Plant metabolomics has been used widely in plant physiology, in particular to analyse metabolic responses to environmental parameters. Derivatization (via trimethylsilylation-methoximation) followed by GC-MS metabolic profiling is a major technique to quantify low molecular weight, common metabolites of primary carbon, sulphur and nitrogen metabolism. There are now excellent opportunities for new generation analyses, using high resolution, exact mass GC-MS spectrometers that are progressively becoming relatively cheap. However, exact mass GC-MS analyses for routine metabolic profiling are not common, there is no dedicated available database. Also, exact mass GC-MS is usually dedicated to structural resolution of targeted secondary metabolites. Here, we present a curated database for exact mass metabolic profiling (made of 336 analytes, 1,064 characteristic exact mass fragments) focused on molecules of primary metabolism. We show advantages of exact mass analyses, in particular to resolve isotopic patterns, localise S-containing metabolites, and avoid identification errors when analytes have common nominal mass peaks in their spectrum. We provide a practical example using leaves of different Arabidopsis ecotypes and show how exact mass GC-MS analysis can be applied to plant samples and identify metabolic profiles.

Microbe associated molecular pattern (MAMP) triggered immunity research has traditionally centred around signal transduction pathways originating from activated membrane localised pattern recognition receptors (PRRs), culminating in nuclear transcription and post translational modifications. More recently, chloroplasts have emerged as key immune signalling hubs. Chloroplasts play a central role in integrating environmental signals. Notably MAMP recognition induces chloroplastic ROS (cROS) which is suppressed by pathogens effectors, which also modify the balance of defence hormone precursors, jasmonic acid (JA), salicylic acid (SA) and abscisic acid (ABA), whose precursors are chloroplast synthesised. This study focuses on how well characterised PRRs and co-receptors modulate chloroplast physiology, examining whether diverse signalling pathways converge to similarly modulate chloroplast function. Pre-treatment of receptor mutant plants with MAMP and D(Damage)AMP peptides usually protect against effector modulation of chlorophyll fluorescence and prevent Pseudomonas syringae effector mediated quenching of cROS and suppression of Fv/Fm. The MAMP-triggered immunity (MTI) co-receptor double mutant, bak1-5/bkk1-1, exhibits a remarkable decrease in Fv/Fm compared to control plants during infection, underlining the importance of MTI mediated signalling in chloroplast immunity. Further probing the role of the chloroplast in immunity we unexpectedly found that high light uncouples plant immune signalling.

Calcium (Ca 2+) is an important second messenger in plants. The activation of Ca 2+ signaling cascades is critical in the activation of adaptive processes in response to perceived environmental stimuli, including biotic stresses. The colonization of roots by the plant growth promoting endophyte Serendipita indica involves the increase of cytosolic Ca 2+ levels in Arabidopsis thaliana. In this study, we investigated transcriptional changes in Arabidopsis roots during symbiosis with S. indica. RNA-seq profiling disclosed the significant induction of CALCINEURIN B-LIKE 7 ( CBL7) during early- and later phases of the interaction. Consistent with the transcriptomics analysis, reverse genetic evidence and yeast two-hybrid studies highlighted the functional relevance of CBL7 and tested the involvement of a CBL7-CBL-INTERACTING PROTEIN KINASE 13 (CIPK13) signaling pathway in the establishment of the mutualistic relationship that promotes plant growth. The loss-of-function of CBL7 abolished the growth promoting effect of S. indica and affected the colonization of the root by the fungus. The subsequent transcriptomics analysis of cbl7 revealed the involvement of this Ca 2+ sensor in activating plant defense responses. Furthermore, we report on the contribution of CBL7 to potassium transport in Arabidopsis. Triggered by the differential expression of a small number of K + channels/transporter genes, we analyzed K + contents in wild-type and cbl7 plants and observed a significant accumulation of K + in root of cbl7 plants, while shoot tissues demonstrated K + depletion. Taken together, our work associates CBL7 with an important role in the mutual interaction between Arabidopsis and S. indica and links the CBL7 Ca 2+ receptor protein to K + transport.

