Peach Leaf Curl Disease, caused by the fungus Taphrina deformans, is characterized by reddish hypertrophic and hyperplasic leaf areas. To comprehend the biochemical imbalances caused by the disease an integrated approach including metabolomics, lipidomics, proteomics and complementary biochemical techniques was undertaken. Symptomatic and asymptomatic areas were dissected from leaves with increasing extension of the disease. A differential metabolic behaviour was identified in symptomatic areas with respect to either asymptomatic areas or healthy leaves. Symptomatic areas showed an altered chloroplastic functioning and composition which differs from the typical senescence process and includes decrease in the photosynthetic machinery, alteration in plastidic lipids, and decreased starch, carotenoid and chlorophyll biosynthesis. In symptomatic areas, alteration in redox-homeostasis proteins and in triacylglycerols content, peroxidation and double bond index were observed. Proteomic data revealed induction of host enzymes involved in auxin and jasmonate biosynthesis together with up-regulation of phenylpropanoid and mevalonate pathways and down-regulation of the plastidic methylerythritol phosphate route. Amino acid pools were affected, with up-regulation of proteins involved in asparagine synthesis. Overall, we conclude that curled areas exhibited a metabolic shift towards functioning as a sink tissue importing sugars and producing energy through fermentation and respiration and reductive power via the pentose phosphate route.

Soybean ( Glycine max [L.] Merr) is among the most important agricultural seed crops and source of vegetable protein. Further yield improvements per unit land area are needed to meet future demand and avoid destruction of more natural lands. Mesophyll conductance ( gm) in C 3 crops quantifies the ease with which CO 2 can transfer from the sub-stomatal cavity to Rubisco within the mesophyll. Increasing gm is in theory most attractive as it would increase photosynthesis, yield potential and water-use efficiency. Most measurements of gm have been made during steady-state light saturated photosynthesis. However, in field crop canopies, light fluctuations are frequent and the speed with which gm can increase following shade to sun transitions is likely important to crop carbon gain. Is there variability in gm that could be used in breeding? If so, indirect selection could be expected to have already increased gm and be apparent when comparing wild ancestors of soybean ( Glycine soja) to a domesticated high-yielding cultivar. The elite LD11 was compared with four ancestor accessions collected from the assumed area of domestication by concurrent measurements of gas exchange and carbon isotope discrimination (∆ 13C). This allowed estimation of gm both through induction following transfer to high light and at steady-state. The results have shown 1) gm was a significant limitation to soybean photosynthesis both at steady-state and through light induction, especially when the major biochemical limitation was in vivo Rubisco activity and, 2) compared to the ancestral accessions, the elite LD11 showed a large and significant increase in gm at both steady-state and through light induction, which also corresponded to a substantial increase in leaf level CO2 assimilation and water use efficiency.

The comprehension of the reciprocal interaction between root development and its co-adapted beneficial microbes in response to elevated CO 2 (eCO 2) will facilitate the identification of nutrient-efficient cultivars for a sustainable agriculture. Here systemically morphological, anatomical, chemical and gene expression assays performed under eCO 2 highlight the divergent root differentiation driven endodermal barrier development with respect to the L-/S-shaped lateral roots under low nitrogen conditions in rice. Next, by metabolome and endodermal-cell specific RNA sequencing we showed that rice adapted to eCO 2 by spatially recruiting diazotrophs through flavonoid secretion in L-shaped lateral roots. To the end, using a rice Casparian strip mutant Oscasp1-1 we validated such root differentiation driven specific recruitment of a diazotrophic family Oxalobacteraceae implicated in plant tolerance to low nitrogen availability. Our work indicates that rice could coordinate nutrient uptake and root differentiation by the recruitment of diazotrophs in L-shaped lateral roots under climate change.

Alfalfa ( Medicago sativa L.) is a crucial and widely grown forage legume that faces yield challenges due to salinity stress. In this study, an R2R3-MYB transcription factor (TF), MsEOBI was characterized from alfalfa. Its function and gene regulatory pathways were studied in alfalfa seedlings. The nuclear-localized MsEOBI acts as a transcriptional activator. MsEOBI enhances salinity tolerance of alfalfa by promoting flavonoids and lignin biosynthesis, as well as scavenging reactive oxygen species (ROS). MsEOBI also promote pollinator attraction and seed yield by activating volatile phenylpropanoid biosynthesis. Yeast one-hybrid, dual-luciferase, and ChIP-qPCR assays showed that MsEOBI binds directly to the promoter of MsPAL1, a key enzyme in the phenylpropanoid pathway to activate its expression. Overexpression of MsPAL1 in alfalfa enhances salinity tolerance. These findings shed light on the functions of the MsEOBI-MsPAL1 module in alfalfa and offer valuable genetic resources for the breeding of salt stress-resistant varieties in the future.

