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Several complex and interconnected megatrends such as climate change, environmental degradation, and stagnating yields threaten crop production and world food security for a growing global population (Maggio et al., 2018). This poses the challenge to develop sustainable and resilient agroecosystems with increased productivity as a key objective for the coming decades. In the past, agriculture has expanded production by breeding as well as by increasing inputs and farming areas. However, the projected scenarios call for considerable reductions in agricultural inputs such as water, fertilizers, and agrochemicals to reduce their environmental burden, whilst also addressing the decreasing land availability in many European countries. Integrated solutions and new technologies to improve plant production, based on knowledge-driven innovations in the farming sector and in agricultural and seed industries, have become the key objectives on the way towards sustainable agriculture (da Silva, 2015; Watt et al., 2020; Morisse et al., 2022).

This article is based upon work from COST Action CA17134 Optical synergies for spatiotemporal SENsing of Scalable ECOphysiological traits (SENSECO), supported by COST. It was supported by European Plant Phenotyping Network (EPPN2020: Grant Agreement 731013), from EMPHASIS-PREP (Grant Agreement: 739514), from EOSC-Life (Grant Agreement: 824087). KB was funded within the EnMAP scientific preparation program (DLR Space and BMWi, Grant Number 50EE1923).

Quantitative analysis of structure and function of plants has become the major bottleneck in basic plant research and applied use of plants in breeding or agricultural management. This is particularly important for sustainable intensification of crop production to ensure the amount and quality of plant biomass for human nutrition and industry in times of climate change. In recent years, significant interdisciplinary approaches have been started to establish plant phenotyping infrastructure with non-invasive methods that allow to quickly and non-invasively assessing the condition and properties of plants in the laboratory, greenhouse or field, make these data accessible through data and computational services and allow data reuse for meta-analysis or modelling.In this presentation, we will outline the recent developments to integrate plant phenotyping across scales from lab to field including common data management approaches. The ESFRI research infrastructure EMPHASIS is developing a pan European infrastructure based of the portfolio of existing national plant phenotyping centers. The goal is to: i) provide a instrumented facilities for user access for quantitative trait assessment, ii) link data acquisition with data management and modelling, iii) develop, evaluate and disseminate knowledge and novel technologies. We will showcase phenotyping of quantitative traits under controlled and specifically field conditions providing novel inside on plant environment interaction for example in dedicated free air CO2 enrichment facilities and illustrate the development of pan-European information system making these data reusable. Finally, we will introduce the latest activities of IPPN e.V. is a networking platform linking the plant phenotyping centers and enabling close interaction across the globe.

This deliverable addresses EOSC-Life WP1's objectives related to publication of data and data resources in cloud repositories by making available resources in EOSC-Life's registries; the implementation of FAIR services and standards, by development of FAIR registries in collaboration with WP6; and evolution of repository infrastructure by making available registry entries deriving from WP3 demonstrators. Use cases for EOSC-Life registries have been defined for general and clinical research data use and the 'EOSC-Life' collection in FAIRsharing has been populated and released comprising more than 100 data resources and standards. A clinical MetaData Repository has also been developed to address challenges of clinical data sharing in Europe. We have engaged with EOSC, sister projects such as FAIRsFAIR and ENVRI to consider the features of registries, cross registry interoperability and use cases which link EOSC projects. We will continue to update the registries as the project progresses and as new dataset and resources are made available and will engage with pan-EOSC registry planning based on our work to date.

International audience

No matter how fascinating the discoveries in the field of molecular biology are, in the end it is the phenotype that matters. In this paper we pay attention to various aspects of plant phenotyping. The challenges to unravel the relationship between genotype and phenotype are discussed, as well as the case where ‘plants do not have a phenotype’. More emphasis has to be placed on automation to match the increased output in the molecular sciences with analysis of relevant traits under laboratory, greenhouse and field conditions. Currently, non-destructive measurements with cameras are becoming widely used to assess plant structural properties, but a wider range of non-invasive approaches and evaluation tools has to be developed to combine physiologically meaningful data with structural information of plants. Another field requiring major progress is the handling and processing of data. A better e-infrastructure will enable easier establishment of links between phenotypic traits and genetic data. In the final part of this paper we briefly introduce the range of contributions that form the core of a special issue of this journal on plant phenotyping.