Recent progress has shown that vacuolar Pi transporters (VPTs) are important for cellular Pi homeostasis against external Pi variations in Arabidopsis and rice, while it is poorly understood for the identity and regulatory mechanism of VPTs in Brassica napus ( B. napus). Here, we identified two vacuolar Pi influx transporters BnA09PHT5;1b and BnCnPHT5;1b in B. napus and uncovered their necessity for cellular Pi homeostasis through functional analysis. BnPHT5;1bs are the homologs of Arabidopsis AtPHT5;1 with the similar sequence, structure, tonoplast localization, and VPT activity. BnPHT5;1b double mutants had smaller shoot growth and higher shoot cellular Pi than the wild-type B. napus, which are largely different from the report in At PHT5;1 mutant, suggesting PHT5;1-VPTs play a distinct mechanism of cellular Pi homeostasis in seedlings of B. napus and Arabidopsis. By contrast, disruption of BnPHT5;1b genes slowed vegetative growth accompanied by Pi toxicity in floral organs, reduced seed yield and impacted seed traits, agreeing with the role of AtPHT5;1 in floral Pi homeostasis. Taken together, our studies identified two vacuolar Pi influx transporters in B. napus and revealed the distinct and conserved regulatory mechanisms of BnPHT5;1bs in cellular Pi homeostasis in this plant species.

Heat stress (HS) caused by ambient high temperature pose a threat to plants. In the natural and agricultural environment, plants often encounter repeated and changeable HS. Moderate HS primes plants to establishment of a molecular ‘thermomemory’ that enables plants to withstand a later-and possibly more extreme-HS attack. Recent years, brassinosteroids (BRs) have been implicated in HS response whereas little is known about whether BRs signal transduction modulates thermomemory. Here, we uncover the positive role of BRs signaling in thermomemory of Arabidopsis thaliana. Heat priming induces de novo synthesis and nuclear accumulation of BRI1-EMS-SUPPRESSOR (BES1), the key regulator of BRs signaling. BRs promote the accumulation of dephosphorylated BES1 during memory phase, blocking BRs synthesis impairs dephosphorylation. During HS memory, BES1 is required to maintain sustained induction of HS memory genes and directly targets APX2 and HSFA3 for activation. In summary, our results reveal a BES1-required, BRs-enhanced transcriptional control module of thermomemory in Arabidopsis thaliana.

Breeding drought stress tolerance is an integral part of our current and future goals of sustainable agricultural production. In the present study, we examined the natural variation of HvP5cs1 and demonstrated the utility of a wild barley allele for drought stress adaptation in cultivated barley. Sequencing the 5-end regulatory region among 49 barley accessions identified a genetically distinct allele of HvP5cs1 promoter from a wild barley ISR42-8. Allele mining of HvP5cs1 indicated quantitative variation in proline accumulation which was associated with promoter polymorphisms across the cluster of abscisic acid-responsive elements (ABRE), ABRE-related coupling elements, and MYB binding motifs. A near-isogenic line (NIL-143) harboring the HvP5cs1 allele from the highest proline accumulating wild barley ISR42-8 was developed in cultivated barley Scarlett through marker-assisted backcrossing (BC6). NIL-143 preserved the genetic competence of ISR42-8 to accumulate proline in higher concentrations under drought conditions at seedling and reproductive stages. Under drought stress, NIL-143 maintained superior membrane integrity, reduced pigment damage, and sustained photosynthetic health compared to Scarlett. NIL-143 presented a remarkable improvement in drought stress recovery than Scarlett. Further, the introgression line exhibited improved yield attributes, especially superior grain weight compared to Scarlett under field drought conditions. In conclusion, the present data uncover the genetic regulation of HvP5cs1 mediated proline accumulation and elucidate its role in drought stress adaptation and yield stability in barley.

Local adaptation is a major driver of biological diversity, and related species may develop analogous (parallel evolution) or alternative (divergent evolution) solutions to similar ecological challenges. We expect these adaptive solutions between closely related organisms would culminate in both phenotypic and genotypic signals. In this study, we employ a reciprocal transplant, glasshouse experiment with two Eucalyptus species ( E. grandis and E. tereticornis) with large, overlapping distributions grown under contrasting ‘local’ temperature conditions (tropic and temperate) to investigate the independent contribution of adaptation, plasticity, and their interaction at molecular, physiological and morphological levels. We find key traits differ in their response. The link between gene expression and traits markedly differed between species. Divergent evolution was the dominant pattern driving adaptation as unique gene responses (91% of all significant genes) was the greatest factor driving differentiation; but overlapping gene (homologous) responses were dependent on the determining factor (plastic, adaptive, or genotype by environment interaction). 98% of the plastic homologs were similarly regulated, while 50% of the adaptive homologs and 100% of the interaction homologs were antagonistically regulated. Therefore, parallel evolution for the adaptive effect in homologous genes was greater than expected but not in favour of divergent evolution. Further, heat shock proteins for E. grandis were almost entirely driven by adaptive responses, while plasticity drove the response in E. tereticornis. These results suggest divergent molecular evolutionary solutions dominated the adaptive mechanisms among species, even in similar ecological circumstances. Thus, trees with overlapping distributions are unlikely to equally persist in the future, suggesting that management of future forests to changing temperature conditions must be species specific.

