Fluctuating Light Interacts with Time of Day and Leaf Development Stage to Reprogram Gene Expression

Translational photobiology: towards dynamic lighting in indoor horticulture

Crop productivity depends on the ability of plants to thrive across different growth environments. In nature, light conditions fluctuate due to diurnal and seasonal changes in direction, duration, intensity, and spectrum. Laboratory studies, predominantly conducted with arabidopsis (Arabidopsis thaliana), have provided valuable insights into the metabolic and regulatory strategies that plants employ to cope with varying light intensities. However, there has been less focus on how horticultural crops tolerate dynamically changing light conditions during the photoperiod. In this review we connect insights from photobiology in model plants to the application of dynamic lighting in indoor horticulture. We explore how model species respond to fluctuating light intensities and discuss how this knowledge could be translated for new lighting solutions in controlled environment agriculture.

Dynamics and interplay of photosynthetic regulatory processes depend on the amplitudes of oscillating light

Plants have evolved multiple regulatory mechanisms to cope with natural light fluctuations. The interplay between these mechanisms leads presumably to the resilience of plants in diverse light patterns. We investigated the energy-dependent nonphotochemical quenching (qE) and cyclic electron transports (CET) in light that oscillated with a 60-s period with three different amplitudes. The photosystem I (PSI) and photosystem II (PSII) function-related quantum yields and redox changes of plastocyanin and ferredoxin were measured in Arabidopsis thaliana wild types and mutants with partial defects in qE or CET. The decrease in quantum yield of qE due to the lack of either PsbS- or violaxanthin de-epoxidase was compensated by an increase in the quantum yield of the constitutive nonphotochemical quenching. The mutant lacking NAD(P)H dehydrogenase (NDH)-like-dependent CET had a transient significant PSI acceptor side limitation during the light rising phase under high amplitude of light oscillations. The mutant lacking PGR5/PGRL1-CET restricted electron flows and failed to induce effective photosynthesis control, regardless of oscillation amplitudes. This suggests that PGR5/PGRL1-CET is important for the regulation of PSI function in various amplitudes of light oscillation, while NDH-like-CET acts' as a safety valve under fluctuating light with high amplitude. The results also bespeak interplays among multiple photosynthetic regulatory mechanisms.

Reprogramming the translatome during daily light transitions as affected by cytosolic glyceraldehyde-3-phosphate dehydrogenases GAPC1/C2

Dark-light and light-dark transitions during the day are switching points of leaf metabolism that strongly affect the regulatory state of the cells, and this change is hypothesized to affect the translatome. The cytosolic glyceraldehyde-3-phosphate dehydrogenases GAPC1 and GAPC2 function in glycolysis, and carbohydrate and energy metabolism, but GAPC1/C2 also shows moonlighting functions in gene expression and post-transcriptional regulation. In this study we examined the rapid reprogramming of the translatome that occurs within 10 min at the end of the night and the end of the day in wild-type (WT) Arabidopsis and a gapc1/c2 double-knockdown mutant. Metabolite profiling compared to the WT showed that gapc1/c2 knockdown led to increases in a set of metabolites at the start of day, particularly intermediates of the citric acid cycle and linked pathways. Differences in metabolite changes were also detected at the end of the day. Only small sets of transcripts changed in the total RNA pool; however, RNA-sequencing revealed major alterations in polysome-associated transcripts at the light-transition points. The most pronounced difference between the WT and gapc1/c2 was seen in the reorganization of the translatome at the start of the night. Our results are in line with the proposed hypothesis that GAPC1/C2 play a role in the control of the translatome during light/dark transitions.

Strong prevalence of light regime-specific QTL in Arabidopsis detected using automated high-throughput phenotyping in fluctuating or constant light

Plants have evolved and adapted under dynamic environmental conditions, particularly to fluctuating light, but plant research has often focused on constant growth conditions. To quantitatively asses the adaptation to fluctuating light, a panel of 384 natural Arabidopsis thaliana accessions was analyzed in two parallel independent experiments under fluctuating and constant light conditions in an automated high-throughput phenotyping system upgraded with supplemental LEDs. While the integrated daily photosynthetically active radiation was the same under both light regimes, plants in fluctuating light conditions accumulated significantly less biomass and had lower leaf area during their measured vegetative growth than plants in constant light. A total of 282 image-derived architectural and/or color-related traits at six common time points, and 77 photosynthesis-related traits from one common time point were used to assess their associations with genome-wide natural variation for both light regimes. Out of the 3000 significant marker-trait associations (MTAs) detected, only 183 (6.1%) were common for fluctuating and constant light conditions. The prevalence of light regime-specific QTL indicates a complex adaptation. Genes in linkage disequilibrium with fluctuating light-specific MTAs with an adjusted repeatability value >0.5 were filtered for gene ontology terms containing "photo" or "light", yielding 15 selected candidates. The candidate genes are involved in photoprotection, PSII maintenance and repair, maintenance of linear electron flow, photorespiration, phytochrome signaling, and cell wall expansion, providing a promising starting point for further investigations into the response of Arabidopsis thaliana to fluctuating light conditions.

Growth in fluctuating light buffers plants against photorespiratory perturbations

Photorespiration (PR) is the pathway that detoxifies the product of the oxygenation reaction of Rubisco. It has been hypothesized that in dynamic light environments, PR provides a photoprotective function. To test this hypothesis, we characterized plants with varying PR enzyme activities under fluctuating and non-fluctuating light conditions. Contrasting our expectations, growth of mutants with decreased PR enzyme levels was least affected in fluctuating light compared with wild type. Results for growth, photosynthesis and metabolites combined with thermodynamics-based flux analysis revealed two main causal factors for this unanticipated finding: reduced rates of photosynthesis in fluctuating light and complex re-routing of metabolic fluxes. Only in non-fluctuating light, mutants lacking the glutamate:glyoxylate aminotransferase 1 re-routed glycolate processing to the chloroplast, resulting in photooxidative damage through H2O2 production. Our results reveal that dynamic light environments buffer plant growth and metabolism against photorespiratory perturbations.

Photosynthetic and transcriptome responses to fluctuating light in Arabidopsis thylakoid ion transport triple mutant

Fluctuating light intensity challenges fluent photosynthetic electron transport in plants, inducing photoprotection while diminishing carbon assimilation and growth, and also influencing photosynthetic signaling for regulation of gene expression. Here, we employed in vivo chlorophyll-a fluorescence and P700 difference absorption measurements to demonstrate the enhancement of photoprotective energy dissipation of both photosystems in wild-type Arabidopsis thaliana after 6 h exposure to fluctuating light as compared with constant light conditions. This acclimation response to fluctuating light was hampered in a triple mutant lacking the thylakoid ion transport proteins KEA3, VCCN1, and CLCe, leading to photoinhibition of photosystem I. Transcriptome analysis revealed upregulation of genes involved in biotic stress and defense responses in both genotypes after exposure to fluctuating as compared with constant light, yet these responses were demonstrated to be largely upregulated in triple mutant already under constant light conditions compared with wild type. The current study illustrates the rapid acclimation of plants to fluctuating light, including photosynthetic, transcriptomic, and metabolic adjustments, and highlights the connection among thylakoid ion transport, photosynthetic energy balance, and cell signaling.