One century ago (1920), Otto Warburg (1883–1970) discovered that in liquid cultures of unicellular green algae (Chlorella sp.) molecular oxygen (O(2)) exerts an inhibitory effect on photosynthesis. Decades later, O(2) dependent suppression of photosynthetic carbon dioxide (CO(2)) assimilation (the “green” Warbur geffect) was confirmed on the leaves of seed plants. Here, we summarize the history of this discovery and elucidate the consequences of the photorespiratory pathway in land plants with reference to unpublished CO(2) exchange data measured on the leaves of sunflower (Helianthus annuus) plants. In addition, we discuss the inefficiency of the key enzyme Rubisco and analyze data concerning the productivity of C3 vs. C4 crop species (sunflower vs. maize, Zea mays). Warburg’s discovery inaugurated a research agenda in the biochemistry of photosynthetic CO(2) assimilation that continues to the present. In addition, we briefly discuss Warburg’s model of metabolic processes in cancer, net primary production (global photosynthesis) with respect to climate change, trees and other land plants as CO(2) removers, and potential climate mitigators in the Anthropocene.

In this study two crop species, winter wheat (Triticum aestivum) and sugar beet (Beta vulgaris), were monitored over the course of five days during the entire season. We investigated the link of the main physiological leaf-level mechanisms, stomatal conductance and efficiency of photosynthetic energy conversion on canopy transpiration and photosynthetic CO2 uptake. The physiological status of 900 leaves of different plants in a natural canopy was characterized on the leaf level using chlorophyll fluorescence. Gas exchange measurements were performed at leaves of 12 individual plants of each species. Eddy covariance flux measurements provided information on CO2, water and energy fluxes on the field scale. The diurnal pattern of stomatal resistance on the leaf level was especially for sugar beet similar to the canopy resistance, which indicates that stomatal resistance may have a large impact on the bulk canopy resistance. The diurnal changes in canopy resistance appeared to have less effect on the evapotranspiration, which was mainly dependent on the amount of incoming radiation. The similar diurnal pattern of water use efficiency on the leaf level and on the canopy level during the day, underline the influence of physiological mechanisms of leaves on the canopy. The greatest difference between water use efficiency on leaf and canopy occurred in the morning, mainly due to an increase of stomatal resistance. Limitation of CO2 uptake occurred in the afternoon when water vapor pressure deficit increased. Maxima of net ecosystem productivity corresponded to the highest values of photosynthetic capacity of single leaves, which occurred before solar noon. Within the course of a few hours, photosynthetic efficiency and stomatal resistance of leaves varied and these variations were the reason for diurnal variations in the carbon fluxes of the whole field. During the seasonal development, the leaf area index was the main factor driving carbon and water exchange, when both crops were still growing. During senescence of winter wheat these structural parameters did not account for changes in canopy fluxes and remaining high green leaf material of sugar beet did not present the reduction in canopy fluxes due to beginning dormancy. We thus hypothesize that the functional status of plants is also important to correctly predict carbon and water fluxes throughout the season. We propose to additionally include the physiological status of plants in carbon flux models in order to improve the quality of the simulation of diurnal patterns of carbon fluxes.