Weeds are among the most significant factors contributing to decreases in crop yield and quality. Glufosinate, a nonselective, broad-spectrum herbicide, has been extensively utilized for weed control in recent decades. However, crops are usually sensitive to glufosinate. Therefore, the development of glufosinate-resistant crops is crucial for effective weed management in agriculture. In this study, we characterized a SQUAMOSA promoter-binding-like (SPL) factor, OsSPL8, which acts as a negative regulator of glufosinate resistance by inhibiting the transcription of OsGS1;1 and OsGS2 and consequently reducing GS activity. Furthermore, the loss of OsSPL8 function enhanced tolerance to drought and salt stresses. Transcriptomic comparisons between the gar18-3 mutant and wild type revealed that OsSPL8 largely downregulates stress-responsive genes and upregulates growth-related genes. We demonstrated that OsSPL8 directly regulates OsOMTN6 and OsNAC17, which influence drought tolerance. Additionally, OsSPL8 directly represses the expression of salt stress tolerance-related genes such as OsHKT1.1 and OsTPP1. Collectively, our results demonstrate that OsSPL8 is a negative regulator of both glufosinate resistance and abiotic stress tolerance.

High seed quality is a prerequisite for successful crop production, making maintenance of seed viability and vigour during storage important. The effects of temperature and humidity on seed ageing are well known, while the negative effect of oxygen in the seed storage environment has been studied less. Here we report on experiments to study the quantitative effect of oxygen on the ageing of seeds. Primed celery seeds were chosen as a model, because of their relatively short shelf life. After equilibration at four relative humidity levels (16, 33, 43 and 60% RH), the seeds were stored at four temperatures (5, 13, 20 and 30°C) and six oxygen levels (1, 5.2, 10, 21, 50 and 99%) for a period up to seven years. Germination tests after storage confirmed a strong shelf life-extending effect of low oxygen conditions, at all four temperatures and the three lower humidity levels. Modelling the viability data revealed a linear double logarithmic relationship between the oxygen concentration and the storage time till a 50% decline in viability (p50), for seeds pe-equilibrated at 16, 33 or 43% RH. The models also showed that each halving of the oxygen concentration increased seed longevity by around 77%. This means that a reduction of the environmental oxygen concentration to a level below 1% increased the shelf life of the primed celery seeds by a factor of twelve. For seeds pre-equilibrated at 60% RH, the effect of lowering the oxygen concentration below 21% was much less or even absent at 30°C, likely due to a different physical or physiological condition of the seeds at this higher humidity level. The large and logarithmic effect of reducing the oxygen level during the dry storage of seeds provides additional opportunities to prolong the shelf life of seeds either for commercial or genebank storage. To estimate the effect of these factors, a model is provided describing the quantitative effect of all three factors, temperature, equilibrium relative humidity and oxygen concentration. Several options for practical application are discussed.

not-yet-known not-yet-known not-yet-known unknown Drought is a critical risk factor that impacts rice growth and yields. Previous studies have focused on the regulatory roles of individual transcription factors in response to drought stress. However, there is limited understanding of multi-factor stresses gene regulatory networks and their mechanisms of action. In this study, we utilized data from the jaspar database to compile a comprehensive dataset of transcription factors and their binding sites in rice, Arabidopsis, and barley genomes. We employed the pytorch framework for machine learning to develop a 9-layer convolutional deep neural network TFBind; its accuracy was 90% through literature review and dual-luciferase assay validation. Subsequently, we obtained rice RNA-seq and ATAC-seq data related to abiotic stress from the public database. Utilizing integrative analysis of WGCNA and ATAC-seq, we effectively identified transcription factors associated with open chromatin regions in response to drought. Interestingly, only 81% of the transcription factors directly bound to the opened genes by testing with TFBind model. By this approach we identified 15 drought-responsive transcription factors corresponding to open chromatin regions of targets, which enriched in the terms related to protein transport, protein allocation, nitrogen compound transport. This approach provides a valuable tool for predicting TF-TAG modules during biological processes.