Dynamic growth QTL action in diverse light environments: characterization of light regime-specific and stable QTL in Arabidopsis

Plant growth is a complex process affected by a multitude of genetic and environmental factors and their interactions. To identify genetic factors influencing plant performance under different environmental conditions, vegetative growth was assessed in Arabidopsis thaliana cultivated under constant or fluctuating light intensities, using high-throughput phenotyping and genome-wide association studies. Daily automated non-invasive phenotyping of a collection of 382 Arabidopsis accessions provided growth data during developmental progression under different light regimes at high temporal resolution. Quantitative trait loci (QTL) for projected leaf area, relative growth rate, and PSII operating efficiency detected under the two light regimes were predominantly condition-specific and displayed distinct temporal activity patterns, with active phases ranging from 2 d to 9 d. Eighteen protein-coding genes and one miRNA gene were identified as potential candidate genes at 10 QTL regions consistently found under both light regimes. Expression patterns of three candidate genes affecting projected leaf area were analysed in time-series experiments in accessions with contrasting vegetative leaf growth. These observations highlight the importance of considering both environmental and temporal patterns of QTL/allele actions and emphasize the need for detailed time-resolved analyses under diverse well-defined environmental conditions to effectively unravel the complex and stage-specific contributions of genes affecting plant growth processes.

Photosynthetic mechanism of maize yield under fluctuating light environments in the field

The photosynthetic mechanism of crop yields in fluctuating light environments in the field remains controversial. To further elucidate this mechanism, we conducted field and simulation experiments using maize (Zea mays) plants. Increased planting density enhanced the light fluctuation frequency and reduced the duration of daily high light, as well as the light-saturated photosynthetic rate, biomass, and yield per plant. Further analysis confirmed a highly significant positive correlation between biomass and yield per plant and the duration of photosynthesis related to daily high light. The simulation experiment indicated that the light-saturated photosynthetic rate of maize leaves decreased gradually and considerably when shortening the daily duration of high light. Under an identical duration of high light exposure, increasing the fluctuation frequency decreased the light-saturated photosynthetic rate slightly. Proteomic data also demonstrated that photosynthesis was mainly affected by the duration of high light and not by the light fluctuation frequency. Consequently, the current study proposes that an appropriate duration of daily high light under fluctuating light environments is the key factor for greatly improving photosynthesis. This is a promising mechanism by which the photosynthetic productivity and yield of maize can be enhanced under complex light environments in the field.

Plasticity of Arabidopsis rosette transcriptomes and photosynthetic responses in dynamic light conditions

With the high variability of natural growth environments, plants exhibit flexibility and resilience in regard to the strategies they employ to maintain overall fitness, including maximizing light use for photosynthesis, while simultaneously limiting light-associated damage. We measured distinct parameters of photosynthetic performance of Arabidopsis thaliana plants under dynamic light regimes. Plants were grown to maturity then subjected to the following 5-day (16 h light, 8 h dark) regime: Day 1 at constant light (CL) intensity during light period, representative of a common lab growth condition; Day 2 under sinusoidal variation in light intensity (SL) during the light period that is representative of changes occurring during a clear sunny day; Day 3 under fluctuating light (FL) intensity during the light period that simulates sudden changes that might occur with the movements of clouds in and out of the view of the sun; Day 4, repeat of CL; and Day 5, repeat of FL. We also examined the global transcriptome profile in these growth conditions based on obtaining RNA-sequencing (RNA-seq) data for whole plant rosettes. Our transcriptomic analyses indicated downregulation of photosystem I (PSI) and II (PSII) associated genes, which were correlated with elevated levels of photoinhibition as indicated by measurements of nonphotochemical quenching (NPQ), energy-dependent quenching (qE), and inhibitory quenching (qI) under both SL and FL conditions. Furthermore, our transcriptomic results indicated downregulation of tetrapyrrole biosynthesis associated genes, coupled with reduced levels of chlorophyll under both SL and FL compared with CL, as well as downregulation of photorespiration-associated genes under SL. We also noticed an enrichment of the stress response gene ontology (GO) terms for genes differentially regulated under FL when compared with SL. Collectively, our phenotypic and transcriptome analyses serve as useful resources for probing the underlying molecular mechanisms associated with plant acclimation to rapid light intensity changes in the natural environment.

Transcriptomic and metabolic signatures of diatom plasticity to light fluctuations

Unlike in terrestrial and freshwater ecosystems, light fields in oceans fluctuate due to both horizontal current and vertical mixing. Diatoms thrive and dominate the phytoplankton community in these fluctuating light fields. However, the molecular mechanisms that regulate diatom acclimation and adaptation to light fluctuations are poorly understood. Here, we performed transcriptome sequencing, metabolome profiling, and 13C-tracer labeling on the model diatom Phaeodactylum tricornutum. The diatom acclimated to constant light conditions was transferred to six different light conditions, including constant light (CL5d), short-term (1 h) high light (sHL1h), and short-term (1 h) and long-term (5 days) mild or severe light fluctuation conditions (mFL1h, sFL1h, mFL5d, and sFL5d) that mimicked land and ocean light levels. We identified 2,673 transcripts (25% of the total expressed genes) expressed differentially under different fluctuating light regimes. We also identified 497 transcription factors, 228 not reported previously, which exhibited higher expression under light fluctuations, including 7 with a light-sensitive PAS domain (Per-period circadian protein, Arnt-aryl hydrocarbon receptor nuclear translocator protein, Sim-single-minded protein) and 10 predicted to regulate genes related to light-harvesting complex proteins. Our data showed that prolonged preconditioning in severe light fluctuation enhanced photosynthesis in P. tricornutum under this condition, as evidenced by increased oxygen evolution accompanied by the upregulation of Rubisco and light-harvesting proteins. Furthermore, severe light fluctuation diverted the metabolic flux of assimilated carbon preferentially toward fatty acid storage over sugar and protein. Our results suggest that P. tricornutum use a series of complex and different responsive schemes in photosynthesis and carbon metabolism to optimize their growth under mild and severe light fluctuations. These insights underscore the importance of using more intense conditions when investigating the resilience of phytoplankton to light fluctuations.

