Nondestructive and intuitive determination of circadian chlorophyll rhythms in soybean leaves using multispectral imaging

Estimation of Biochemical Pigment Content in Poplar Leaves Using Proximal Multispectral Imaging and Regression Modeling Combined with Feature Selection

Monitoring the biochemical pigment contents in individual plants is crucial for assessing their health statuses and physiological states. Fast, low-cost measurements of plants' biochemical traits have become feasible due to advances in multispectral imaging sensors in recent years. This study evaluated the field application of proximal multispectral imaging combined with feature selection and regressive analysis to estimate the biochemical pigment contents of poplar leaves. The combination of 6 spectral bands and 26 vegetation indices (VIs) derived from the multispectral bands was taken as the group of initial variables for regression modeling. Three variable selection algorithms, including the forward selection algorithm with correlation analysis (CORR), recursive feature elimination algorithm (RFE), and sequential forward selection algorithm (SFS), were explored as candidate methods for screening combinations of input variables from the 32 spectral-derived initial variables. Partial least square regression (PLSR) and nonlinear support vector machine regression (SVR) were both applied to estimate total chlorophyll content (Chla+b) and carotenoid content (Car) at the leaf scale. The results show that the nonlinear SVR prediction model based on optimal variable combinations, selected by SFS using multiple scatter correction (MSC) preprocessing data, achieved the best estimation accuracy and stable prediction performance for the leaf pigment content. The Chla+b and Car models developed using the optimal model had R2 and RMSE predictive statistics of 0.849 and 0.825 and 5.116 and 0.869, respectively. This study demonstrates the advantages of using a nonlinear SVR model combined with SFS variable selection to obtain a more reliable estimation model for leaf biochemical pigment content.

Growth-limiting drought stress induces time-of-day-dependent transcriptome and physiological responses in hybrid poplar

Drought stress negatively impacts the health of long-lived trees. Understanding the genetic mechanisms that underpin response to drought stress is requisite for selecting or enhancing climate change resilience. We aimed to determine how hybrid poplars respond to prolonged and uniform exposure to drought; how responses to moderate and more severe growth-limiting drought stresses differed; and how drought responses change throughout the day. We established hybrid poplar trees (Populus × 'Okanese') from unrooted stem cutting with abundant soil moisture for 6 weeks. We then withheld water to establish well-watered, moderate and severe growth-limiting drought conditions. These conditions were maintained for 3 weeks during which growth was monitored. We then measured photosynthetic rates and transcriptomes of leaves that had developed during the drought treatments at two times of day. The moderate and severe drought treatments elicited distinct changes in growth and development, photosynthetic rates and global transcriptome profiles. Notably, the time of day of sampling produced the strongest effect in the transcriptome data. The moderate drought treatment elicited global transcriptome changes that were intermediate to the severe and well-watered treatments in the early evening but did not elicit a strong drought response in the morning. Stable drought conditions that are sufficient to limit plant growth elicit distinct transcriptional profiles depending on the degree of water limitation and on the time of day at which they are measured. There appears to be a limited number of genes and functional gene categories that are responsive to all of the tested drought conditions in this study emphasizing the complex nature of drought regulation in long-lived trees.

Mutations that alter Arabidopsis flavonoid metabolism affect the circadian clock

Flavonoids are a well-known class of specialized metabolites that play key roles in plant development, reproduction, and survival. Flavonoids are also of considerable interest from the perspective of human health, as both phytonutrients and pharmaceuticals. RNA sequencing analysis of an Arabidopsis null allele for chalcone synthase (CHS), which catalyzes the first step in flavonoid metabolism, has uncovered evidence that these compounds influence the expression of genes associated with the plant circadian clock. Analysis of promoter-luciferase constructs further showed that the transcriptional activity of CCA1 and TOC1, two key clock genes, is altered in CHS-deficient seedlings across the day/night cycle. Similar findings for a mutant line lacking flavonoid 3'-hydroxylase (F3'H) activity, and thus able to synthesize mono- but not dihydroxylated B-ring flavonoids, suggests that the latter are at least partially responsible; this was further supported by the ability of quercetin to enhance CCA1 promoter activity in wild-type and CHS-deficient seedlings. The effects of flavonoids on circadian function were also reflected in photosynthetic activity, with chlorophyll cycling abolished in CHS- and F3'H-deficient plants. Remarkably, the same phenotype was exhibited by plants with artificially high flavonoid levels, indicating that neither the antioxidant potential nor the light-screening properties of flavonoids contribute to optimal clock function, as has recently also been demonstrated in animal systems. Collectively, the current experiments point to a previously unknown connection between flavonoids and circadian cycling in plants and open the way to better understanding of the molecular basis of flavonoid action.