Changing environments can alter plant functional traits in agricultural ecosystems, leading to shifts in plant resource utilization strategies. The plant trait network can integrate economic, hydraulic, and anatomical traits to reflect plants’ adaptation and responses to environmental changes from multiple perspectives. This study quantitatively analyzed the economic and hydraulic traits of leaves and roots in three cotton varieties under changing environments with different CO 2 concentrations and water or salt stress, exploring the impact of changing environments on plant functional traits and resource utilization strategies. The results showed that under water or salt stress, the leaf economic spectrum (LES) exhibited a conservative strategy, while the root economic spectrum (RES) displayed an acquisitive strategy. Under elevated CO 2 concentration, LES, RES, and hydraulic traits of both leaf and root showed conservative strategies. Additionally, under changing environments, the trade-off between LES and leaf hydraulic traits demonstrates a congruent resource utilization pattern, whereas the trade-off between RES and root hydraulic traits demonstrates an inverse pattern. We also found that changing environments altered the centrality of the plant traits network. Overall, the multi-faceted study of plant functional traits and their interrelationships provides a crucial basis for understanding the response of crops in agroecosystems to environmental changes.

Drought is an important abiotic factor constricting crop production globally. Although the role of JAZ proteins in regulating jasmonic acid signaling and plant responses to environmental stress is well documented, their specific functions and underlying mechanisms in plants remains little known. In this study, JAZ proteins in barley were thoroughly analyzed, revealing a total of 11 members classified into three phylogenetic subgroups. HvJAZ2, based on its distinct expression patterns, is considered as a key candidate gene for regulating drought tolerance in barley. Using the HvJAZ2 knockout mutants, we revealed that the gene negatively regulates drought tolerance by inhibiting barley root growth. Notably, the jaz2 mutants up-regulated expression of root development genes, including SHR1, PLT1, PLT2, and PLT6. plt2 and plt1/plt2 mutants exhibited suppressed root development and reduced drought tolerance. Analysis of interactions between HvJAZ2 and other proteins showed that HvJAZ2 is not directly interacted with HvPLT1/2/6, but interacts with some other proteins. BIFC and LCA assays further confirmed the nuclear interaction between HvJAZ2 and HvMYC2. Y1H and Dual-Luciferase experiments demonstrated that HvMYC2 can bind to and activates the HvPLT2 promoter. In summary, HvJAZ2 negatively regulates root development and drought tolerance in barley by suppressing HvPLT2 expression through interacting with HvMYC2.

The impact of nitrogen (N) and phosphorus (P) on the physiological and biochemical processes crucial for tree seedling growth is substantial. Although the study of plant hydraulic traits in response to N and P is growing, comprehensive research on their combined effects remains limited. Malus sieversii, a key ancestral species of modern apples and a dominant species in Xinjiang’s Tianshan wild fruit forest, is witnessing a decline due to climate change, pests and diseases, compounded by challenges in seedling regeneration. Addressing this, a four-year study was conducted to determine the optimal fertilization method for it. The experiment explored varying levels of N (N10, N20, N40) and P (P2, P4, P8), and their combined effects (N20Px: N20P2, N20P4, N20P8; NxP4: N10P4, N20P4, N40P4), assessing their impact on gas exchange, hydraulic traits, and the interplay among functional traits in Tianshan Mountains’ M. sieversii seedlings. Our study revealed that all nitrogen treatments enhanced gas exchange, while phosphorus addition negatively impacted it. N10 significantly increasing leaf hydraulic conductivity. All phosphorus-inclusive fertilizers adversely affected hydraulic conductivity. P8, N20P4 and N20P8 notably increased seedlings’ vulnerability to embolism. Seedlings can adaptively adjust multiple functional traits in response to nutrient changes. The research suggests N10 and N20 as the most effective fertilization treatments for M. sieversii seedlings in this region, while fertilization involving phosphorus is less suitable. This study contributes valuable insights into the specific nutrient needs of it, vital for conservation and cultivation efforts in the Tianshan region.

A document by Michael Blatt. Click on the document to view its contents.

