by the inactivation of the endogenous MEP pathway via Cas9 counter‐selection. The resulting strain showed increased amorphadiene yields compared to the parental strain. Therefore replacement of endogenous pathways with non‐native counterparts is suggested for rational design of microbial cell factories.

In plants, epigenetic regulation is critical for silencing transposons and maintaining proper gene expression. However, its impact on the genome-wide transcription initiation landscape remains elusive. By conducting a genome-wide analysis of transcription start sites (TSSs) using cap analysis of gene expression (CAGE) sequencing, we show that thousands of TSSs are exclusively activated in various epigenetic mutants of Arabidopsis thaliana and referred to as cryptic TSSs. Many have not been identified in previous studies, of which up to 65% are contributed by transposons. They possess similar genetic features to regular TSSs and their activation is strongly associated with the ectopic recruitment of RNAPII machinery. The activation of cryptic TSSs significantly alters transcription of nearby TSSs, including those of genes important for development and stress responses. Our study, therefore, sheds light on the role of epigenetic regulation in maintaining proper gene functions in plants by suppressing transcription from cryptic TSSs., Epigenetic regulation can silence transposons and maintain gene expression. Here the authors survey Arabidopsis mutants defective in epigenetic regulation and show ectopic activation of thousands of cryptic TSSs and altered expression of nearby genes demonstrating the importance of suppressing spurious transcription.

Drought reduces the availability of soil water and the mobility of nutrients, thereby limiting the growth and productivity of rice. Under drought, arbuscular mycorrhizal fungi (AMF) increase P uptake and sustain rice growth. However, we lack knowledge of how the AMF symbiosis contributes to drought tolerance of rice. In the greenhouse, we investigated mechanisms of AMF symbiosis that confer drought tolerance, such as enhanced nutrient uptake, stomatal conductance, chlorophyll fluorescence, and hormonal balance (abscisic acid (ABA) and indole acetic acid (IAA)). Two greenhouse pot experiments comprised three factors in a full factorial design with two AMF treatments (low- and high-AMF colonization), two water treatments (well-watered and drought), and three rice varieties. Soil water potential was maintained at 0 kPa in the well-watered treatment. In the drought treatment, we reduced soil water potential to − 40 kPa in experiment 1 (Expt 1) and to − 80 kPa in experiment 2 (Expt 2). Drought reduced shoot and root dry biomass and grain yield of rice in both experiments. The reduction of grain yield was less with higher AMF colonization. Plants with higher AMF colonization showed higher leaf P concentrations than plants with lower colonization in Expt 1, but not in Expt 2. Plants with higher AMF colonization exhibited higher stomatal conductance and chlorophyll fluorescence than plants with lower colonization, especially under drought. Drought increased the levels of ABA and IAA, and AMF colonization also resulted in higher levels of IAA. The results suggest both nutrient-driven and plant hormone-driven pathways through which AMF confer drought tolerance to rice. Electronic supplementary material The online version of this article (10.1007/s00572-020-00953-z) contains supplementary material, which is available to authorized users.

Araucaria angustifolia (Bertol.) Kuntze is a representative species of the Mixed Ombrophilous Forest in the Atlantic Forest Biome of Brazil. The development of a germplasm conservation protocol for long-term seed bank storage is compromised for this species, as it is sensitive to desiccation. Furthermore, in situ establishment of a soil seed bank in its natural habitat may be limited. This study evaluates the storability of two provenances of A. angustifolia seeds and their behavior in an artificial soil seed bank in two forest environments (understory and edge). Results show that both seed provenances may be stored at 5 °C for approximately 12 months, retaining high viability. The subsequent decrease in germination was associated with a reduction and an increase in seed water content, as well as with increased electrical conductivity. In the understory environment, seed viability was above 85% for the first 60 days, and at the end of the experiment (270 days), seedlings emerged. However, at the forest edge, there was a total loss of seed viability after 120 days associated with a reduction in water content and high predation. It is concluded, therefore, that short-term storage of A. angustifolia seeds is possible in a cold room, which is fundamental to supply seed demand outside the production period. Forest cover conservation is important for regeneration and conservation of the species.

Did you know that a group of early-career researchers launched an initiative enabling open dialog on new plant breeding techniques, such as genome editing? We developed a wide-ranging initiative that aims to facilitate public engagement and provide a platform for young plant scientists to encourage participation in science communication.

The metabolic-oxidative stress profile of the rice flag leaf during drought stress in the reproductive stage is highly predictive for grain yield loss sensitivity of 292 accessions at harvest time., Crop yield stability requires an attenuation of the reduction of yield losses caused by environmental stresses such as drought. Using a combination of metabolomics and high-throughput colorimetric assays, we analysed central metabolism and oxidative stress status in the flag leaf of 292 indica rice (Oryza sativa) accessions. Plants were grown in the field and were, at the reproductive stage, exposed to either well-watered or drought conditions to identify the metabolic processes associated with drought-induced grain yield loss. Photorespiration, protein degradation, and nitrogen recycling were the main processes involved in the drought-induced leaf metabolic reprogramming. Molecular markers of drought tolerance and sensitivity in terms of grain yield were identified using a multivariate model based on the values of the metabolites and enzyme activities across the population. The model highlights the central role of the ascorbate–glutathione cycle, particularly dehydroascorbate reductase, in minimizing drought-induced grain yield loss. In contrast, malondialdehyde was an accurate biomarker for grain yield loss, suggesting that drought-induced lipid peroxidation is the major constraint under these conditions. These findings highlight new breeding targets for improved rice grain yield stability under drought.

