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.

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.

Phenotypic plasticity is the ability of organisms to respond to environmental changes. Understanding and leveraging crop phenotypic plasticity is crucial for mitigating the threats caused by climate change. Here, we assessed phenotypic plasticity in multi-environment trials over 4 years, covering a wide geographical area, using 505 inbred lines from a Brassica napus genetic diversity panel. The observed phenotypic variation for seed oil content (SOC) was influenced by three environmental indices (precipitation, diurnal temperature range, and ultraviolet B) during the flowering or pod-filling stage alongside five plasticity genes. Leveraging this information with climate records, we developed a predictive model to estimate SOC for various planting dates in seven major production regions, and validated the accuracy of our predictions in new environments. With the quantified plasticity conferred by genetic variation in the five plasticity genes, we identified an optimal haplotype for each production region for adaptability to future climate projections. This study offers valuable insights and selection of materials to mitigate the adverse effects of climate change on agriculture.

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 includes decrease in the photosynthetic machinery, alteration in plastidic lipids, and decreased starch, carotenoid and chlorophyll biosynthesis. In symptomatic areas, decreases in chloroplast redox-homeostasis proteins and in triacylglycerols double bond index were observed. Proteomic data revealed an 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. 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. As the disease progresses, reduced asymptomatic areas and healthy leaves diminishes photosynthates production thereby limiting fruit production and ultimately tree survival.

Plant density significantly impacts photosynthesis, canopy structure, crop growth, and yield, thereby shaping the [CO 2] fertilization effect and intricate physiological interactions in rice. An association panel of 171 rice genotypes was evaluated for physiological and yield-related traits, including the cumulative response index, under both normal planting density (NPD) and low planting density (LPD) conditions. LPD, serving as a proxy for elevated atmospheric [CO 2], significantly increased all trait values, except for harvest index, compared to NPD. For the genome-wide association study, 386,817 high-quality SNPs were considered, employing both single-locus and multi-locus models, which collectively identified 172 QTNs, including 12 QTNs associated with at least two different traits under NPD or LPD conditions. A significant r­elationship between the percentage of favorable alleles in the genotypes and their performance under NPD and LPD conditions was observed. Potential haplotypes were validated using genotypes with contrasting [CO 2] responses, grown under LPD and Free-Air CO 2 Enrichment facility. These findings can enable efforts to selectively breed genotypes with favorable alleles and/or superior haplotypes for enhancing [CO 2] responsiveness in rice. Climate smart rice varieties, with increased [CO 2] responsiveness, have the potential to simultaneously enhance grain yield and quality while mitigating losses induced by high night temperatures.

Plants are an intrinsic part of the soil community and the “one health concept” considers that human health is intimately connected to the health of animals, plants, and microbial environments. Plant-microbe interactions are a cornerstone of one health, the soil microbiome being comprised of a diverse range of organisms, interacts in the rhizosphere through continuous molecular communications. Soils are a source and reservoir of pathogens, as well as beneficial microorganisms. Hence, the molecular dialogue at the rhizosphere interface is crucial not only for successful plant-microbe interactions but also for crop resilience and stress tolerance. The plant-microbe continuum forms a network of underground “nutrient highways” that benefit both plant and microbial communities. It also serves as a significant sink for atmospheric CO 2. While microbial diversity is generally positively associated with one health, the host range of beneficial microbes currently limits their successful exploitation with a wide range of microbial communities. We consider the possibility of increasing the host range of beneficial microbes, including arbuscular mycorrhiza fungi (AMF) and rhizobia, and how current genetic incompatibility and/or activation of robust plant defenses, can be overcome while accepting that significant challenges exist in translating laboratory findings into the field. We consider why AMF inoculants and plant growth-promoting microbes are not always beneficial under field conditions and suggest possible approaches for tailoring plant-microbe interactions to assist plant breeding efforts in crop resilience.

Plant responses to multifactorial stress combinations are seldom studied, but combinations of abiotic and biotic stresses may cause drastic yield reductions in crops. While an abiotic stress, the salinization of agricultural soil, affects crop production, added pressures of insect herbivores could lead to further losses. In this paper, we investigate the effects of salinity on an insect herbivore, the corn earworm caterpillar ( Helicoverpa zea), feeding on tomato ( Solanum lycopersicum cv. Better Boy) plants. We show that salt-stressed tomato plants are poor hosts for H. zea, impacting caterpillar growth rates, caterpillar feeding preference, and moth oviposition. We further show that these observations are best explained by reductions in both relative leaf water content and leaf total protein content, along with ionic toxicity and imbalance. We observe that salt stress does not influence anti-insect herbivory defense protein (PPO and TPI) levels. Finally, we observe that salt treatment leads to differences in specific volatiles, with lower emissions of 2-carene, α-phellandrene, β-phellandrene, α-humulene, and β-caryophyllene in salt-treated plants. We demonstrate that salt exposure changes tomato plant quality and chemical composition, which in turn negatively affects insect herbivores feeding on these plants.