Role of Circadian Rhythms in Major Plant Metabolic and Signaling Pathways

Plants require an endogenous regulatory network and mechanism to cope with diurnal environmental changes and compensate for their sessile nature. Plants use the circadian clock to anticipate diurnal changes. Circadian rhythm predicts a 24-h cycle with 16 h of light and 8 h of darkness in response to abiotic and biotic factors as well as the appropriate temperature. For a plant's fitness, proper growth, and development, these rhythms synchronize the diurnal photoperiodic changes. Input pathway, central oscillator, and output pathway are the three components that make up the endogenous clock. There are also transcriptional and translational feedback loops (TTFLs) in the clock, which are dependent on the results of gene expression. Several physiological processes, such as stress acclimatization, hormone signaling, morphogenesis, carbon metabolism, and defense response, are currently being investigated for their interactions with the circadian clock using phenotypic, genomic, and metabolic studies. This review examines the role of circadian rhythms in the regulation of plant metabolic pathways, such as photosynthesis and carbon metabolism, as well as developmental and degenerative processes, such as flowering and senescence. Furthermore, we summarized signaling pathways related to circadian rhythms, such as defense response and gene regulatory pathways.

Dynamic physiological and transcriptome changes reveal a potential relationship between the circadian clock and salt stress response in Ulmus pumila

Despite the important role the circadian clock plays in numerous critical physiological responses in plants, such as hypocotyl elongation, leaf movement, stomatal opening, flowering, and stress responses, there have been no investigations into the effect of the circadian clock on physiological and transcriptional networks under salt stress. Ulmus pumila L. has been reported to tolerate 100-150 mM NaCl treatment. We measured the diurnal variation in photosynthesis and chlorophyll fluorescence parameters and performed a time-course transcriptome analysis of 2-years-old U. pumila seedlings under salt treatment to dissect the physiological regulation and potential relationship between the circadian network and the salt stress response. Seedlings in 150 mM NaCl treatment exhibited salt-induced physiological enhancement compared to the control group. A total of 7009 differentially expressed unigenes (DEGs) were identified under salt stress, of which 16 DEGs were identified as circadian rhythm-related DEGs (crDEGs). Further analysis of dynamic expression changes revealed that DEGs involved in four crucial pathways-photosynthesis, thiamine metabolism, abscisic acid synthesis and metabolism, and the hormone-MAPK signal crosstalk pathway-are closely related to the circadian clock. Finally, we constructed a co-expression network between the circadian clock and these four crucial pathways. Our results help shed light on the molecular link between the circadian network and salt stress tolerance in U. pumila.

Daily dynamics of intermediate metabolite profiles lead to time-dependent phenylethanoid glycosides production in Scrophularia striata during the day/night cycle

Phenylethanoid glycosides (PhGs) are important medicinal compounds found in Scrophularia striata, one of the plant species native to Iran. Since almost all aspects of plant life are controlled by night/light cycle, studying its relationship to valuable plant metabolites production will help us to determine the right time for their extraction. Therefore, the aim of this investigation is to figure out whether the diel light oscillations control PhGs production and how it relates to daily changes in upstream metabolic reactions and circadian clock in S. striata. For this, daily rhythms of metabolic pathways were examined every 4 h during a day/night cycle in 3 groups of control (16 h light/8 h dark), continuous light and darkness. The results showed that acteoside and echinacoside levels in each group peaked during the night and day, respectively. Thus, the PhGs production follows a rhythmic behavior in S. striata, which is probably controlled by circadian clock. Also, the levels of photosynthetic pigments, carbohydrates, amino acids, phenolic acids, phytohormones and phenylalanine ammonia-lyase (PAL) and tyrosine ammonia-lyase (TAL) enzyme activities varied diel in a similar or different way among study groups. The observations revealed that light/dark cycle controls the carbon and energy flow from light reception to the production and consumption of starch, biosynthesis of phenylalanine, tyrosine, cinnamic acid and coumaric acid, activation of hormonal signaling pathways and enzymes involved in phenylpropanoid pathway. Overall, it can be concluded that PhGs accumulation time-dependent patterns is likely due to daily fluctuations in upstream metabolic reactions induced by light/dark cycle.