Field phenotyping conceptually can be divided in five pillars 1) traits of interest 2) sensors to measure these traits 3) positioning systems to allow high-throughput measurements by the sensors 4) experimental sites and 5) environmental monitoring. In this paper we will focus on photosynthesis as trait of interest, measured by remote active fluorescence in ‘BreedFACE’, an infrastructure for field phenotyping under elevated CO2 (eCO 2 ). The sensor used is the Light Induced Fluorescence Transient (LIFT) device mounted on a manual operated field4cycle positioning system. In direct response to eCO2 at 600ppm for winter wheat, NDVI and photosynthetic efficiency (Fq‘/F m ’) did not change whereas the QA reoxidation efficiency (F r2 /F m ) decreased at eCO2. This study further demonstrates the completion of BreedFAce with an example of proximal sensing of photosynthetic traits by the LIFT.

A new spatially scanning TDLAS in situ hygrometer based on a 2.7-µm DFB diode laser was constructed and used to analyse the water vapour concentration boundary layer structure at the surface of a single plant leaf. Using an absorption length of only 5.4 cm, the TDLAS hygrometer permits a H2O vapour concentration resolution of 31 ppmv. This corresponds to a normalized precision of 1.7 ppm m. In order to preserve and control the H2O boundary layer on an individual leaf and to study the boundary layer dependence on the wind speed to which the leaf might be exposed in nature, we also constructed a new, application specific, small-scale, wind tunnel for individual plant leaves. The rectangular, closed-loop tunnel has overall dimensions of 1.2 × 0.6 m and a measurement chamber dimension of 40 × 54 mm (H × W). It allows to generate a laminar flow with a precisely controlled wind speed at the plant leaf surface. Combining honeycombs and a miniaturized compression orifice, we could generate and control stable wind speeds from 0.1 to 0.9 m/s, and a highly laminar and homogeneous flow with an excellent relative spatial homogeneity of 0.969 ± 0.03. Combining the spectrometer and the wind tunnel, we analysed (for the first time) non-invasively the wind speed-dependent vertical structure of the H2O vapour distribution within the boundary layer of a single plant leaf. Using our time-lag-free data acquisition procedure for phase locked signal averaging, we achieved a temporal resolution of 0.2 s for an individual spatial point, while a complete vertical spatial scan at a spatial resolution of 0.18 mm took 77 s. The boundary layer thickness was found to decrease from 6.7 to 3.6 mm at increasing wind speeds of 0.1–0.9 m/s. According to our knowledge, this is the first experimental quantification of wind speed-dependent H2O vapour boundary layer concentration profiles of single plant leaves.

'Summary' I. 'Introduction' 839 II. 'Phenotypic differences between lab- and field-grown plants' 839 III. 'The shoot environment' 841 IV. 'The root environment' 845 V. 'Effects of plant density' 847 VI. 'Consistency among species or genotypes in ranking between lab and field' 848 VII. 'Translation of lab results to the field' 849 VIII. 'Conclusions' 851 'Acknowledgements' 851 'Author contributions' 852 References 852 Appendix A1 854 Summary Plant biologists often grow plants in growth chambers or glasshouses with the ultimate aim to understand or improve plant performance in the field. What is often overlooked is how results from controlled conditions translate back to field situations. A meta-analysis showed that lab-grown plants had faster growth rates, higher nitrogen concentrations and different morphology. They remained smaller, however, because the lab plants had grown for a much shorter time. We compared glasshouse and growth chamber conditions with those in the field and found that the ratio between the daily amount of light and daily temperature (photothermal ratio) was consistently lower under controlled conditions. This may strongly affect a plant's source : sink ratio and hence its overall morphology and physiology. Plants in the field also grow at higher plant densities. A second meta-analysis showed that a doubling in density leads on average to 34% smaller plants with strong negative effects on tiller or side-shoot formation but little effect on plant height. We found the r2 between lab and field phenotypic data to be rather modest (0.26). Based on these insights, we discuss various alternatives to facilitate the translation from lab results to the field, including several options to apply growth regimes closer to field conditions.