As a well-conserved histone variant, H2A.Z epigenetically regulates plant growth and development as well as the interaction with environmental factors. However, the role of H2A.Z in response to salt stress remains unclear, and whether nucleosomal H2A.Z occupancy work on the gene responsiveness upon salinity is obscure. Here, we elucidate the involvement of H2A.Z in salt response by analyzing H2A.Z disorder plants with impaired or overloaded H2A.Z deposition. The salt tolerance is dramatically accompanied by H2A.Z deficiency and reacquired in H2A.Z OE lines. H2A.Z disorder changes the expression profiles of large-scale of salt responsive genes, announcing that H2A.Z is required for plant salt response. Genome-wide H2A.Z mapping shows that H2A.Z level is induced by salt condition across promoter, TSS and TES (-1 kb to +1kb), the peaks preferentially enrich at promoter regions near TSS. We further show that H2A.Z deposition within TSS provides a direct role on transcriptional control, which has both repressive and activating effects, while it is found generally H2A.Z enrichment negatively correlate with gene expression level response to salt stress. This study shed light on the H2A.Z function in salt tolerance, highlighting the complex regulatory mechanisms of H2A.Z on transcriptional activity for yielding appropriate responses to particularly environmental stress.

Reactive oxygen species are important signaling molecules that influence many aspects of plant biology. One way in which ROS influence plant growth and development is by modifying intercellular trafficking through plasmodesmata (PD). Viruses have evolved to use plasmodesmata for their local cell-to-cell spread between plant cells, so it is therefore not surprising that they have found ways to modulate ROS and redox signaling to optimize plasmodesmata function for their benefit. This review examines how intracellular signaling via ROS and redox pathways regulate intercellular trafficking via PD during development and stress. The relationship between viruses and ROS-redox systems, and the strategies viruses employ to control PD function by interfering with ROS-redox in plants is also discussed.

Stomata play a pivotal role in regulating gas exchange between terrestrial plants and the atmosphere controlling water and carbon cycles at organismal, ecosystem and global levels. Accordingly, our objective was to investigate the impact of ultraviolet-B radiation, a neglected environmental factor varying with ongoing global change, on stomatal morphology and function by means of a comprehensive meta-analysis. We found 45 peer-reviewed publications containing altogether 143 case studies for analysis. The overall UV effect at the leaf level is to decrease stomatal conductance, stomatal aperture and stomatal size, although stomatal density was increased. The significant decline in conductance is marked in short-term experiments, with more modest decreases noted in long-term UV studies. We found that short-term experiments in growth chambers are not representative of long-term field UV effects on stomatal conductance. Further, we found a stronger UV effect in grasses than in herbs, while the reduction of stomatal conductance was insignificant in trees. It is hypothesised that these alterations in stomatal function have important potential consequences for plant life. In the short term, UV-mediated stomatal closure may reduce transpiration and alleviate drought stress. However, in the long term more complex changes in stomatal aperture, size and density may reduce carbon sink capacity, and enhance leaf and surface warming, potentially exacerbating the negative effects of drought and/or heatwaves on plant ecosystems and endangering long-term plant survival.

Xylem conduits have lignified walls to resist crushing pressures. The thicker the double-wall ( T) relative to its maximum diameter ( D), the greater the collapse/implosion resistance. Having xylem that is more resistant than necessary incurs high costs and reduced flow, while having xylem not resistant enough may lead to catastrophic collapse under drought. Despite the importance of xylem implosion safety in determining plant drought resistance, it is still unclear how leaves scale Tx D to trade-off among implosion safety, flow efficiency, mechanical support, and construction cost. We measured T and D in over 7,000 leaf xylem conduits of 122 ferns and angiosperms species to investigate how the Tx D scaling varies across species, clades, habitats, growth forms, and vein orders. Overall, leaf xylem conduits grow wider than thicker, potentially resulting in high flow efficiency and lower cost, but at the expense of high vulnerability to implosion. Conduits seem particularly vulnerable to implosion in monocots, aquatic species and in species from hydric habitats, as well as in major veins. The absence of strong trade-offs within the leaf functional traits examined suggests that implosion safety at the whole-leaf level cannot be easily predicted by the sum of the individual conduits’ resistance to collapse.