A comparative study on the circadian rhythm of the electrical signals of Broussonetia papyrifera and Morus alba

The circadian clock regulates a wide range of physiological processes in plants. Here we showed the circadian variations of the electrical signals in Broussonetia papyrifera L. and Morus alba L. in a natural state, which were analyzed using the day-night cycle method. The circadian characteristics of different plant electrical signals were compared by constructing a coupling model for the circadian rhythm of plant electrical signals. The electrical signal sensor had two electrode plates, which were fixed on the two ends of the splint, leaves could then be clamped and measured. The clamping force between the two electrode plates was uniform, which enabled continuous and nondestructive measurements. The results showed that an electric cyclic behavior was observed (circadian cycle) with the circadian variation in the plants within 24 h. Both the resistance (R) and the impedance (Z) increased firstly in the early morning and then decreased subsequently, while the capacitance (C) showed an opposite variation. Under different weather conditions, plant electrical signals showed periodic changes when the temperature and light intensity in the environment slightly changed within the physiological tolerance of plant. This indicated that the circadian clock of plant electrical signals could be maintained endogenously. The variation curves of plant electrical signals as time increased were fitted using the sine equation. The characteristic parameters of circadian rhythm of plant electrical signals were obtained. We found that although all plant electrical signals exhibited electric cyclic behavior, but the characteristics of circadian rhythms of electrical signals were different. This study provided a scientific basic for precisely monitoring plant electrical signals, and a reference for revealing circadian rhythms of plant electrical signals and their occurrence rules.

Arabidopsis CHLOROPHYLLASE 1 protects young leaves from long-term photodamage by facilitating FtsH-mediated D1 degradation in photosystem II repair

The proteolytic degradation of the photodamaged D1 core subunit during the photosystem II (PSII) repair cycle is well understood, but chlorophyll turnover during D1 degradation remains unclear. Here, we report that Arabidopsis thaliana CHLOROPHYLLASE 1 (CLH1) plays important roles in the PSII repair process. The abundance of CLH1 and CLH2 peaks in young leaves and is induced by high-light exposure. Seedlings of clh1 single and clh1-1/2-2 double mutants display increased photoinhibition after long-term high-light exposure, whereas seedlings overexpressing CLH1 have enhanced light tolerance compared with the wild type. CLH1 is localized in the developing chloroplasts of young leaves and associates with the PSII-dismantling complexes RCC1 and RC47, with a preference for the latter upon exposure to high light. Furthermore, degradation of damaged D1 protein is retarded in young clh1-1/2-2 leaves after 18-h high-light exposure but is rescued by the addition of recombinant CLH1 in vitro. Moreover, overexpression of CLH1 in a variegated mutant (var2-2) that lacks thylakoid protease FtsH2, with which CLH1 interacts, suppresses the variegation and restores D1 degradation. A var2-2 clh1-1/2-2 triple mutant shows more severe variegation and seedling death. Taken together, these results establish CLH1 as a long-sought chlorophyll dephytylation enzyme that is involved in PSII repair and functions in long-term adaptation of young leaves to high-light exposure by facilitating FtsH-mediated D1 degradation.

Circadian Rhythms in Legumes: What Do We Know and What Else Should We Explore?

The natural timing devices of organisms, commonly known as biological clocks, are composed of specific complex folding molecules that interact to regulate the circadian rhythms. Circadian rhythms, the changes or processes that follow a 24-h light–dark cycle, while endogenously programmed, are also influenced by environmental factors, especially in sessile organisms such as plants, which can impact ecosystems and crop productivity. Current knowledge of plant clocks emanates primarily from research on Arabidopsis, which identified the main components of the circadian gene regulation network. Nonetheless, there remain critical knowledge gaps related to the molecular components of circadian rhythms in important crop groups, including the nitrogen-fixing legumes. Additionally, little is known about the synergies and trade-offs between environmental factors and circadian rhythm regulation, especially how these interactions fine-tune the physiological adaptations of the current and future crops in a rapidly changing world. This review highlights what is known so far about the circadian rhythms in legumes, which include major as well as potential future pulse crops that are packed with nutrients, particularly protein. Based on existing literature, this review also identifies the knowledge gaps that should be addressed to build a sustainable food future with the reputed “poor man’s meat”.