Iron (Fe) deficiency restricts crop yields in calcareous soil. Thus, a novel Fe chelator, proline-2′-deoxymugineic acid (PDMA), based on the natural phytosiderophore 2′-deoxymugineic acid (DMA), was developed to solve the Fe deficiency problem. However, the effects and mechanisms of PDMA relevant to the Fe nutrition and yield of dicots grown under field conditions require further exploration. In this study, pot and field experiments with calcareous soil were conducted to investigate the effects of PDMA on the Fe nutrition and yield of peanuts. The results demonstrate that PDMA could dissolve insoluble Fe in the rhizosphere and up-regulate expression of the yellow stripe-like family gene AhYSL1 to improve the Fe nutrition of peanuts. Moreover, the chlorosis and growth inhibition induced by Fe deficiency were significantly diminished. Importantly, under field conditions, the peanut yield and kernel micronutrition were notably promoted by PDMA application. Our results indicate that PDMA promotes the dissolution of insoluble Fe and a rich supply of Fe in the rhizosphere, increasing yields through integrated improvements in soil–plant Fe nutrition at the molecular and ecological levels. In conclusion, the efficacy of PDMA for improving the Fe nutrition and yield of peanut indicates its outstanding potential for agricultural applications.

Triose-phosphate utilization (TPU) limits the maximum rate at which plants can photosynthesize. However, TPU is almost never found to be limiting photosynthesis under ambient conditions for plants. This, along with previous results showing adaptability of TPU at low temperature, suggest that TPU capacity is regulated to be just above the photosynthetic rate achievable under the prevailing conditions. A set of experiments were performed to study the adaptability of TPU capacity when plants are acclimated to elevated CO 2 concentrations. Plants held at 1500 ppm CO 2 were initially TPU limited. After 30 hours they no longer exhibited TPU limitations but they did not elevate their TPU capacity. Instead, the maximum rates of carboxylation and electron transport declined. A timecourse of regulatory responses was established. A step increase of CO 2 first caused PSI to be oxidized but after 40 s both PSI and PSII had excess electrons as a result of acceptor-side limitations. Electron flow to PSI slowed and the proton motive force increased. Eventually, non-photochemical quenching reduced electron flow sufficiently to balance the TPU limitation. Over several minutes rubisco deactivated contributing to regulation of metabolism to overcome the TPU limitation.

Group VII Ethylene Response Factors (ERF-VII) are plant-specific transcription factors (TFs) known for their role in the activation of hypoxia-responsive genes under low oxygen stress but also in plant endogenous hypoxic niches. However, their function in the microaerophilic nitrogen-fixing nodules of legumes has not yet been investigated. We investigated regulation and the function of the two Medicago truncatula ERF-VII TFs ( MtERF74 and MtERF75) in roots and nodules, MtERF74 and MtERF75 in response to hypoxia stress and during the nodulation process using an RNA interference strategy and targeted proteolysis of MtERF75. Knockdown of MtERF74 and MtERF75 partially blocked the induction of hypoxia-responsive genes in roots exposed to hypoxia stress. In addition, a significant reduction in nodulation capacity and nitrogen fixation activity was observed in mature nodules of double knockdown transgenic roots. Overall, the results indicate that MtERF74 and MtERF75 are involved in the induction of MtNR1 and Pgb1.1 expression for efficient Phytogb-NO respiration in the nodule.