The plant cell wall is a plastic structure of variable composition that constitutes the first line of defense against environmental challenges. Lodging and drought are two stressful conditions that severely impact on maize yield. In a previous work, we characterized the cell walls of two maize inbreds susceptible (EA2024) or resistant (B73) to stalk-lodging. Here, we show that drought induces phenotypical, physiological, cell wall, and transcriptional changes with distinct dynamics in the two inbreds, and that B73 is less tolerant than EA2024 to this stress. While in control conditions, stalk of EA2024 had higher levels of cellulose, uronic acids and p-coumarate than B73, upon drought these displayed increased levels of arabinose-enriched polymers, such as pectin-arabinans and arabinogalactan proteins, and a decreased lignin content. By contrast, a deeper rearrangement of cell walls including the modification of lignin composition and an increase of uronic acids was observed in B73. Drought induced higher changes in gene expression in B73 compared to EA2024, particularly in cell wall-related genes, that were altered in an inbred-specific manner. Transcription factor enrichment assays unveiled inbred-specific regulatory networks coordinating cell wall genes expression. Altogether, these findings reveal that B73 and EA2024 inbreds, with opposite stalk-lodging phenotypes, undertake different cell wall modification strategies in response to drought. We propose that the specific cell wall composition that confers lodging resistance to B73 compromises its cell wall plasticity and renders this inbred more susceptible to drought.

Nucleotide-binding, leucine-rich repeat (NLR) genes play a pivotal role in shaping plant effector-triggered immunity in response to pathogen invasions. However, the mechanisms governing the expression and behavior of NLRs, particularly in the context of head-to-head NLR gene pairs, in the presence of pathogens, remain uncovered. In this study, we dissected the Pik-H4 promoter (P Pik-H4) at the TATA boxes and conducted an in-depth investigation into split promoter activity using Agro-infiltration assays. The segments spanning 593-1232 bp and 2016-2492 bp (starting from -1 bp of Pik1-H4) within P Pik-H4 emerged as core regions for expressing Pik1-H4 and Pik1-H4 respectively. Nevertheless, merging these two core fragments failed to recover the promoter activity in both directions. Employing Gus staining, promoter activity assays and qRT-PCR, we unveiled the co-expression of Pik1-H4 and Pik2-H4 throughout the whole plant. Additionally, in the presence of the rice blast fungus, their co-amplification was observed in leaves and leaf sheaths. Strikingly, Pik-H4 exhibited heightened expression within vascular bundles. Moreover, perturbing the Pik1-H4 and Pik2-H4 co-expression relationship via overexpression in rice or Nicotiana did not disrupt the immune response. Upon infection, the singleton Pik 1-H4 localized within vesicles, while Pik 2-H4 predominantly occupied the nucleus within leaf sheath cells. Transcriptome analysis highlighted Pik-H4-mediated resistance triggering a transcriptome reprogramming between 12 and 24 hours post-inoculation. Notably, overexpression of Pik1-H4 or Pik2-H4 enriches various pathways compared to the Pik-H4 Lijiangheituanxingu near-isogenic lines. In summary, these findings unravel the intricate dynamics of co-expression and singular functionality within NLR bidirectional gene pairs upon pathogen invasion.

High temperature negatively impacts the yield and quality of fruit crops. Exogenous melatonin (MT) application has shown the capability to enhance heat tolerance, but the response of endogenous MT to heat stress, particularly in perennial fruit trees, remains elusive. This study investigated the effects of high temperatures on transgenic apple plants overexpressing the MT biosynthetic gene N-acetylserotonin methyltransferase 9 ( MdASMT9). Endogenous MT protected transgenic plants from heat stress, scavenging reactive oxygen species (ROS) and increasing soluble carbohydrates and amino acids levels. MdASMT9-overexpressing plants also maintained higher photosynthetic activity by protecting the chloroplasts from damage. Transcriptome sequencing indicates that MdASMT9 overexpression promoting the expression of HSFA1d, HSFA2-like, and HSFA9b, and inhibiting the transcription of HSFB1 and HSFB2b. Application of MT and overexpression of MdASMT9 reduced abscisic acid (ABA) accumulation through promoting MdWRKY33-mediated transcriptional inhibition of MdNCED1 and MdNCED3, thus promoting stomatal opening for better heat dissipation. Furthermore, melatonin enhanced autophagic activity through promoting MdWRKY33-mediated transcriptional enhancement of MdATG18a under heat stress . These findings provide new sight into the regulation of endogenous MT and its role in improving heat tolerance in perennial fruit trees.