Assessing Global Circadian Rhythm Through Single-Time-Point Transcriptomic Analysis

Plant circadian clock has emerged as a central hub integrating various endogenous signals and exogenous stimuli to coordinate diverse plant physiological processes. The intimate relationship between crop circadian clock and key agronomic traits has been increasingly appreciated. However, due to the lack of fundamental genetic resources, more complex genome structures and the high cost of large-scale time-course circadian expression profiling, our understanding of crop circadian clock is still very limited. To study plant circadian clock, conventional methods rely on time-course experiments, which can be expensive and time-consuming. Different from these conventional approaches, the molecular timetable method can estimate the global rhythm using single-time-point transcriptome datasets, which has shown great promises in accelerating studies of crop circadian clock. Here we describe the application of the molecular timetable method in soybean and provide key technical caveats as well as related R Markdown scripts.

The Modification of Circadian Clock Components in Soybean During Domestication and Improvement

Agricultural production is greatly dependent on daylength, which is determined by latitude. Living organisms align their physiology to daylength through the circadian clock, which is made up of input sensors, core and peripheral clock components, and output. The light/dark cycle is the major input signal, moderated by temperature fluctuations and metabolic changes. The core clock in plants functions mainly through a number of transcription feedback loops. It is known that the circadian clock is not essential for survival. However, alterations in the clock components can lead to substantial changes in physiology. Thus, these clock components have become the de facto targets of artificial selection for crop improvement during domestication. Soybean was domesticated around 5,000 years ago. Although the circadian clock itself is not of particular interest to soybean breeders, specific alleles of the circadian clock components that affect agronomic traits, such as plant architecture, sensitivity to light/dark cycle, flowering time, maturation time, and yield, are. Consequently, compared to their wild relatives, cultivated soybeans have been bred to be more adaptive and productive at different latitudes and habitats for acreage expansion, even though the selection processes were made without any prior knowledge of the circadian clock. Now with the advances in comparative genomics, known modifications in the circadian clock component genes in cultivated soybean have been found, supporting the hypothesis that modifications of the clock are important for crop improvement. In this review, we will summarize the known modifications in soybean circadian clock components as a result of domestication and improvement. In addition to the well-studied effects on developmental timing, we will also discuss the potential of circadian clock modifications for improving other aspects of soybean productivity.

Hyperspectral imaging combined with machine learning as a tool to obtain high-throughput plant salt-stress phenotyping

The rapid selection of salinity-tolerant crops to increase food production in salinized lands is important for sustainable agriculture. Recently, high-throughput plant phenotyping technologies have been adopted that use plant morphological and physiological measurements in a non-destructive manner to accelerate plant breeding processes. Here, a hyperspectral imaging (HSI) technique was implemented to monitor the plant phenotypes of 13 okra (Abelmoschus esculentus L.) genotypes after 2 and 7 days of salt treatment. Physiological and biochemical traits, such as fresh weight, SPAD, elemental contents and photosynthesis-related parameters, which require laborious, time-consuming measurements, were also investigated. Traditional laboratory-based methods indicated the diverse performance levels of different okra genotypes in response to salinity stress. We introduced improved plant and leaf segmentation approaches to RGB images extracted from HSI imaging based on deep learning. The state-of-the-art performance of the deep-learning approach for segmentation resulted in an intersection over union score of 0.94 for plant segmentation and a symmetric best dice score of 85.4 for leaf segmentation. Moreover, deleterious effects of salinity affected the physiological and biochemical processes of okra, which resulted in substantial changes in the spectral information. Four sample predictions were constructed based on the spectral data, with correlation coefficients of 0.835, 0.704, 0.609 and 0.588 for SPAD, sodium concentration, photosynthetic rate and transpiration rate, respectively. The results confirmed the usefulness of high-throughput phenotyping for studying plant salinity stress using a combination of HSI and deep-learning approaches.