Photosynthetic Apparatus of Hydrocharis morsus-ranae in Different Solar Lighting

Hydrocharis morsus-ranae is a free-floating species growing in lakes and slow-flowing rivers near the shore in Europe and Western Asia, and as an invasive plant in the USA and Canada. Light-requiring plants of this species can also grow in the shade, up to about 30% of full sunlight. In this paper we present the data about the photosynthetic apparatus of sunny and shady H. morsus-ranae plants grown in the sun and in the shade in nature. Methods of light and transmission electron microscopy, biochemistry, chlorophyll fluorescence induction as well as the principal component analysis were used. It was found that leaves of plants growing in shade differed from those in the sun with such traits as thickness of a blade, palisade and spongy parenchyma, ultrastructure of chloroplasts, and quantum efficiency of photosynthetic electron transport, the content of chlorophylls and carotenoids, anthocyanins and phenilpropanoids. By these traits, H. morsus-ranae shady plants are similar with shade-bearing plants that indicates their adaptation to light intensity lowering. The ordination plots (PCA) suggested a clear structural and functional shift of plants growing in different lighting showing relationship to light changes in the natural environment. Thus, our results displayed the high phenotypic plasticity of the H. morsus-ranae photosynthetic apparatus, which ensures its acclimation to changing light environment and wide distribution of this species.

Fast chlorophyll a fluorescence induction (OJIP) phenotyping of chlorophyll-deficient wheat suggests that an enlarged acceptor pool size of Photosystem I helps compensate for a deregulated photosynthetic electron flow

The wheat lines affected by a decrease in the leaf chlorophyll content typically experience a biomass loss. A known major problem of the chlorophyll-deficient wheat mutants is their limited prevention of Photosystem I (PSI) over-reduction brought about by an insufficient cyclic electron flow, potentially exposing them to a higher sensitivity to light fluctuations. However, the resistance of some mutant lines against fluctuating light suggests the occurrence of regulatory processes compensating for the defect in cyclic electron flow. In this study, a phenotyping approach based on fast chlorophyll a fluorescence induction (OJIP transient), corroborated by P700 redox kinetics, was applied to a collection of chlorophyll-deficient wheat lines, grown under continuous or fluctuating light. Quantitative parameters calculated from the OJIP transient are considered informative about Photosystem II (PSII) functional antenna size and photochemistry, as well as the functioning of the entire photosynthetic electron transport chain. The mutants tended to recover a wild-type-like chlorophyll content, and mature plants could hardly be distinguished based on their effective PSII antenna size. Nevertheless, specific OJIP-derived parameters were strongly correlated with the phenotype severity, in particular the amplitude of the I-P phase and the I-P/J-P amplitude ratio, which are indicative of a more capacitive pool of PSI final electron acceptors (ferredoxin and ferredoxin-NADP⁺ oxidoreductase, FNR). We propose that the enlargement of such pool of electron carriers is a compensatory response operating at the acceptor side of PSI to alleviate potentially harmful over-reduced states of PSI. Our results also suggest that, in chlorophyll-deficient mutants, higher F_V /F_M cannot prove a superior PSII photochemistry and wider I-P phase is not indicative of a higher relative content of PSI.

Fillable and unfillable gaps in plant transcriptome under field and controlled environments

The differences between plants grown in field and in controlled environments have long been recognized. However, few studies have addressed the underlying molecular mechanisms. To evaluate plant responses to fluctuating environments using laboratory equipment, we developed SmartGC, a high-performance growth chamber that reproduces the fluctuating irradiance, temperature and humidity of field environments. We analysed massive transcriptome data of rice plants grown under field and SmartGC conditions to clarify the differences in plant responses to field and controlled environments. Rice transcriptome dynamics in SmartGC mimicked those in the field, particularly during the morning and evening but those in conventional growth chamber conditions did not. Further analysis revealed that fluctuation of irradiance affects transcriptome dynamics in the morning and evening, while fluctuation of temperature affects transcriptome dynamics only in the morning. We found upregulation of genes related to biotic and abiotic stress, and their expression was affected by environmental factors that cannot be mimicked by SmartGC. Our results reveal fillable and unfillable gaps in the transcriptomes of rice grown in field and controlled environments and can accelerate the understanding of plant responses to field environments for both basic biology and agricultural applications.

Cia Zeaxanthin Biosynthesis, OsZEP and OsVDE Regulate Striped Leaves Occurring in Response to Deep Transplanting of Rice

The rice leaf color mutant B03S was previously generated from the photoperiod- and thermo-sensitive genic male sterile (PTGMS) rice line Efeng 1S, of which male sterility manifests by photoperiod and temperature but exhibits mainly temperature-sensitive characteristics. After these plants were deeply transplanted, the new leaves manifested typical zebra stripe patterns. Here, B03S was subjected to deep and shallow transplanting, shading with soil and aluminum foil, and control conditions in situ to determine the cause of the striped-leaf trait. The direct cause of striped leaves is the base of the leaf sheath being under darkness during deep transplanting, of which the critical shading range reached or exceeds 4 cm above the base. Moreover, typical striped leaves were analyzed based on the targeted metabolome method by ultra-performance liquid chromatography/tandem mass spectrometry (UPLC–MS/MS) combined with transcriptome and real-time quantitative PCR (qPCR)-based verification to clarify the metabolic pathways and transcriptional regulation involved. Carotenoids enter the xanthophyll cycle, and the metabolites that differentially accumulate in the striped leaves include zeaxanthin and its derivatives for photooxidative stress protection, driven by the upregulated expression of OsZEP. These findings improve the understanding of the physiological and metabolic mechanisms underlying the leaf color mutation in rice plants, enrich the theoretical foundation of the nonuniform leaf color phenomenon widely found in nature and highlight key advancements concerning rice production involving the transplanting of seedlings or direct broadcasting of seeds.

A Comparison of Photoprotective Mechanism in Different Light-Demanding Plants Under Dynamic Light Conditions

Light intensity is highly heterogeneous in nature, and plants have evolved a series of strategies to acclimate to dynamic light due to their immobile lifestyles. However, it is still unknown whether there are differences in photoprotective mechanisms among different light-demanding plants in response to dynamic light, and thus the role of non-photochemical quenching (NPQ), electron transport, and light energy allocation of photosystems in photoprotection needs to be further understood in different light-demanding plants. The activities of photosystem II (PSII) and photosystem I (PSI) in shade-tolerant species Panax notoginseng, intermediate species Polygonatum kingianum, and sun-demanding species Erigeron breviscapus were comparatively measured to elucidate photoprotection mechanisms in different light-demanding plants under dynamic light. The results showed that the NPQ and PSII maximum efficiency (F v'/F m') of E. breviscapus were higher than the other two species under dynamic high light. Meanwhile, cyclic electron flow (CEF) of sun plants is larger under transient high light conditions since the slope of post-illumination, P700 dark reduction rate, and plastoquinone (PQ) pool were greater. NPQ was more active and CEF was initiated more readily in shade plants than the two other species under transient light. Moreover, sun plants processed higher quantum yield of PSII photochemistry (ΦPSII), quantum yield of photochemical energy conversion [Y(I)], and quantum yield of non-photochemical energy dissipation due to acceptor side limitation (Y(NA), while the constitutive thermal dissipation and fluorescence (Φf,d) and quantum yield of non-photochemical energy dissipation due to donor side limitation [Y(ND)] of PSI were higher in shade plants. These results suggest that sun plants had higher NPQ and CEF for photoprotection under transient high light and mainly allocated light energy through ΦPSII and ΦNPQ, while shade plants had a higher Φf,d and a larger heat dissipation efficiency of PSI donor. Overall, it has been demonstrated that the photochemical efficiency and photoprotective capacity are greater in sun plants under transient dynamic light, while shade plants are more sensitive to transient dynamic light.