Five decades ago, a novel mode of CO2 assimilation that was later described as C4-photosynthesis was discovered on mature leaves of maize (Zea mays L.) plants. Here we show that 3- to 5-day-old developing maize leaves recapitulate the evolutionary advance from the ancient, inefficient C3 mode of photosynthesis to the C4 pathway, a mechanism for overcoming the wasteful process of photorespiration. Chlorophyll fluorescence measurements documented that photorespiration was high in 3-day-old juvenile primary leaves with non-specialized C3-like leaf anatomy and low in 5-day-old organs with the typical "Kranz-anatomy" of C4 leaves. Photosynthetic gas (CO2)-exchange measurements on 5-day-old leaves revealed the characteristic features of C4 photosynthesis, with a CO2 compensation point close to zero and little inhibition of photosynthesis by the normal oxygen concentration in the air. This indicates a very low photorespiratory activity in contrast to control experiments conducted with mature C3 sunflower (Helianthus annuus L.) leaves, which display a high rate of photorespiration.

The terrestrial hydrological cycle is strongly influenced by transpiration—water loss through the stomatal pores of leaves. In this report we present studies showing that the energy content of radiation absorbed by the leaf influences stomatal control of transpiration. This observation is at odds with current concepts of how stomata sense and control transpiration, and we suggest an alternative model. Specifically, we argue that the steady-state water potential of the epidermis in the intact leaf is controlled by the difference between the radiation-controlled rate of water vapor production in the leaf interior and the rate of transpiration. Any difference between these two potentially large fluxes is made up by evaporation from (or condensation on) the epidermis, causing its water potential to pivot around this balance point. Previous work established that stomata in isolated epidermal strips respond by opening with increasing (and closing with decreasing) water potential. Thus, stomatal conductance and transpiration rate should increase when there is condensation on (and decrease when there is evaporation from) the epidermis, thus tending to maintain homeostasis of epidermal water potential. We use a model to show that such a mechanism would have control properties similar to those observed with leaves. This hypothesis provides a plausible explanation for the regulation of leaf and canopy transpiration by the radiation load and provides a unique framework for studies of the regulation of stomatal conductance by CO 2 and other factors.

The light use efficiency (LUE) of photosynthesis dynamically adapts to environmental factors, and this leads to complex spatio-temporal variations of photosynthesis on various scales from the leaf to the canopy level. These spatio-temporal pattern formations not only help to understand the regulatory properties of photosynthesis, but may also have a constructive role in maintaining stability in metabolic pathways and during development. Optical remote sensing techniques have the potential to detect physiological and biochemical changes in plant ecosystems, and non-invasive detection of changes in photosynthetic energy conversion may be of great potential for managing agricultural production in a future bio-based economy. Here we review the results from selected remote sensing projects for their potential to quantify LUE from the level of single leaves to the canopy scale. In a case study with soybean grown under elevated CO2 conditions at the SoyFACE facility, we tested the photochemical reflectance index (PRI) for its capacity to quantify higher photosynthetic efficiency. In this study the PRI failed to detect differences in photosynthetic light conversion, most likely because of the variable canopy structure of the soybean canopy. We thus conclude that at the current state of the art the PRI cannot serve as an easy remote sensing approach to detect changes in photosynthetic energy conversion in agriculture. As an alternative we present approaches that aim to quantify the fluorescence signal of chlorophyll and thus estimate photosynthetic efficiency. In a second case study, using avocado as a model species, an active laser induced fluorescence transient (LIFT) method was applied to deliver maps of different photosynthetic efficiency within the canopy. Cold-induced down-regulation of photosynthesis in the upper canopy was detected, so active fluorescence may prove its potential for non-invasive monitoring of crops. With a view to the future, we present a method for large scale managing of agricultural practices within the framework of the FLuorescence EXplorer (FLEX) mission, which proposed launching a satellite for the global monitoring of steady-state chlorophyll fluorescence in terrestrial vegetation. This mission was selected for inclusion in pre-phase A by the European Space Agency.