CO2 uptake and chlorophyll a fluorescence of Suaeda fruticosa grown under diurnal rhythm and after transfer to continuous dark

Although only 2-4% of absorbed light is emitted as chlorophyll (Chl) a fluorescence, its measurement provides valuable information on photosynthesis of the plant, particularly of Photosystem II (PSII) and Photosystem I (PSI). In this paper, we have examined photosynthetic parameters of Suaeda fruticosa L. (family: Amaranthaceae), surviving under extreme xerohalophytic conditions, as influenced by diurnal rhythm or continuous dark condition. We report here CO₂ gas exchange and the kinetics of Chl a fluorescence of S. fruticosa, made every 3 hours (hrs) for 3 days, using a portable infra-red gas analyzer and a Handy PEA fluorimeter. Our measurements on CO₂ gas exchange show the maximum rate of photosynthesis to be at 08:00 hrs under diurnal condition and at 05:00 hrs under continuous dark. From the OJIP phase of Chl a fluorescence transient, we have inferred that the maximum quantum yield of PSII photochemistry must have increased during the night under diurnal rhythm, and between 11:00 and 17:00 hrs under constant dark. Overall, our study has revealed novel insights into how photosynthetic reactions are affected by the photoperiodic cycles in S. fruticosa under high salinity. This study has further revealed a unique strategy operating in this xero-halophyte where the repair mechanism for damaged PSII operates during the dark, which, we suggest, contributes to its ecological adaptation and ability to survive and reproduce under extreme saline, high light, and drought conditions. We expect these investigations to help in identifying key genes and pathways for raising crops for saline and dry areas.

A Clustering Framework for Monitoring Circadian Rhythm in Structural Dynamics in Plants From Terrestrial Laser Scanning Time Series

Terrestrial Laser Scanning (TLS) can be used to monitor plant dynamics with a frequency of several times per hour and with sub-centimeter accuracy, regardless of external lighting conditions. TLS point cloud time series measured at short intervals produce large quantities of data requiring fast processing techniques. These must be robust to the noise inherent in point clouds. This study presents a general framework for monitoring circadian rhythm in plant movements from TLS time series. Framework performance was evaluated using TLS time series collected from two Norway maples (Acer platanoides) and a control target, a lamppost. The results showed that the processing framework presented can capture a plant's circadian rhythm in crown and branches down to a spatial resolution of 1 cm. The largest movements in both Norway maples were observed before sunrise and at their crowns' outer edges. The individual cluster movements were up to 0.17 m (99th percentile) for the taller Norway maple and up to 0.11 m (99th percentile) for the smaller tree from their initial positions before sunset.

Evaluation of Informative Bands Used in Different PLS Regressions for Estimating Leaf Biochemical Contents from Hyperspectral Reflectance

Partial least squares (PLS) regression models are widely applied in spectroscopy to estimate biochemical components through hyperspectral reflected information. To build PLS regression models based on informative spectral bands, rather than strongly collinear bands contained in the full spectrum, is essential for upholding the performance of models. Yet no consensus has ever been reached on how to select informative bands, even though many techniques have been proposed for estimating plant properties using the vast array of hyperspectral reflectance. In this study, we designed a series of virtual experiments by introducing a dummy variable (Cd) with convertible specific absorption coefficients (SAC) into the well-accepted leaf reflectance PROSPECT-4 model for evaluating popularly adopted informative bands selection techniques, including stepwise-PLS, genetic algorithms PLS (GA-PLS) and PLS with uninformative variable elimination (UVE-PLS). Such virtual experiments have clearly defined responsible wavelength regions related to the dummy input variable, providing objective criteria for model evaluation. Results indicated that although all three techniques examined may estimate leaf biochemical contents efficiently, in most cases the selected bands, unfortunately, did not exactly match known absorption features, casting doubts on their general applicability. The GA-PLS approach was comparatively more efficient at accurately locating the informative bands (with physical and biochemical mechanisms) for estimating leaf biochemical properties and is, therefore, recommended for further applications. Through this study, we have provided objective evaluations of the potential of PLS regressions, which should help to understand the pros and cons of PLS regression models for estimating vegetation biochemical parameters.

Field-grown soybean transcriptome shows diurnal patterns in photosynthesis-related processes

Many plant physiological processes have diurnal patterns regulated by diurnal environmental changes and circadian rhythms, but the transcriptional underpinnings of many of these cycles have not been studied in major crop species under field conditions. Here, we monitored the transcriptome of field-grown soybean (Glycine max) during daylight hours in the middle of the growing season with RNA-seq. The analysis revealed 21% of soybean genes were differentially expressed over the course of the day. Expression of some circadian-related genes in field-grown soybean differed from previously reported expression patterns measured in controlled environments. Many genes in functional groups contributing to and/or depending on photosynthesis showed differential expression, with patterns particularly evident in the chlorophyll synthesis pathway. Gene regulatory network inference also revealed seven diurnally sensitive gene nodes involved with circadian rhythm, transcription regulation, cellular processes, and water transport. This study provides a diurnal overview of the transcriptome for an economically important field-grown crop and a basis for identifying pathways that could eventually be tailored to optimize diurnal regulation of carbon gain.