Photosynthesis under fluctuating light in the CAM plant Vanilla planifolia

Photosynthetic induction after a sudden increase in illumination affects carbon gain. Photosynthetic dynamics under fluctuating light (FL) have been widely investigated in C3 and C4 plants but are little known in CAM plants. In our present study, the chlorophyll fluorescence, P700 redox state and electrochromic shift signals were measured to examine photosynthetic characteristics under FL in the CAM orchid Vanilla planifolia. The light use efficiency was maximized in the morning but was restricted in the afternoon, indicating that the pool of malic acid dried down in the afternoon. During photosynthetic induction in the morning, electron flow through photosystem I rapidly reached the 95% of the maximum value in 4-6 min, indicating that V. planifolia showed a fast photosynthetic induction when compared with C3 and C4 plants reported previously. Upon a sudden transition from dark to actinic light, a rapid re-oxidation of P700 was observed in V. planifolia, indicating the fast outflow of electrons from PSI to alternative electron acceptors, which was attributed to the O₂ photo-reduction mediated by water-water cycle. The functioning of water-water cycle prevented photosystem I over-reduction after transitioning from low to high light and thus protected PSI under FL. In the afternoon, cyclic electron flow was stimulated under FL to fine-tune photosynthetic apparatus when photosynthetic CO₂ was restricted. Therefore, water-water cycle cooperates with cyclic electron flow to regulate the photosynthesis under FL in the CAM orchid V. planifolia.

The biology of time: dynamic responses of cell types to developmental, circadian and environmental cues

As sessile organisms, plants are finely tuned to respond dynamically to developmental, circadian and environmental cues. Genome-wide studies investigating these types of cues have uncovered the intrinsically different ways they can impact gene expression over time. Recent advances in single-cell sequencing and time-based bioinformatic algorithms are now beginning to reveal the dynamics of these time-based responses within individual cells and plant tissues. Here, we review what these techniques have revealed about the spatiotemporal nature of gene regulation, paying particular attention to the three distinct ways in which plant tissues are time sensitive. (i) First, we discuss how studying plant cell identity can reveal developmental trajectories hidden in pseudotime. (ii) Next, we present evidence that indicates that plant cell types keep their own local time through tissue-specific regulation of the circadian clock. (iii) Finally, we review what determines the speed of environmental signaling responses, and how they can be contingent on developmental and circadian time. By these means, this review sheds light on how these different scales of time-based responses can act with tissue and cell-type specificity to elicit changes in whole plant systems.

Ocean acidification exacerbates the inhibition of fluctuating light on the productivity of Ulva prolifera

Ulva prolifera, a common species of green macroalgae, is often harmful-algal-bloom causative and significantly impacts local marine ecosystems. Previous studies on the physiological characteristics of U. prolifera have been conducted under constant light (CL). However, light in the natural environment continually changes, and little is known about fluctuating light (FL). Ocean acidification (OA) has been proposed to interact with dynamic surrounding environments to affect the physiological performance of macroalgae. Therefore, we investigated the combined effects of FL (80/300, alternating between 80 μmol photons m^-2 s^-1 for 2.5 h and 300 μmol photons m^-2 s^-1 for 1.5 h, with an average light intensity of 160 μmol photons m^-2 s^-1 and OA (1000 ppm CO₂) on U. prolifera. The results clearly showed that FL had no significant effect on the relative growth rate (RGR), whereas OA obviously improved RGR. However, under FL-OA combination conditions, RGR was inhibited significantly, accompanied by a concomitant downgraded photosynthetic performance, while the photoprotective abilities were enhanced. The results would help us accurately predict the primary productivity of macroalgae in coastal waters under future OA conditions with irradiance fluctuations.

Indirect Export of Reducing Equivalents From the Chloroplast to Resupply NADP for C3 Photosynthesis-Growing Importance for Stromal NAD(H)?

Plant productivity greatly relies on a flawless concerted function of the two photosystems (PS) in the chloroplast thylakoid membrane. While damage to PSII can be rapidly resolved, PSI repair is complex and time-consuming. A major threat to PSI integrity is acceptor side limitation e.g., through a lack of stromal NADP ready to accept electrons from PSI. This situation can occur when oscillations in growth light and temperature result in a drop of CO2 fixation and concomitant NADPH consumption. Plants have evolved a plethora of pathways at the thylakoid membrane but also in the chloroplast stroma to avoid acceptor side limitation. For instance, reduced ferredoxin can be recycled in cyclic electron flow or reducing equivalents can be indirectly exported from the organelle via the malate valve, a coordinated effort of stromal malate dehydrogenases and envelope membrane transporters. For a long time, the NADP(H) was assumed to be the only nicotinamide adenine dinucleotide coenzyme to participate in diurnal chloroplast metabolism and the export of reductants via this route. However, over the last years several independent studies have indicated an underappreciated role for NAD(H) in illuminated leaf plastids. In part, it explains the existence of the light-independent NAD-specific malate dehydrogenase in the stroma. We review the history of the malate valve and discuss the potential role of stromal NAD(H) for the plant survival under adverse growth conditions as well as the option to utilize the stromal NAD(H) pool to mitigate PSI damage.

Defining date palm leaf pruning line in bearing status by tracking physiological markers and expression of senescence-related genes

The physiological and molecular markers were evaluated for defining leaf pruning line in bearing status of date palm (Phoenix dactylifera cv. Mazafati). Our results showed that the higher expression of the chlorophyllase (Chlase) gene was concomitant with lower expression of chlorophyll synthase (ChlG) and oxygen-evolving enhancer protein (PSBO) genes in the 6-year-old leaf line. In addition, the 6-year-old leaf line resulted in a lower Hill reaction rate, chlorophyll a/b ratio, photosystem Ⅱ quantum efficiency, and photosynthesis rate. Also, lower expression and activities of catalase (CAT), ascorbate peroxidase (APX), and glutathione peroxidase (GPX) was associated with higher malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) accumulation in 6-year-old leaf line. These results suggested that the physiological maturity termination, senescence stage initiation, and source to sink transition could occur in 6-year-old leaves. Furthermore, delayed 5-year-old leaf pruning line adjustment in consecutive years could increase quantitative and qualitative yield loss, decrease water use efficiency, and promote alternate bearing and fruit abscission, which is considered a common problem of date growing areas. Further, the senescence-related markers in the alternate bearing trees pruned in pruning line 5 showed a tendency to normal trees. The five-year-old pruning line also resulted in the balance of bunching and loading the alternate bearing trees.