Background and Aims Leaf gas exchange is influenced by stomatal size, density, distribution between the leaf adaxial and abaxial sides, as well as by pore dimensions. This study aims to quantify which of these traits mainly underlie genetic differences in operating stomatal conductance (gs) and addresses possible links between anatomical traits and regulation of pore width. Methods Stomatal responsiveness to desiccation, gs-related anatomical traits of each leaf side and estimated gs (based on these traits) were determined for 54 introgression lines (ILs) generated by introgressing segments of Solanum pennelli into the S. lycopersicum ‘M82’. A quantitative trait locus (QTL) analysis for stomatal traits was also performed. Key Results A wide genetic variation in stomatal responsiveness to desiccation was observed, a large part of which was explained by stomatal length. Operating gs ranged over a factor of five between ILs. The pore area per stomatal area varied 8-fold among ILs (2–16 %), and was the main determinant of differences in operating gs between ILs. Operating gs was primarily positioned on the abaxial surface (60–83 %), due to higher abaxial stomatal density and, secondarily, to larger abaxial pore area. An analysis revealed 64 QTLs for stomatal traits in the ILs, most of which were in the direction of S. pennellii. Conclusions The data indicate that operating and maximum gs of non-stressed leaves maintained under stable conditions deviate considerably (by 45–91 %), because stomatal size inadequately reflects operating pore area (R2 = 0·46). Furthermore, it was found that variation between ILs in both stomatal sensitivity to desiccation and operating gs is associated with features of individual stoma. In contrast, genotypic variation in gs partitioning depends on the distribution of stomata between the leaf adaxial and abaxial epidermis.

The process of domestication has led to dramatic morphological and physiological changes in crop species due to adaptation to cultivation and to the needs of farmers. To investigate the phenotypic architecture of shoot- and root-related traits and quantify the impact of primary and secondary domestication, we examined a collection of 36 wheat genotypes under optimal and nitrogen-starvation conditions. These represented three taxa that correspond to key steps in the recent evolution of tetraploid wheat (i.e. wild emmer, emmer, and durum wheat). Overall, nitrogen starvation reduced the shoot growth of all genotypes, while it induced the opposite effect on root traits, quantified using the automated phenotyping platform GROWSCREEN-Rhizo. We observed an overall increase in all of the shoot and root growth traits from wild emmer to durum wheat, while emmer was generally very similar to wild emmer but intermediate between these two subspecies. While the differences in phenotypic diversity due to the effects of primary domestication were not significant, the secondary domestication transition from emmer to durum wheat was marked by a large and significant decrease in the coefficient of additive genetic variation. In particular, this reduction was very strong under the optimal condition and less intense under nitrogen starvation. Moreover, although under the optimal condition both root and shoot traits showed significantly reduced diversity due to secondary domestication, under nitrogen starvation the reduced diversity was significant only for shoot traits. Overall, a considerable amount of phenotypic variation was observed in wild emmer and emmer, which could be exploited for the development of pre-breeding strategies.

Gas exchange is generally regarded to occur between the leaf interior and ambient air, i.e. in vertical (anticlinal) directions of leaf blades. However, inside homobaric leaves, gas movement occurs also in lateral directions. The aim of the present study was to ascertain whether lateral CO 2 diffusion affects leaf photosynthesis when illuminated leaves are partially shaded. • Measurements using gas exchange and chlorophyll fluorescence imaging techniques were performed on homobaric leaves of Vicia faba and Nicotiana tabacum or on heterobaric leaves of Glycine max and Phaseolus vulgaris . • For homobaric leaves, gas exchange inside a clamp-on leaf chamber was affected by shading the leaf outside the chamber. The quantum yield of photosystem II ( Φ PSII ) was highest directly adjacent to a light/shade border (LSB). Φ PSII decreased in the illuminated leaf parts with distance from the LSB, while the opposite was observed for nonphotochemical quenching. These effects became most pronounced at low stomatal conductance. They were not observed in heterobaric leaves. • The results suggest that plants with homobaric leaves can benefit from lateral CO 2 flux, in particular when stomata are closed (e.g. under drought stress). This may enhance photosynthetic, instead of nonphotochemical, processes near LSBs in such leaves and reduce the photoinhibitory effects of excess light.