Degradation of chlorophyll and synthesis of flavonols during autumn senescence-the story told by individual leaves

Autumn senescence of deciduous trees is characterized by chlorophyll degradation and flavonoid synthesis. In the present study, chlorophyll and flavonol contents were measured every morning and evening during the whole autumn with a non-destructive method from individual leaves of Sorbus aucuparia, Acer platanoides, Betula pendula and Prunus padus. In most of the studied trees, the chlorophyll content of each individual leaf remained constant until a phase of rapid degradation commenced. The fast phase lasted only ~1 week and ended with abscission. In S. aucuparia, contrary to the other species, the chlorophyll content of leaflets slowly but steadily decreased during the whole autumn, but rapid chlorophyll degradation commenced only prior to leaflet abscission also in this species. An increase in flavonols commonly accompanied the rapid degradation of chlorophyll. The results may suggest that each individual tree leaf retains its photosynthetic activity, reflected by a high chlorophyll content, until a rapid phase of chlorophyll degradation and flavonoid synthesis begins. Therefore, in studies of autumn senescence, leaves whose chlorophyll content is decreasing and leaves with summertime chlorophyll content (i.e. the leaves that have not yet started to degrade chlorophyll) should be treated separately.

Non-destructive Determination of Shikimic Acid Concentration in Transgenic Maize Exhibiting Glyphosate Tolerance Using Chlorophyll Fluorescence and Hyperspectral Imaging

The development of transgenic glyphosate-tolerant crops has revolutionized weed control in crops in many regions of the world. The early, non-destructive identification of superior plant phenotypes is an important stage in plant breeding programs. Here, glyphosate-tolerant transgenic maize and its parental wild-type control were studied at 2, 4, 6, and 8 days after glyphosate treatment. Visible and near-infrared hyperspectral imaging and chlorophyll fluorescence imaging techniques were applied to monitor the performance of plants. In our research, transgenic maize, which was highly tolerant to glyphosate, was phenotyped using these high-throughput non-destructive methods to validate low levels of shikimic acid accumulation and high photochemical efficiency of photosystem II as reflected by maximum quantum yield and non-photochemical quenching in response to glyphosate. For hyperspectral imaging analysis, the combination of spectroscopy and chemometric methods was used to predict shikimic acid concentration. Our results indicated that a partial least-squares regression model, built on optimal wavelengths, effectively predicted shikimic acid concentrations, with a coefficient of determination value of 0.79 for the calibration set, and 0.82 for the prediction set. Moreover, shikimic acid concentration estimates from hyperspectral images were visualized on the prediction maps by spectral features, which could help in developing a simple multispectral imaging instrument for non-destructive phenotyping. Specific physiological effects of glyphosate affected the photochemical processes of maize, which induced substantial changes in chlorophyll fluorescence characteristics. A new data-driven method, combining mean fluorescence parameters and featuring a screening approach, provided a satisfactory relationship between fluorescence parameters and shikimic acid content. The glyphosate-tolerant transgenic plants can be identified with the developed discrimination model established on important wavelengths or sensitive fluorescence parameters 6 days after glyphosate treatment. The overall results indicated that both hyperspectral imaging and chlorophyll fluorescence imaging techniques could provide useful tools for stress phenotyping in maize breeding programs and could enable the detection and evaluation of superior genotypes, such as glyphosate tolerance, with a non-destructive high-throughput technique.