Iron (Fe) deficiency severely limits plant growth in calcareous soils. Plants have evolved two main strategies to acquire sparingly available Fe under these conditions. These strategies may show natural variations that can be exploited for agriculture but remain unexplored since most research has focused on crops and model plants. To find such variations, we cultivated various plant species in a high throughput manner under Fe-sufficient and deficient media and compared their Fe deficiency responses. We discovered that Veronica officinalis, a species adapted to non-calcareous soils, failed to induce the accumulation of fluorescent phenolic compounds in roots, a common response to Fe deficiency in several species, when grown in a Fe-deficient medium. On the other hand, Trifolium montanum, a legume adapted to calcareous soils, showed pronounced root fluorescence even when cultivated in a Fe-sufficient medium. T. montanum plants also showed constitutive ferric chelate reductase activity and rhizosphere acidification, indicating a general defect in turning off Fe deficiency-induced responses. These findings suggest that adaptation to contrasting environments with predictable Fe availability can lead to a loss of plasticity in Fe deficiency responses. While V. officinalis benefits by giving up a Fe-acquisition component that is non-essential where it is adapted, T. montanum benefits from constitutive Fe acquisition in chronically Fe-deficient calcareous soils. These contrasting adaptations highlight the trade-offs inherent in maintaining plasticity and underline the importance of studying stress responses in wild species of diverse natural settings, which can contribute to developing stress-tolerant crops.

Leaf photosynthesis models are used extensively in photosynthesis research and are embedded in many larger scale models. Typical photosynthesis models simplify light intensity as the integrated intensity over the 400 to 700 nm waveband (Photosynthetic Active Radiation; PAR). However, far-red light (700-750 nm, FR) also drives photosynthesis when supplied in addition to light within the PAR spectrum. Currently, it is unknown how much far-red light contributes to carbon assimilation under various spectral light conditions. We developed a combined experimental and computational method to quantify FR stimulation. Gas-exchange parameters and incident light spectra were measured simultaneously and analysed with wavelength-dependent modelling of light harvesting. Hereto, separate excitation of Photosystem I and Photosystem II was calculated from incident light spectra. The effect of FR supplementation on photosynthesis was subsequently modelled and expressed as a single parameter ρ. We tested our method on Solanum dulcamara, Lactuca sativa and Phaseolus vulgaris under various light conditions. Results show consistent species-specific ρ-values across a range of FR levels. Our method provides an approach to consistently quantify the effect of FR stimulation on photosynthesis and harmonize the interpretation of photosynthesis measurements under different light regimes, for example in (experimental) setups with artificial FR supplementation or in canopies.

The massive leaf shedding in monoculture soybeans post-anthesis detrimentally impacts production, whereas relay strip intercropping can extend leaf area duration to enhance overall productivity. To reveal the reasons for leaf shedding in monoculture soybeans and how it affects the physiological and biochemical functions of source and sink organs, we conducted a four-year field experiment and a leaf-removal simulation experiment in relay strip intercropped soybeans to measure the phenotypic and physiological traits of leaves and nodules. The results showed that the strong self-shading of leaves in monoculture soybeans led to extensive defoliation, while the superior light environment in relay strip intercropped soybeans can promote the maintenance of a higher leaf area, nodule growth, and photosynthetic carbon allocation. With increasing leaf removal, leaf growth increased first and then decreased, and leaf defoliation gradually decreased. Extensive leaf-removal reduced Rubisco activity and sucrose phosphate synthase (SPS) activity in leaves, as well as the content of sucrose, malate, ATP, and energy charge (EC) in nodules, with a trade-off between leaf mass enhancement and weakened nodule growth. Notably, moderate leaf-removal could balance compensation and consumption. The total non-structural carbohydrates (TNC) in roots, N and Ureide in leaves and pods increased in unison, achieving the synergies between leaves and nodules to maintain a higher energy status and growth rate. Our study highlights that the favorable light environment in relay strip intercropping system shapes the coordinated functioning of above-ground and below-ground source-sink organs and effectively promoting photosynthesis and nitrogen fixation. These findings contribute to a better understanding of the underlying mechanisms of effective resource utilization in different cropping patterns, aiding in the sustainable development of food production.