The Complementary Roles of Chloroplast Cyclic Electron Transport and Mitochondrial Alternative Oxidase to Ensure Photosynthetic Performance

Chloroplasts use light energy and a linear electron transport (LET) pathway for the coupled generation of NADPH and ATP. It is widely accepted that the production ratio of ATP to NADPH is usually less than required to fulfill the energetic needs of the chloroplast. Left uncorrected, this would quickly result in an over-reduction of the stromal pyridine nucleotide pool (i.e., high NADPH/NADP⁺ ratio) and under-energization of the stromal adenine nucleotide pool (i.e., low ATP/ADP ratio). These imbalances could cause metabolic bottlenecks, as well as increased generation of damaging reactive oxygen species. Chloroplast cyclic electron transport (CET) and the chloroplast malate valve could each act to prevent stromal over-reduction, albeit in distinct ways. CET avoids the NADPH production associated with LET, while the malate valve consumes the NADPH associated with LET. CET could operate by one of two different pathways, depending upon the chloroplast ATP demand. The NADH dehydrogenase-like pathway yields a higher ATP return per electron flux than the pathway involving PROTON GRADIENT REGULATION5 (PGR5) and PGR5-LIKE PHOTOSYNTHETIC PHENOTYPE1 (PGRL1). Similarly, the malate valve could couple with one of two different mitochondrial electron transport pathways, depending upon the cytosolic ATP demand. The cytochrome pathway yields a higher ATP return per electron flux than the alternative oxidase (AOX) pathway. In both Arabidopsis thaliana and Chlamydomonas reinhardtii, PGR5/PGRL1 pathway mutants have increased amounts of AOX, suggesting complementary roles for these two lesser-ATP yielding mechanisms of preventing stromal over-reduction. These two pathways may become most relevant under environmental stress conditions that lower the ATP demands for carbon fixation and carbohydrate export.

Evaluation of Light-Dependent Photosynthetic Reactions in Reynoutria japonica Houtt. Leaves Grown at Different Light Conditions

The Japanese knotweed (Reynoutria japonica Houtt.) is considered as one of the most aggressive and highly successful invasive plants with a negative impact on invaded habitats. Its uncontrolled expansion became a significant threat to the native species throughout Europe. Due to its extensive rhizome system, rapid growth, and allelopathic activity, it usually forms monocultures that negatively affect the nearby vegetation. The efficient regulation of partitioning and utilization of energy in photosynthesis enables invasive plants to adapt rapidly a variety of environmental conditions. Therefore, we aimed to determine the influence of light conditions on photosynthetic reactions in the Japanese knotweed. Plants were grown under two different light regimes, namely, constant low light (CLL, 40 μmol/m²/s) and fluctuating light (FL, 0-1,250 μmol/m²/s). To evaluate the photosynthetic performance, the direct and modulated chlorophyll a fluorescence was measured. Plants grown at a CLL served as control. The photosynthetic measurements revealed better photosystem II (PSII) stability and functional oxygen-evolving center of plants grown in FL. They also exhibited more efficient conversion of excitation energy to electron transport and an efficient electron transport beyond the primary electron acceptor Q_A, all the way to PSI. The enhanced photochemical activity of PSI suggested the formation of a successful adaptive mechanism by regulating the distribution of excitation energy between PSII and PSI to minimize photooxidative damage. A faster oxidation at the PSI side most probably resulted in the generation of the cyclic electron flow around PSI. Besides, the short-term exposure of FL-grown knotweeds to high light intensity increased the yield induced by downregulatory processes, suggesting that the generation of the cyclic electron flow protected PSI from photoinhibition.

Age-Dependent Abiotic Stress Resilience in Plants

Developmental age is a strong determinant of stress responses in plants. Differential susceptibility to various environmental stresses is widely observed at both the organ and whole-plant level. While it is clear that age determines stress susceptibility, the causes, regulatory mechanisms, and functions are only now beginning to emerge. Compared with concepts on age-related biotic stress resilience, advancements in the abiotic stress field are relatively limited. In this review, we focus on current knowledge of ontogenic resistance to abiotic stresses, highlighting examples at the organ (leaf) and plant level, preceded by an overview of the relevant concepts in plant aging. We also discuss age-related abiotic stress resilience mechanisms, speculate on their functional relevance, and outline outstanding questions.

Stromal NADH supplied by PHOSPHOGLYCERATE DEHYDROGENASE3 is crucial for photosynthetic performance

During photosynthesis, electrons travel from light-excited chlorophyll molecules along the electron transport chain to the final electron acceptor nicotinamide adenine dinucleotide phosphate (NADP) to form NADPH, which fuels the Calvin-Benson-Bassham cycle (CBBC). To allow photosynthetic reactions to occur flawlessly, a constant resupply of the acceptor NADP is mandatory. Several known stromal mechanisms aid in balancing the redox poise, but none of them utilizes the structurally highly similar coenzyme NAD(H). Using Arabidopsis (Arabidopsis thaliana) as a C3-model, we describe a pathway that employs the stromal enzyme PHOSPHOGLYCERATE DEHYDROGENASE 3 (PGDH3). We showed that PGDH3 exerts high NAD(H)-specificity and is active in photosynthesizing chloroplasts. PGDH3 withdrew its substrate 3-PGA directly from the CBBC. As a result, electrons become diverted from NADPH via the CBBC into the separate NADH redox pool. pgdh3 loss-of-function mutants revealed an overreduced NADP(H) redox pool but a more oxidized plastid NAD(H) pool compared to wild-type plants. As a result, photosystem I acceptor side limitation increased in pgdh3. Furthermore, pgdh3 plants displayed delayed CBBC activation, changes in nonphotochemical quenching, and altered proton motive force partitioning. Our fluctuating light-stress phenotyping data showed progressing photosystem II damage in pgdh3 mutants, emphasizing the significance of PGDH3 for plant performance under natural light environments. In summary, this study reveals an NAD(H)-specific mechanism in the stroma that aids in balancing the chloroplast redox poise. Consequently, the stromal NAD(H) pool may provide a promising target to manipulate plant photosynthesis.

Phosphoglycerate dehydrogenase genes differentially affect Arabidopsis metabolism and development

Unlike animals, plants possess diverse L-serine (Ser) biosynthetic pathways. One of them, the Phosphorylated Pathway of Serine Biosynthesis (PPSB) has been recently described as essential for embryo, pollen and root development, and required for ammonium and sulfur assimilation. The first and rate limiting step of PPSB is the reaction catalyzed by the enzyme phosphoglycerate dehydrogenase (PGDH). In Arabidopsis, the PGDH family consists of three genes, PGDH1, PGDH2 and PGDH3. PGDH1 is characterized as being the essential gene of the family. However, the biological significance of PGDH2 and PGDH3 remains unknown. In this manuscript, we have functionally characterized PGDH2 and PGDH3. Phenotypic, metabolomic and gene expression analysis in PGDH single, double and triple mutants indicate that both PGDH2 and PGDH3 are functional, affecting plant metabolism and development. PGDH2 has a stronger effect on plant growth than PGDH3, having a partial redundant role with PGDH1. PGDH3, however, could have additional functions in photosynthetic cells unrelated to Ser biosynthesis.