The photosynthesis of various species or even a single plant varies dramatically in time and space, creating great spatial heterogeneity within a plant canopy. Continuous and spatially explicit monitoring is, therefore, required to assess the dynamic response of plant photosynthesis to the changing environment. This is a very challenging task when using the existing portable fi eld i nstrumentation. T his p aper r eports o n t he a pplication of a t echnique, l aser-induced fl uorescence t ransient ( LIFT), developed fo r gr ound re mote me asurement of ph otosynthetic ef ficiency at a di stance of up to 50 m. Th e LI FT te chnique wa s used to monitor the seasonal dynamics of selected leaf groups within inaccessible canopies of deciduous and evergreen tree species. Electron tr ansport ra tes co mputed fr om LI FT me asurements va ried ov er th e gr owth pe riod be tween th e di fferent species studied. Th e LI FT ca nopy da ta an d lig ht-use ef ficiency me asured un der fie ld co nditions co rrelated re asonably we ll with the single-leaf pu lse am plitude-modulated me asurements of br oadleaf sp ecies, bu t di ffered si gnificantly in th e ca se of conifer tree sp ecies. Th e LI FT me thod ha s pr oven to be ap plicable fo r a re mote se nsing as sessment of ph otosynthetic parameters on a di urnal an d se asonal sc ale; fu rther in vestigation is , ho wever, ne eded to ev aluate th e in fluence of co mplex heterogeneous canopy structures on LIFT-measured chlorophyll fluorescence parameters.

International audience; In determining vase life (VL), it is often not considered that the measured VL in a particular experiment may greatly depend on both the preharvest and evaluation environmental conditions. This makes the comparison between studies difficult and may lead to erroneous interpretation of results. In this review, we critically discuss the effect of the growth environment on the VL of cut roses. This effect is mainly related to changes in stomatal responsiveness, regulating water loss, whereas cut flower carbohydrate status appears less critical. When comparing cultivars, postharvest water loss and VL often show no correlation, indicating that components such as variation in the tissue resistance to cavitate and/or collapse at low water potential play an important role in the incidence of water stress symptoms. The effect of the growth environment on these components remains unknown. Botrytis cinerea sporulation and infection, as well as cut rose susceptibility to the pathogen are also affected by the growth environment, with the latter being largely unexplored. A huge variability in the choices made with respect to the experimental setup (harvest/conditioning methods, test room conditions and VL terminating symptoms) is reported. We highlight that these decisions, though frequently overlooked, influence the outcome of the study. Specifications for each of these factors are proposed as necessary to achieve a common VL protocol. Documentation of both preharvest conditions and a number of postharvest factors, including the test room conditions, is recommended not only for assisting comparisons between studies, but also to identify factors with major effects on VL. (c) 2012 Elsevier B.V. All rights reserved.

The interaction of plants with their environment is very dynamic. Studying the underlying processes is important for understanding and modeling plant response to changing environmental conditions. Photosynthesis varies largely between different plants and at different locations within a canopy of a single plant. Thus, continuous and spatially distributed monitoring is necessary to assess the dynamic response of photosynthesis to the environment. Limited scale of observation with portable instrumentation makes it difficult to examine large numbers of plants under different environmental conditions. We report here on the application of a recently developed technique, laser-induced fluorescence transient (LIFT), for continuous remote measurement of photosynthetic efficiency of selected leaves at a distance of up to 50 m. The ability to make continuous, automatic, and remote measurements of photosynthetic efficiency of leaves with the LIFT provides a new approach for studying the interaction of plants with the environment and may become an important tool in phenotyping photosynthetic properties in field applications.