β-Glucosidase is validated as an elicitor for early immune responses in plants and it was detected in the salivary glands of Frankliniella occidentalis in previous research. Seven differentially expressed genes encoding β-Glucosidase were obtained by comparing the transcriptomes of F. occidentalis adults grown under two different CO 2 concentrations (800 ppm vs. 400 ppm), which might be associated with the differences in the interaction between F. occidentalis adults and its host plant, Phaseolus vulgaris under different CO 2 levels. To verify this speculation, changes in defense responses based on the production and elimination of reactive oxygen species (ROS) in P. vulgaris leaves treated with three levels of β-Glucosidase activity under ambient CO 2 (aCO 2) and elevated CO 2 (eCO 2) were measured in this study. The results showed that both leaves infested with thrips and those sprayed with the pure β-Glucosidase solution showed significant increases in ROS levels under aCO 2 and eCO 2, and the activities of antioxidant enzymes including superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) were increased correspondingly, while in leaves infested with FoβGlu-1-silenced thrips, the ROS levels and activities of these enzymes did not change significantly during the first 12 hours of injury regardless of CO 2 level. Besides, significantly higher levels of ROS and lower activities of SOD, POD and CAT in injured leaves under eCO 2 compared to aCO 2 were noticed, which would negatively affect P. vulgaris leaves and facilitate thrips damage.

Increasing rice yield has always been one of the primary objectives of rice breeding. However, panicle degeneration, a complex phenomenon regulated by many genetic and environmental factors, often occurs in rice-growing regions and severely curbs rice yield. In this study, we obtained a new apical panicle degeneration mutant named ym48, which induces a marked degeneration rate and diminishes the final grain yield. Cellular and physiological analyses revealed that the apical panicle in ym48 undergoes programmed cell death, accompanied by excessive accumulations of peroxides. Following, the panicle degeneration gene OsCAX1a was identified, which was involved in Ca2+ transport in the ym48 mutant. In OsCAX1a, a relative conserved T to A substitution was noted at the 64th amino acid, which disrupted Ca2+ transport. Hydroponics assays and Ca2+ quantification confirmed that Ca2+ transport and distribution to apical tissues were restricted and over-accumulated in mutant sheath. Ca2+ transport between cytoplasm and vacuole was affected, and the reduced content of Ca2+ in vacuole and cell wall and the decreased of Ca2+ absorption were appeared in ym48 mutant. RNA-Seq data indicated that the abnormal CBL (calcineurin b-like proteins) pathway mediated by deficient Ca2+ might occur in mutant, resulting in the burst of ROS and programmed cell death in panicles. Our results explained the key role of OsCAX1a in Ca2+ transport and distribution and laid a foundation to further explore the genetic and molecular mechanisms of panicle degeneration and the efficiency of Ca2+ fertilization in rice.

A key to achieve the goals put forward in the UN's 2030 Agenda for Sustainable Development, it will need transformative change to our agrifood systems. We must mount to the global challenge to achieve food security in a sustainable manner in the context of climate change, population growth, urbanization, and depletion of natural resources. Rice is one of the major staple cereal crops that has contributed, is contributing, and will still contribute to the global food security. To date, rice yield has held pace with increasing demands, due to advances in both fundamental and biological studies, as well as genomic and molecular breeding practices. However, future rice production depends largely on the planting of resilient cultivars that can acclimate and adapt to changing environmental conditions. This Special Issue highlight with reviews and original research articles the exciting and growing field of rice-environment interactions that could benefit future rice breeding. We also outline open questions and propose future directions of 2050 rice research, calling for more attentions to develop environment resilient rice especially hybrid rice, upland rice and perennial rice.

Heightened by the COVID-19 pandemic there has been a global increase in urban greenspace appreciation. Indoor plants are equally important for improving mental health and air quality but despite evolving in humid (sub)tropical environments with aerial root types, planting systems ignore aerial resource supply. This study directly compared nutrient uptake preferences of aerial and soil-formed roots of three common houseplant species under high and ambient relative humidities. Growth and physiology parameters were measured weekly for Anthurium andreanum, Epipremnum aureum and Philodendron scandens grown in custom made growth chambers. Both aerial and soil-formed roots were then fed mixtures of nitrate, ammonium and glycine, with one source labelled with 15N to determine uptake rates and maximum capacities. Aerial roots were consistently better at nitrogen uptake than soil roots but no species, root type or humidity condition showed a preference for a particular nitrogen source. All three species grew more in high humidity, with aerial roots demonstrating the greatest biomass increase. Higher humidities for indoor niches, together with fertiliser applications to aerial roots will support indoor plant growth, creating lush calming indoor environments for people inhabitants.