Photosynthesis is the foundation of all life on Earth, providing oxygen and energy. However, if not well regulated, it can also generate toxic reactive oxygen species (ROS), which can cause photodamage. Regulation of photosynthesis is highly dynamic, responding to both environmental and metabolic cues, and occurs at many levels, from light capture to energy storage and metabolic processes. One general mechanism of regulation involves the reversible oxidation and reduction of protein thiol groups, which can affect the activity of enzymes and the stability of proteins. Such redox regulation has been well studied in stromal enzymes, but more recently evidence has emerged of redox control of thylakoid lumenal enzymes. This review/hypothesis paper summarizes the latest research and discusses several open questions and challenges to achieving effective redox control in the lumen, focusing on the distinct environments and regulatory components of the thylakoid lumen, including the need to transport electrons across the thylakoid membrane, the effects of pH changes in the stromal and lumenal compartments, and the observed differences in redox states. These constraints suggest that activated oxygen species are likely to be major regulatory contributors to lumenal thiol redox regulation, with key components and processes yet to be discovered.

Leaf gas exchange measurements provide an important tool for inferring a plant’s photosynthetic biochemistry. In most cases, the responses of photosynthetic CO 2 assimilation to variable intercellular CO 2 concentrations ( A/ Ci response curves) are used to model the maximum rate of carboxylation by ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco, V cmax) and the rate of electron transport at a given photosynthetically active radiation (PAR; J PAR). The standard Farquhar-Von Caemmerer-Berry model is typically used with default parameters of Rubisco kinetic values and mesophyll conductance to CO 2 ( g m) derived from tobacco that impairs analytical reliability across species. To study this, here we measured the temperature responses of key in vitro Rubisco catalytic properties and g m in cotton ( Gossypium hirsutum cv. Sicot 71) and derived V cmax and J 2000 ( J at 2000 µmol m -2 s -1 PAR) from cotton A/ Ci curves incrementally measured at 15°C to 40°C using cotton and tobacco parameters with our new automated fitting R package ‘OptiFitACi’. When applied to cotton, the tobacco parameters produced unrealistic J 2000: V cmax ratio of <1 at 25°C, two- to three-fold higher estimates of V cmax, approximately 50% higher estimates of J 2000 and more variable estimates of V cmax and J 2000, compared to model parameterisation with cotton-derived values. We determined that errors arise when using a g m of 0.23 mol m -2 s -1 bar -1 or below and Rubisco CO 2-affinities under ambient O 2 ( K C 21%O2) outside 461 µbar to 627 µbar to model A/ C i responses in cotton. We show how the multi- A/ C i modelling capabilities of ‘OptiFitACi’ serves as a robust, user-friendly extension of ‘plantecophys’ by providing simplified temperature-sensitivity and species-specificity parameterisation capabilities to enable higher accuracy estimates of V cmax and J 2000.

D-amino acids are the D stereoisomers of common L-amino acids found in proteins. In the past two decades, the occurrence of D-amino acids in plants has been reported and circumstantial evidence for a role in several processes has been provided, including the interaction with soil microorganisms or an interference with cellular signalling. However, examples are relatively scarce and D-amino acids can also be detrimental, some of them inhibiting growth and development. Thus, the persistence of a D-amino acid metabolism in plants is rather surprising and evolutive origins of D-amino acid metabolism is presently unclear. Systemic analysis of sequences associated with enzymes of D-amino acid metabolism shows that they are not simply inherited from cyanobacterial metabolism. In effect, the history of enzymes of plant D-amino acid metabolism likely involves several steps, cellular compartments, gene transfers and losses. Regardless of evolutive steps, enzymes of D-amino acid metabolism like D-amino acid transferases or racemases have been kept by higher plants and not simply eliminated, hence it is likely that they fulfil important metabolic roles, which can be illustrated with serine, tryptophan, and folate metabolism. We suggest that D-amino acid metabolism was perhaps crucial to support metabolic functions required during land plants evolution.

Early flowering is a survival strategy in wheat ( Triticum aestivum L.) that sacrifices grain yield under long photoperiod conditions, and this contradiction is greatly affected by floral growth and development. However, little is known about the regulatory mechanisms that remove the barrier between “early flowering” and “high yielding” during floret development. Here, we showed high-resolution analyses of the number and morphology of floret primordia and the transcriptomes of wheat spikes in three light regimens. The development of all floret primordia in a spike could be divided into four distinct stages: differentiation (Stage I), differentiation and morphology development concurrently (Stage II), morphology development (Stage III), and polarization (Stage IV). Compared to the controls, the long photoperiod supplemented with red light treatment shortened the time required to complete Stage I-II, then improved assimilates in the spike and promoted anther development, thereby increasing fertile floret primordia during Stage III, and maintained fertile floret primordia development during Stage IV until they became fertile florets (grains) via a dynamic gene network centered on ubiquitin, calcium signaling, aldehyde dehydrogenase, zinc finger proteins, and heat shock proteins. Our findings proposed a light regimen, critical stages, and candidate regulators that promoted early flowering and high yield in wheat.