A Holistic Approach to Study Photosynthetic Acclimation Responses of Plants to Fluctuating Light

Plants in natural environments receive light through sunflecks, the duration and distribution of these being highly variable across the day. Consequently, plants need to adjust their photosynthetic processes to avoid photoinhibition and maximize yield. Changes in the composition of the photosynthetic apparatus in response to sustained changes in the environment are referred to as photosynthetic acclimation, a process that involves changes in protein content and composition. Considering this definition, acclimation differs from regulation, which involves processes that alter the activity of individual proteins over short-time periods, without changing the abundance of those proteins. The interconnection and overlapping of the short- and long-term photosynthetic responses, which can occur simultaneously or/and sequentially over time, make the study of long-term acclimation to fluctuating light in plants challenging. In this review we identify short-term responses of plants to fluctuating light that could act as sensors and signals for acclimation responses, with the aim of understanding how plants integrate environmental fluctuations over time and tailor their responses accordingly. Mathematical modeling has the potential to integrate physiological processes over different timescales and to help disentangle short-term regulatory responses from long-term acclimation responses. We review existing mathematical modeling techniques for studying photosynthetic responses to fluctuating light and propose new methods for addressing the topic from a holistic point of view.

Light acts as a stressor and influences abiotic and biotic stress responses in plants

Light is important for plants as an energy source and a developmental signal, but it can also cause stress to plants and modulates responses to stress. Excess and fluctuating light result in photoinhibition and reactive oxygen species (ROS) accumulation around photosystems II and I, respectively. Ultraviolet light causes photodamage to DNA and a prolongation of the light period initiates the photoperiod stress syndrome. Changes in light quality and quantity, as well as in light duration are also key factors impacting the outcome of diverse abiotic and biotic stresses. Short day or shady environments enhance thermotolerance and increase cold acclimation. Similarly, shade conditions improve drought stress tolerance in plants. Additionally, the light environment affects the plants' responses to biotic intruders, such as pathogens or insect herbivores, often reducing growth-defence trade-offs. Understanding how plants use light information to modulate stress responses will support breeding strategies to enhance crop stress resilience. This review summarizes the effect of light as a stressor and the impact of the light environment on abiotic and biotic stress responses. There is a special focus on the role of the different light receptors and the crosstalk between light signalling and stress response pathways.

Chloroplast immunity illuminated

The chloroplast has recently emerged as pivotal to co-ordinating plant defence responses and as a target of plant pathogens. Beyond its central position in oxygenic photosynthesis and primary metabolism - key targets in the complex virulence strategies of diverse pathogens - the chloroplast integrates, decodes and responds to environmental signals. The capacity of chloroplasts to synthesize phytohormones and a diverse range of secondary metabolites, combined with retrograde and reactive oxygen signalling, provides exquisite flexibility to both perceive and respond to biotic stresses. These processes also represent a plethora of opportunities for pathogens to evolve strategies to directly or indirectly target 'chloroplast immunity'. This review covers the contribution of the chloroplast to pathogen associated molecular pattern and effector triggered immunity as well as systemic acquired immunity. We address phytohormone modulation of immunity and surmise how chloroplast-derived reactive oxygen species underpin chloroplast immunity through indirect evidence inferred from genetic modification of core chloroplast components and direct pathogen targeting of the chloroplast. We assess the impact of transcriptional reprogramming of nuclear-encoded chloroplast genes during disease and defence and look at future research challenges.

Leaf photosynthetic and anatomical insights into mechanisms of acclimation in rice in response to long-term fluctuating light

Long-term fluctuating light (FL) conditions are very common in natural environments. The physiological and biochemical mechanisms for acclimation to FL differ between species. However, most of the current conclusions regarding acclimation to FL were made based on studies in algae or Arabidopsis thaliana. It is still unclear how rice (Oryza sativa L.) integrate multiple physiological changes to acclimate to long-term FL. In this study, we found that rice growth was repressed under long-term FL. By systematically measuring phenotypes and physiological parameters, we revealed that: (a) under short-term FL, photosystem I (PSI) was inhibited, while after 1-7 days of long-term FL, both PSI and PSII were inhibited. Higher acceptor-side limitation in electron transport and higher overall nonphotochemical quenching (NPQ) explained the lower efficiencies of PSI and PSII, respectively. (b) An increase in pH differences across the thylakoid membrane and a decrease in thylakoid proton conductivity revealed a reduction of ATP synthase activity. (c) Using electron microscopy, we showed a decrease in membrane stacking and stomatal opening after 7 days of FL treatment. Taken together, our results show that electron flow, ATP synthase activity and NPQ regulation are the major processes determining the growth performance of rice under long-term FL conditions.

Salt stress and fluctuating light have separate effects on photosynthetic acclimation, but interactively affect biomass

In nature, soil salinity and fluctuating light (FL) often occur concomitantly. However, it is unknown whether salt stress interacts with FL on leaf photosynthesis, architecture, biochemistry, pigmentation, mineral concentrations, as well as whole-plant biomass. To elucidate this, tomato (Solanum lycopersicum) seedlings were grown under constant light (C, 200 μmol m^-2 s^-1 ) or FL (5-650 μmol m^-2 s^-1 ), in combination with no (0 mM NaCl) or moderate (80 mM NaCl) salinity, for 14 days, at identical photoperiods and daily light integrals. FL and salt stress had separate effects on leaf anatomy, biochemistry and photosynthetic capacity: FL reduced leaf thickness as well as nitrogen, chlorophyll and carotenoid contents per unit leaf area, but rarely affected steady-state and dynamic photosynthetic properties along with abundance of key proteins in the electron transport chain. Salt stress, meanwhile, mainly disorganized chloroplast grana stacking, reduced stomatal density, size and aperture as well as photosynthetic capacity. Plant biomass was affected interactively by light regime and salt stress: FL reduced biomass in salt stressed plants by 17%, but it did not affect biomass of non-stressed plants. Our results stress the importance of considering FL when inferring effects of salt-stress on photosynthesis and productivity under fluctuating light intensities.

Light in the transcription landscape: chromatin, RNA polymerase II and splicing throughout Arabidopsis thaliana's life cycle

Plants have a high level of developmental plasticity that allows them to respond and adapt to changes in the environment. Among the environmental cues, light controls almost every aspect of A. thaliana's life cycle, including seed maturation, seed germination, seedling de-etiolation and flowering time. Light signals induce massive reprogramming of gene expression, producing changes in RNA polymerase II transcription, alternative splicing, and chromatin state. Since splicing reactions occur mainly while transcription takes place, the regulation of RNAPII transcription has repercussions in the splicing outcomes. This cotranscriptional nature allows a functional coupling between transcription and splicing, in which properties of the splicing reactions are affected by the transcriptional process. Chromatin landscapes influence both transcription and splicing. In this review, we highlight, summarize and discuss recent progress in the field to gain a comprehensive insight on the cross-regulation between chromatin state, RNAPII transcription and splicing decisions in plants, with a special focus on light-triggered responses. We also introduce several examples of transcription and splicing factors that could be acting as coupling factors in plants. Unravelling how these connected regulatory networks operate, can help in the design of better crops with higher productivity and tolerance.