The thylakoid membrane is in a temperature-sensitive equilibrium that shifts repeatedly during the life cycle in response to ambient temperature or solar irradiance. Plants respond to seasonal temperature by changing their thylakoid lipid composition, while a more rapid mechanism for short-term heat exposure is required. The emission of the small organic molecule isoprene has been postulated as one such possible rapid mechanism. The protective mechanism of isoprene is not known, but some plants emit isoprene during periods of high-temperature stress. In this work, we investigate the dynamics and structure for lipids within a thylakoid membrane at different temperatures and varied isoprene content using classical molecular dynamics simulations. The results are compared with experimental findings from across the literature for temperature-dependent changes in the lipid composition and shape of thylakoids. We find that the surface area, volume, and flexibility of the membrane, as well as the lipid diffusion, increase with temperature, while the membrane thickness decreases. Saturated thylakoid 34:3 glycolipids derived from eukaryotic synthesis pathways exhibit significantly different dynamics than lipids from prokaryotic synthesis paths, which could explain the upregulation of specific lipid synthesis pathways at different temperatures. Increasing isoprene concentration was not observed to have a significant thermoprotective effect on the thylakoid membranes, and that isoprene readily permeated the membrane models tested here.

Conservative flowering behaviors, such as flowering during long days in summer or late flowering at a high leaf number, are often proposed to protect against variable winter and spring temperatures which lead to frost damage if premature flowering occurs. Yet, due the many factors in natural environments relative to the number of individuals compared, assessing which climate characteristics drive these flowering traits has been difficult. We applied a multidisciplinary approach to ten winter-annual Arabidopsis thaliana populations originating along a wide climactic gradient in Norway. We used a variable reduction strategy to assess which of 100 climate descriptors from their home sites correlated most to their behaviors when grown in common garden and assessed sequence variation of 19 known environmental-response flowering genes. Photoperiod sensitivity inversely correlated with interannual variation in timing of growing season onset (start of favorable spring temperatures). Time to flowering appeared driven by growing season length, curtailed by cold fall temperatures. The distribution of FLM, TFL2, and HOS1 haplotypes, genes involved in ambient temperature response, correlated with growing-season climate. We show that long-day sensitivity and late flowering may be driven not by risk of spring frosts, but by growing season temperature and length perhaps to opportunistically maximize growth.

Phloem sap transport, velocity and allocation have been proposed to play a role in physiological limitations of crop yield, along with photosynthetic activity or water use efficiency. Although there is clear evidence that carbon allocation to grains effectively drives yield in cereals like wheat (as reflected by the harvest index), the influence of phloem transport rate and velocity is less clear. Here, we took advantage of previously published data on yield, respiration, carbon isotope composition, nitrogen content and water consumption in winter wheat cultivars grown across several sites with or without irrigation, to express grain production in terms of phloem sucrose transport and compare with xylem water transport. Our results suggest that phloem sucrose transport rate follows the same relationship with phloem N transport regardless of irrigation conditions and cultivars, and seems to depend mostly on grain weight (i.e. mg per grain). When compared to xylem sap water movement, phloem sap velocity (in m s -1) was 5.8 to 7.7 times lower. Depending on the assumption made for phloem sap sucrose concentration, either phloem sap velocity or its proportionality coefficient to xylem velocity change little with environmental conditions. Taken as a whole, phloem transport from leaves to grains seems to be homeostatic within a narrow range of values and following relationships with other plant physiological parameters across cultivars and conditions. This suggests that phloem transport per se is not a limitation for yield in wheat but rather, is controlled to sustain grain filling.

Control of plant virus diseases largely depends on the induced plant defense achieved by the external application of synthetic chemical inducers with the ability to modify defense-signaling pathways. However, most of the molecular mechanisms underlying these chemical inducers remain unknown. Here, we developed a lentinan-loaded hydrogel with a core-shell structure and discovered how it protects plants from different virus infections. The hydrogel was synthesized by adding a chitosan shell on the surface of the polyanion sodium alginate-Ca 2+-lentinan (LNT) hydrogel (SL-gel) to form a CSL-gel. CSL-gels exhibit the capacity to prolong the stable release of lentinan and promote Ca 2+ release. Application of CSL-gels on the root of plants induces broad-spectrum resistance against TMV, TRV, PVX and TuMV). RNA-seq analysis identified that the calmodulin-like protein 19 gene ( NbCML19) is upregulated by the sustained release of Ca 2+ from the CSL-gel, and silencing and overexpression of NbCML19 alter the susceptibility and resistance of tobacco to TMV. Our findings provide evidence that this novel and synthetic CSL-gel strongly inhibits the infection of plant viruses by the sustainable release of LNT and Ca 2+. This study uncovers a novel mode of action by which CSL-gels trigger NbCML19 expression through the stable and sustained release of Ca 2+.