The interaction of plants with their environment is very dynamic. Studying the underlying processes is important for understanding and modeling plant response to changing environmental conditions. Photosynthesis varies largely between different plants and at different locations within a canopy of a single plant. Thus, continuous and spatially distributed monitoring is necessary to assess the dynamic response of photosynthesis to the environment. Limited scale of observation with portable instrumentation makes it difficult to examine large numbers of plants under different environmental conditions. We report here on the application of a recently developed technique, laser-induced fluorescence transient (LIFT), for continuous remote measurement of photosynthetic efficiency of selected leaves at a distance of up to 50 m. The ability to make continuous, automatic, and remote measurements of photosynthetic efficiency of leaves with the LIFT provides a new approach for studying the interaction of plants with the environment and may become an important tool in phenotyping photosynthetic properties in field applications.

We systematically analyzed a developmental gradient of the third maize (Zea mays) leaf from the point of emergence into the light to the tip in 10 continuous leaf slices to study organ development and physiological and biochemical functions. Transcriptome analysis, oxygen sensitivity of photosynthesis, and photosynthetic rate measurements showed that the maize leaf undergoes a sink-to-source transition without an intermediate phase of C3 photosynthesis or operation of a photorespiratory carbon pump. Metabolome and transcriptome analysis, chlorophyll and protein measurements, as well as dry weight determination, showed continuous gradients for all analyzed items. The absence of binary on–off switches and regulons pointed to a morphogradient along the leaf as the determining factor of developmental stage. Analysis of transcription factors for differential expression along the leaf gradient defined a list of putative regulators orchestrating the sink-to-source transition and establishment of C4 photosynthesis. Finally, transcriptome and metabolome analysis, as well as enzyme activity measurements, and absolute quantification of selected metabolites revised the current model of maize C4 photosynthesis. All data sets are included within the publication to serve as a resource for maize leaf systems biology.

Plant phenotyping is an emerging discipline in plant biology. Quantitative measurements of functional and structural traits help to better understand gene–environment interactions and support breeding for improved resource use efficiency of important crops such as bean (Phaseolus vulgaris L.). Here we provide an overview of state-of-the-art phenotyping approaches addressing three aspects of resource use efficiency in plants: belowground roots, aboveground shoots and transport/allocation processes. We demonstrate the capacity of high-precision methods to measure plant function or structural traits non-invasively, stating examples wherever possible. Ideally, high-precision methods are complemented by fast and high-throughput technologies. High-throughput phenotyping can be applied in the laboratory using automated data acquisition, as well as in the field, where imaging spectroscopy opens a new path to understand plant function non-invasively. For example, we demonstrate how magnetic resonance imaging (MRI) can resolve root structure and separate root systems under resource competition, how automated fluorescence imaging (PAM fluorometry) in combination with automated shape detection allows for high-throughput screening of photosynthetic traits and how imaging spectrometers can be used to quantify pigment concentration, sun-induced fluorescence and potentially photosynthetic quantum yield. We propose that these phenotyping techniques, combined with mechanistic knowledge on plant structure–function relationships, will open new research directions in whole-plant ecophysiology and may assist breeding for varieties with enhanced resource use efficiency varieties.

The light use efficiency of photosynthesis dynamically adapts to environmental factors and is one major factor determining crop yield. Optical remote sensing techniques have the potential to detect physiological and biochemical changes in plant ecosystems, and non-invasive detection of changes in photosynthetic energy conversion may be of great potential for managing agricultural production in a future bio-based economy. Here we give an overview on the principles of optical remote sensing in crop systems with a special emphasis on investigating hyperspectral reflectance data and the sun-induced fluorescence signal. Especially sun-induced fluorescence as a parameter, which becomes important in remote sensing research may have great potential quantifying the physiological status of the photosynthetic apparatus. Both remote sensing principles were applied during the CEFLES2 campaign in Southern France, where the structural and functional status of several crops was measured on the ground and using state-of-the-art optical remote sensing techniques. Sun-induced fluorescence measurements over a variety of crops showed that additional information can be retrieved also over dense canopies, where classical remote sensing signals often saturate. With a view to the future, we discuss how hyperspectral reflectance and sun-induced fluorescence can quantitatively be related to photosynthetic efficiency and help to measure and manage productivity of natural and agricultural ecosystems.