Moderate heat stress accelerates photoinhibition of photosystem I under fluctuating light in tobacco young leaves

Moderate heat stress and fluctuating light are typical conditions in summer in tropical and subtropical regions. This type of stress can cause photodamage to photosystems I and II (PSI and PSII). However, photosynthetic responses to the combination of heat and fluctuating light in young leaves are little known. In this study, we investigated chlorophyll fluorescence and P700 redox state under fluctuating light at 25 °C and 42 °C in young leaves of tobacco. Our results indicated that fluctuating light caused selective photodamage to PSI in the young leaves at 25 °C and 42 °C. Furthermore, the moderate heat stress significantly accelerated photoinhibition of PSI under fluctuating light. Within the first 10 s after transition from low to high light, cyclic electron flow (CEF) around PSI was highly stimulated at 25 °C but was slightly activated at 42 °C. Such depression of CEF activation at moderate heat stress were unable to maintain energy balance under high light. As a result, electron flow from PSI to NADP+ was restricted, leading to the over-reduction of PSI electron carriers. These results indicated that moderate heat stress altered the CEF performance under fluctuating light and thus accelerated PSI photoinhibition in tobacco young leaves.

Improved stomatal opening enhances photosynthetic rate and biomass production in fluctuating light

It has been reported that stomatal conductance often limits the steady-state photosynthetic rate. On the other hand, the stomatal limitation of photosynthesis in fluctuating light remains largely unknown, although in nature light fluctuates due to changes in sun position, cloud cover, and the overshadowing canopy. In this study, we analysed three mutant lines of Arabidopsis with increased stomatal conductance to examine to what extent stomatal opening limits photosynthesis in fluctuating light. The slac1 (slow anion channel-associated 1) and ost1 (open stomata 1) mutants with stay-open stomata, and the PATROL1 (proton ATPase translocation control 1) overexpression line with faster stomatal opening responses exhibited higher photosynthetic rates and plant growth in fluctuating light than the wild-type, whereas these four lines showed similar photosynthetic rates and plant growth in constant light. The slac1 and ost1 mutants tended to keep their stomata open in fluctuating light, resulting in lower water-use efficiency (WUE) than the wild-type. However, the PATROL1 overexpression line closed stomata when needed and opened stomata immediately upon irradiation, resulting in similar WUE to the wild-type. The present study clearly shows that there is room to optimize stomatal responses, leading to greater photosynthesis and biomass accumulation in fluctuating light in nature.

Photosynthetic Acclimation to Fluctuating Irradiance in Plants

Unlike the short-term responses of photosynthesis to fluctuating irradiance, the long-term response (i.e., acclimation) at the chloroplast, leaf, and plant level has received less attention so far. The ability of plants to acclimate to irradiance fluctuations and the speed at which this acclimation occurs are potential limitations to plant growth under field conditions, and therefore this process deserves closer study. In the first section of this review, we look at the sources of natural irradiance fluctuations, their effects on short-term photosynthesis, and the interaction of these effects with circadian rhythms. This is followed by an overview of the mechanisms that are involved in acclimation to fluctuating (or changes of) irradiance. We highlight the chain of events leading to acclimation: retrograde signaling, systemic acquired acclimation (SAA), gene transcription, and changes in protein abundance. We also review how fluctuating irradiance is applied in experiments and highlight the fact that they are significantly slower than natural fluctuations in the field, although the technology to achieve realistic fluctuations exists. Finally, we review published data on the effects of growing plants under fluctuating irradiance on different plant traits, across studies, spatial scales, and species. We show that, when plants are grown under fluctuating irradiance, the chlorophyll a/b ratio and plant biomass decrease, specific leaf area increases, and photosynthetic capacity as well as root/shoot ratio are, on average, unaffected.

Photoprotective Acclimation of the Arabidopsis thaliana Leaf Proteome to Fluctuating Light

Plants are subjected to strong fluctuations in light intensity in their natural growth environment, caused both by unpredictable changes due to weather conditions and movement of clouds and upper canopy leaves and predictable changes during day-night cycle. The mechanisms of long-term acclimation to fluctuating light (FL) are still not well understood. Here, we used quantitative mass spectrometry to investigate long-term acclimation of low light-grown Arabidopsis thaliana to a FL condition that induces mild photooxidative stress. On the third day of exposure to FL, young and mature leaves were harvested in the morning and at the end of day for proteome analysis using a stable isotope labeling approach. We identified 2,313 proteins, out of which 559 proteins exhibited significant changes in abundance in at least one of the four experimental groups (morning-young, morning-mature, end-of-day-young, end-of-day-mature). A core set of 49 proteins showed significant responses to FL in three or four experimental groups, which included enhanced accumulation of proteins involved in photoprotection, cyclic electron flow around photosystem I, photorespiration, and glycolysis, while specific glutathione transferases and proteins involved in translation and chlorophyll biosynthesis were reduced in abundance. In addition, we observed pathway- and protein-specific changes predominantly at the end of day, whereas few changes were observed exclusively in the morning. Comparison of the proteome data with the matching transcript data revealed gene- and protein-specific responses, with several chloroplast-localized proteins decreasing in abundance despite increased gene expression under FL. Together, our data shows moderate but widespread alterations of protein abundance during acclimation to FL and suggests an important role of post-transcriptional regulation of protein abundance.

Growth under Fluctuating Light Reveals Large Trait Variation in a Panel of Arabidopsis Accessions

The capacity of photoautotrophs to fix carbon depends on the efficiency of the conversion of light energy into chemical potential by photosynthesis. In nature, light input into photosynthesis can change very rapidly and dramatically. To analyze how genetic variation in Arabidopsis thaliana affects photosynthesis and growth under dynamic light conditions, 36 randomly chosen natural accessions were grown under uniform and fluctuating light intensities. After 14 days of growth under uniform or fluctuating light regimes, maximum photosystem II quantum efficiency (Fv/Fm) was determined, photosystem II operating efficiency (ΦPSII) and non-photochemical quenching (NPQ) were measured in low light, and projected leaf area (PLA) as well as the number of visible leaves were estimated. Our data show that ΦPSII and PLA were decreased and NPQ was increased, while Fv/Fm and number of visible leaves were unaffected, in most accessions grown under fluctuating compared to uniform light. There were large changes between accessions for most of these parameters, which, however, were not correlated with genomic variation. Fast growing accessions under uniform light showed the largest growth reductions under fluctuating light, which correlated strongly with a reduction in ΦPSII, suggesting that, under fluctuating light, photosynthesis controls growth and not vice versa.