Endoplasmic Reticulum-Plasma Membrane contact sites (ER-PM CS) are evolutionarily conserved membrane domains found in all eukaryotes, where the endoplasmic reticulum (ER) closely interfaces with the plasma membrane (PM). This short distance is achieved in plants through the action of tether proteins such as Synaptotagmins (SYTs). Arabidopsis comprises five SYT members ( SYT1-SYT5), but whether they possess overlapping or distinct biological functions remains elusive. SYT1, the best-characterized member, plays essential roles in the resistance to abiotic stress. This study reveals that the functionally redundant SYT1 and SYT3 genes, but not SYT5, are involved in salt and cold stress resistance. We also show that, unlike SYT5, SYT1 and SYT3 are not required for Pseudomonas syringae resistance . Since SYT1 and SYT5 interact in vivo via their SMP domains , the distinct functions of these proteins cannot be caused by differences in their localization. Interestingly, structural phylogenetic analysis indicates that SYT1 and SYT5 clades emerged early in the evolution of land plants. We also show that SYT1 and SYT5 clades exhibit different structural features, rationalizing their distinct biological roles.

The increased production and use of plastics have negative impacts on the environment. However, not only the polymers themselves, but also smaller particles used for instance in cosmetics or derived from decomposition are toxicologically relevant. In recent years, research has focused on the occurrence of micro- and nanoplastics (MNPs) in air, soil and water, whereas the entry into plants has hardly been investigated. To determine the load, translocation of MNPs and their effects on metabolism, pak choi, tomato, radish and asparagus have been exposed with fluorescent-labeled particles; poly(methyl methacrylate) (PMMA) or polystyrene (PS) of different sizes and surface modifications. By means of fluorescence microscopy the entry of NP regardless of their size (100 nm – 500 nm) and surface modification (unmodified, COOH or NH 2) has been demonstrated. Additionally, metabolic changes induced by MNPs have been determined by metabolomics. The entry could pose a potential risk to food safety as well as quality and needs greater concern and further research.

Plants share their habitats with a multitude of different microbes. This close vicinity promoted the evolution of inter-organismic interactions between plants and many different microorganisms that provide mutual growth benefits both to the plant and the microbial partner. The symbiosis of Arabidopsis thaliana with the beneficial root colonizing endophyte Serendipita indica represents a well-studied system. Co-colonization of Arabidopsis roots with S. indica significantly promotes plant growth. Due to the notable phenotypic alterations of fungus-infected root systems, the involvement of a reprogramming of plant hormone levels, especially that of indole-3-acetic acid, has been suggested earlier. However, until now, the molecular mechanism by which S. indica promotes plant growth remains largely unknown. This study used comprehensive transcriptomics, metabolomics, reverse genetics, and life cell imaging to reveal the intricacies of auxin-related processes that affect root growth in the symbiosis between A. thaliana and S. indica. Our experiments revealed the essential role of tightly controlled auxin conjugation in the plant–fungus interaction. It particularly highlighted the importance of two GRETCHEN HAGEN 3 ( GH3) genes, GH3.5 and GH3.17, for the fungus infection-triggered stimulation of biomass production, thus broadening our knowledge about the function of GH3s in plants. Furthermore, we provide evidence for the transcriptional alteration of the PIN2 auxin transporter gene in roots of Arabidopsis seedlings infected with S. indica and demonstrate that this transcriptional adjustment affects auxin signaling in roots, which results in increased plant growth.

Tree transpiration dynamics and mechanisms in karst habitats are not fully understood due to the heterogeneous environmental features and complex species composition. Two common coexisting tree species, Mallotus philippensis and Celtis biondii, were examined in soil- and rock-dominated (SD and RD) karst habitats. Soil moisture, plant transpiration, root distribution, and leaf water potential were measured over two years (2021 and 2022). The mean water content was significantly lower in the RD than in the SD habitat. Transpiration patterns also differed between habitats, although species-specific distinctions were driven by leaf and root physiological traits. M. philippensis showed an isohydric tendency in both habitats and a lower density of fine roots, mostly in the soil zone, in the RD habitat. The transpiration of M. philippensis followed the variation in soil moisture, being lower in the RD habitat. Conversely, an anisohydric tendency in both habitats and a higher density of fine roots in both the soil and bedrock zones in the RD habitat were found in C. biondii. This species showed higher transpiration in the RD habitat, arising from ample water availability from soil and epikarst. Our findings reveal the regulatory mechanisms of species-specific root-zone water availability in transpiration patterns across karst habitats.