Integration of multi-omics techniques and physiological phenotyping within a holistic phenomics approach to study senescence in model and crop plants

The study of senescence in plants is complicated by diverse levels of temporal and spatial dynamics as well as the impact of external biotic and abiotic factors and crop plant management. Whereas the molecular mechanisms involved in developmentally regulated leaf senescence are very well understood, in particular in the annual model plant species Arabidopsis, senescence of other organs such as the flower, fruit, and root is much less studied as well as senescence in perennials such as trees. This review addresses the need for the integration of multi-omics techniques and physiological phenotyping into holistic phenomics approaches to dissect the complex phenomenon of senescence. That became feasible through major advances in the establishment of various, complementary 'omics' technologies. Such an interdisciplinary approach will also need to consider knowledge from the animal field, in particular in relation to novel regulators such as small, non-coding RNAs, epigenetic control and telomere length. Such a characterization of phenotypes via the acquisition of high-dimensional datasets within a systems biology approach will allow us to systematically characterize the various programmes governing senescence beyond leaf senescence in Arabidopsis and to elucidate the underlying molecular processes. Such a multi-omics approach is expected to also spur the application of results from model plants to agriculture and their verification for sustainable and environmentally friendly improvement of crop plant stress resilience and productivity and contribute to improvements based on postharvest physiology for the food industry and the benefit of its customers.

Circadian clock component, LHY, tells a plant when to respond photosynthetically to light in nature

The circadian clock is known to increase plant growth and fitness, and is thought to prepare plants for photosynthesis at dawn and dusk; whether this happens in nature was unknown. We transformed the native tobacco, Nicotiana attenuata to silence two core clock components, NaLHY (irLHY) and NaTOC1 (irTOC1). We characterized growth and light- and dark-adapted photosynthetic rates (Ac ) throughout a 24 h day in empty vector-transformed (EV), irLHY, and irTOC1 plants in the field, and in NaPhyA- and NaPhyB1-silenced plants in the glasshouse. The growth rates of irLHY plants were lower than those of EV plants in the field. While irLHY plants reduced Ac earlier at dusk, no differences between irLHY and EV plants were observed at dawn in the field. irLHY, but not EV plants, responded to light in the night by rapidly increasing Ac . Under controlled conditions, EV plants rapidly increased Ac in the day compared to dark-adapted plants at night; irLHY plants lost these time-dependent responses. The role of NaLHY in gating photosynthesis is independent of the light-dependent reactions and red light perceived by NaPhyA, but not NaPhyB1. In summary, the circadian clock allows plants not to respond photosynthetically to light at night by anticipating and gating red light-mediated in native tobacco.

Endogenous circadian rhythms in pigment composition induce changes in photochemical efficiency in plant canopies

There is increasing evidence that the circadian clock is a significant driver of photosynthesis that becomes apparent when environmental cues are experimentally held constant. We studied whether the composition of photosynthetic pigments is under circadian regulation, and whether pigment oscillations lead to rhythmic changes in photochemical efficiency. To address these questions, we maintained canopies of bean and cotton, after an entrainment phase, under constant (light or darkness) conditions for 30-48 h. Photosynthesis and quantum yield peaked at subjective noon, and non-photochemical quenching peaked at night. These oscillations were not associated with parallel changes in carbohydrate content or xanthophyll cycle activity. We observed robust oscillations of Chl a/b during constant light in both species, and also under constant darkness in bean, peaking when it would have been night during the entrainment (subjective nights). These oscillations could be attributed to the synthesis and/or degradation of trimeric light-harvesting complex II (reflected by the rhythmic changes in Chl a/b), with the antenna size minimal at night and maximal around subjective noon. Considering together the oscillations of pigments and photochemistry, the observed pattern of changes is counterintuitive if we assume that the plant strategy is to avoid photodamage, but consistent with a strategy where non-stressed plants maximize photosynthesis.

Correlations between Circadian Rhythms and Growth in Challenging Environments

In plants, the circadian system controls a plethora of processes, many with agronomic importance, such as photosynthesis, photoprotection, stomatal opening, and photoperiodic development, as well as molecular processes, such as gene expression. It has been suggested that modifying circadian rhythms may be a means to manipulate crops to develop improved plants for agriculture. However, there is very little information on how the clock influences the performance of crop plants. We used a noninvasive, high-throughput technique, based on prompt chlorophyll fluorescence, to measure circadian rhythms and demonstrated that the technique works in a range of plants. Using fluorescence, we analyzed circadian rhythms in populations of wild barley (Hordeum vulgare ssp. spontaneum) from widely different ecogeographical locations in the Southern Levant part of the Fertile Crescent, an area with a high proportion of the total genetic variation of wild barley. Our results show that there is variability for circadian traits in the wild barley lines. We observed that circadian period lengths were correlated with temperature and aspect at the sites of origin of the plants, while the amplitudes of the rhythms were correlated with soil composition. Thus, different environmental parameters may exert selection on circadian rhythms.