Comparative transcriptome analysis reveals the molecular regulation underlying the adaptive mechanism of cherry (Cerasus pseudocerasus Lindl.) to shelter covering

BACKGROUND

Rain-shelter covering is widely applied during cherry fruit development in subtropical monsoon climates with the aim of decreasing the dropping and cracking of fruit caused by excessive rainfall. Under rain-shelter covering, the characteristics of the leaves and fruit of the cherry plant may adapt to the changes in the microclimate. However, the molecular mechanism underlying such adaptation remains unclear, although clarifying it may be helpful for improving the yield and quality of cherry under rain-shelter covering.

RESULTS

To better understand the regulation and adaptive mechanism of cherry under rain-shelter covering, 38,621 and 3584 differentially expressed genes were identified with a combination of Illumina HiSeq and single-molecule real-time sequencing in leaves and fruits, respectively, at three developmental stages. Among these, key genes, such as those encoding photosynthetic-antenna proteins (Lhca and Lhcb) and photosynthetic electron transporters (PsbP, PsbR, PsbY, and PetF), were up-regulated following the application of rain-shelter covering, leading to increased efficiency of light utilization. The mRNA levels of genes involved in carbon fixation, namely, rbcL and rbcS, were clearly increased compared with those under shelter-free conditions, resulting in improved CO₂ utilization. Furthermore, the transcription levels of genes involved in chlorophyll (hemA, hemN, and chlH) and carotenoid synthesis (crtB, PDS, crtISO, and lcyB) in the sheltered leaves peaked earlier than those in the unsheltered leaves, thereby promoting organic matter accumulation in leaves. Remarkably, the expression levels of key genes involved in the metabolic pathways of phenylpropanoid (PAL, C4H, and 4CL) and flavonoid (CHS, CHI, F3'H, DFR, and ANS) in the sheltered fruits were also up-regulated earlier than of those in the unsheltered fruits, conducive to an increase in anthocyanin content in the fruits.

CONCLUSIONS

According to the physiological indicators and transcriptional expression levels of the related genes, the adaptive regulation mechanism of cherry plants was systematically revealed. These findings can help understand the effect of rain-shelter covering on Chinese cherry cultivation in rainy regions.

Alginate Oligosaccharide (AOS) induced resistance to Pst DC3000 via salicylic acid-mediated signaling pathway in Arabidopsis thaliana

Alginate Oligosaccharide (AOS) is a natural biological carbohydrate extracted from seaweed. In our study, Arabidopsis thaliana was used to evaluate the AOS-induced resistance to Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). Resistance was vitally enhanced at 25 mg/L in wild type (WT), showing the decreased disease index and bacteria colonies, burst of ROS and NO, high transcription expression of resistance genes PR1 and increased content of salicylic acid (SA). In SA deficient mutant (sid2), AOS-induced disease resistance dropped obviously compared to WT. The disease index was significantly higher than WT and the expression of recA and avrPtoB are two and four times lower than WT, implying that AOS induces disease resistance injecting Pst DC3000 after three days treatment by arousing the SA pathway. Our results provide a reference for the profound research and application of AOS in agriculture.

High-yielding rice Takanari has superior photosynthetic response to a commercial rice Koshihikari under fluctuating light

Leaves within crop canopies experience variable light over the course of a day, which greatly affects photosynthesis and crop productivity. Little is known about the mechanisms of the photosynthetic response to fluctuating light and their genetic control. Here, we examined gas exchange, metabolite levels, and chlorophyll fluorescence during the photosynthetic induction response in an Oryza sativa indica cultivar with high yield (Takanari) and a japonica cultivar with lower yield (Koshihikari). Takanari had a faster induction response to sudden increases in light intensity than Koshihikari, as demonstrated by faster increases in net CO2 assimilation rate, stomatal conductance, and electron transport rate. In a simulated light regime that mimicked a typical summer day, the faster induction response in Takanari increased daily CO2 assimilation by 10%. The faster response of Takanari was explained in part by its maintenance of a larger pool of Calvin-Benson cycle metabolites. Together, the rapid responses of electron transport rate, metabolic flux, and stomatal conductance in Takanari contributed to the greater daily carbon gain under fluctuating light typical of natural environments.

Comparative Transcriptome Analysis of Gene Expression Patterns in Tomato Under Dynamic Light Conditions

Plants grown under highly variable natural light regimes differ strongly from plants grown under constant light (CL) regimes. Plant phenotype and adaptation responses are important for plant biomass and fitness. However, the underlying regulatory mechanisms are still poorly understood, particularly from a transcriptional perspective. To investigate the influence of different light regimes on tomato plants, three dynamic light (DL) regimes were designed, using a CL regime as control. Morphological, photosynthetic, and transcriptional differences after five weeks of treatment were compared. Leaf area, plant height, shoot /root weight, total chlorophyll content, photosynthetic rate, and stomatal conductance all significantly decreased in response to DL regimes. The biggest expression difference was found between the treatment with the highest light intensity at the middle of the day with a total of 1080 significantly up-/down-regulated genes. A total of 177 common differentially expressed genes were identified between DL and CL conditions. Finally, significant differences were observed in the levels of gene expression between DL and CL treatments in multiple pathways, predominantly of plant–pathogen interactions, plant hormone signal transductions, metabolites, and photosynthesis. These results expand the understanding of plant development and photosynthetic regulations under DL conditions by multiple pathways.

Fluctuating light experiments and semi-automated plant phenotyping enabled by self-built growth racks and simple upgrades to the IMAGING-PAM

BACKGROUND

Over the last years, several plant science labs have started to employ fluctuating growth light conditions to simulate natural light regimes more closely. Many plant mutants reveal quantifiable effects under fluctuating light despite being indistinguishable from wild-type plants under standard constant light. Moreover, many subtle plant phenotypes become intensified and thus can be studied in more detail. This observation has caused a paradigm shift within the photosynthesis research community and an increasing number of scientists are interested in using fluctuating light growth conditions. However, high installation costs for commercial controllable LED setups as well as costly phenotyping equipment can make it hard for small academic groups to compete in this emerging field.

RESULTS

We show a simple do-it-yourself approach to enable fluctuating light growth experiments. Our results using previously published fluctuating light sensitive mutants, stn7 and pgr5, confirm that our low-cost setup yields similar results as top-prized commercial growth regimes. Moreover, we show how we increased the throughput of our Walz IMAGING-PAM, also found in many other departments around the world. We have designed a Python and R-based open source toolkit that allows for semi-automated sample segmentation and data analysis thereby reducing the processing bottleneck of large experimental datasets. We provide detailed instructions on how to build and functionally test each setup.

CONCLUSIONS

With material costs well below USD$1000, it is possible to setup a fluctuating light rack including a constant light control shelf for comparison. This allows more scientists to perform experiments closer to natural light conditions and contribute to an emerging research field. A small addition to the IMAGING-PAM hardware not only increases sample throughput but also enables larger-scale plant phenotyping with automated data analysis.