Proteins from cashew nut can elicit mild to severe allergic reactions. Three allergenic proteins have already been identified, and it is expected that additional allergens are present in cashew nut. pathogenesis‐related protein 10 (PR10) allergens from pollen have been found to elicit similar allergic reactions as those from nuts and seeds. Therefore, we investigated the presence of PR10 genes in cashew nut. Using RNA‐seq analysis, we were able to identify several PR10‐like transcripts in cashew nut and clone six putative PR10 genes. In addition, PR10 protein expression in raw cashew nuts was confirmed by immunoblotting and liquid chromatography–mass spectrometry (LC–MS/MS) analyses. An in silico allergenicity assessment suggested that all identified cashew PR10 proteins are potentially allergenic and may represent three different isoallergens.

Canopy temperature, detected by thermal imaging, is a good predictor of rice yield performance under drought and shows genetic variation in an association mapping panel., Drought-stressed plants display reduced stomatal conductance, which results in increased leaf temperature by limiting transpiration. In this study, thermal imaging was used to quantify the differences in canopy temperature under drought in a rice diversity panel consisting of 293 indica accessions. The population was grown under paddy field conditions and drought stress was imposed for 2 weeks at flowering. The canopy temperature of the accessions during stress negatively correlated with grain yield (r= –0.48) and positively with plant height (r=0.56). Temperature values were used to perform a genome-wide association (GWA) analysis using a 45K single nucleotide polynmorphism (SNP) map. A quantitative trait locus (QTL) for canopy temperature under drought was detected on chromosome 3 and fine-mapped using a high-density imputed SNP map. The candidate genes underlying the QTL point towards differences in the regulation of guard cell solute intake for stomatal opening as the possible source of temperature variation. Genetic variation for the significant markers of the QTL was present only within the tall, low-yielding landraces adapted to drought-prone environments. The absence of variation in the shorter genotypes, which showed lower leaf temperature and higher grain yield, suggests that breeding for high grain yield in rice under paddy conditions has reduced genetic variation for stomatal response under drought.

In plants, prenylation of aromatic compounds, such as (iso)flavonoids and stilbenoids, by membrane-bound prenyltransferases (PTs), is an essential step in the biosynthesis of many bioactive compounds. Prenylated aromatic compounds have various health-beneficial properties that are interesting for industrial applications, but their exploitation is limited due to their low abundance in nature. Harnessing plant aromatic PTs for prenylation in microbial cell factories may be a sustainable and economically viable alternative. Limitations in prenylated aromatic compound production have been identified, including availability of prenyl donor substrate. In this review, we summarize the current knowledge about plant aromatic PTs and discuss promising strategies towards the optimized production of prenylated aromatic compounds by microbial cell factories.

Artemisinin is a natural bioactive sesquiterpene lactone containing an unusual endoperoxide 1, 2, 4-trioxane ring. It is derived from the herbal medicinal plant Artemisia annua and is best known for its use in treatment of malaria. However, recent studies also indicate the potential for artemisinin and related compounds, commonly referred to as artemisinins, in combating viral infections, inflammation and certain cancers. Moreover, the different potential modes of action of artemisinins make these compounds also potentially relevant to the challenges the world faces in the COVID-19 pandemic. Initial studies indicate positive effects of artemisinin or Artemisia spp. extracts to combat SARS-CoV-2 infection or COVID-19 related symptoms and WHO-supervised clinical studies on the potential of artemisinins to combat COVID-19 are now in progress. However, implementing multiple potential new uses of artemisinins will require effective solutions to boost production, either by enhancing synthesis in A. annua itself or through biotechnological engineering in alternative biosynthesis platforms. Because of this renewed interest in artemisinin and its derivatives, here we review its modes of action, its potential application in different diseases including COVID-19, its biosynthesis and future options to boost production.

White asparagus (A. officinalis) is a popular vegetable consumed worldwide and its cooked spears are appreciated for their distinct flavour profile. During asparagus harvesting, around one-third of the total material is usually discarded. This significant waste stream partially consists of the stem bases which are cut off to produce spears with the same desired length for delivery to the supermarket. This waste stream could become a valuable resource of food ingredients. Asparagus waste was used to generate an asparagus concentrate, and this was spray-dried in different carrier formulations in which maltodextrin was partially replaced by cellulose-based carriers, i.e. asparagus fibre, citrus fibre or microcrystalline cellulose. Powders obtained from feed solutions with an initial solids content of 40 % w/w showed better physical properties and aroma retention than 30 % w/w. Partial replacement of maltodextrin by cellulose-based carriers resulted in powders with similar physical properties to the control and did not detrimentally influence the aroma profiles as analysed by headspace solid-phase microextraction and gas chromatography-mass spectrometry. Aroma analysis was focused on asparagus key volatiles based on previous studies. This research showed that fibre obtained from asparagus waste streams could potentially be used as a carrier to produce spray-dried asparagus powder with retained key asparagus odorants such as 2-methoxy-3-isopropyl pyrazine. Valorisation of these materials could reduce the amount of agricultural waste while generating aroma-rich natural food products.