Leaves within a canopy are exposed to a spatially and temporally fluctuating light environment which may cause lateral gradients in leaf internal CO(2) concentration and diffusion between shaded and illuminated areas. In previous studies it was hypothesized that lateral CO(2) diffusion may support leaf photosynthesis, but the magnitude of this effect is still not well understood. In the present study homobaric leaves of Vicia faba or heterobaric leaves of Glycine max were illuminated with lightflecks of different sizes, mimicking sunflecks. Photosynthetic properties of the lightfleck areas were assessed with combined gas exchange measurements and chlorophyll fluorescence imaging. Lateral diffusion in homobaric leaves with an interconnected intercellular air space stimulated photosynthesis and the effect was largest in small lightfleck areas, in particular when plants were under drought stress. Such effects were not observed in the heterobaric leaves with strongly compartmented intercellular gas spaces. It is concluded that lateral diffusion may significantly contribute to photosynthesis of lightfleck areas of homobaric leaves depending on lightfleck size, lateral diffusivity, and stomatal conductance. Since homobaric leaf structures have been reported for many plant species, it is hypothesized that leaf homobary may have an impact on overall plant performance under conditions with a highly heterogeneous light environment.

This study examines the extent to which lateral gas diffusion can influence intercellular CO(2) concentrations (c(i)) and thus photosynthesis in leaf areas with closed stomata. Leaves were partly greased to close stomata artificially, and effects of laterally diffusing CO(2) into the greased areas were studied by gas-exchange measurement and chlorophyll fluorescence imaging. Effective quantum yields (Delta F/F(m)') across the greased areas were analysed with an image-processing tool and transposed into c(i) profiles, and lateral CO(2) diffusion coefficients (D(C'lat)), directly proportional to lateral conductivities (), were estimated using a one-dimensional (1D) diffusion model. Effective CO(2) diffusion distances in Vicia faba (homobaric), Commelina vulgaris (homobaric) and Phaseolus vulgaris (heterobaric) leaves clearly differed, and were dependent on D(C'lat), light intensity, [CO(2)], and [O(2)]: largest distances were approx. 7.0 mm for homobaric leaves (with high D(C'lat)) and approx. 1.9 mm for heterobaric leaves (low D(C'lat)). Modeled lateral CO(2) fluxes indicate large support of photosynthesis over submillimeter distances for leaves with low D(C'lat), whereas in leaves with large D(C'lat), photosynthesis can be stimulated over distances of several millimeters. For the plant species investigated, the surplus CO(2) assimilation rates of the greased leaf areas (A(gr)) differed clearly, depending on lateral conductivities of the respective leaves.

The Interaction Of Phototrophic Organisms With Their Environment Is A Dynamic And Variable System. Studying The Underlying Processes Is Important For Understanding And Modeling The Response To Changing Environmental Conditions And Requires Continuous And Spatially Distributed Monitoring. Limited Access To Many Canopies And Scale Of Observation With Portable Instrumentation Make It Difficult To Examine Dynamics Of Canopy Photosynthesis. We Report Here On The Application Of A Recently Developed Technique, Laser Induced Fluorescence Transient (Lift), For Continuous Remote Measurement Of Photosynthetic Efficiency Of Selected Leaves Within An Oak Tree Canopy, Grass Community Below This Tree And, Thalli Of Lichen On Branches Of The Tree Over 50 Days In Spring. While The Oak Tree Showed Very Little Variation Of Quantum Yield Throughout The Measuring Period, A Reduction Of Photosynthetic Efficiency Of The Grass Community Was Observed And, The Photosynthetic Efficiency Of Lichens Was Strongly Correlated With Relative Humidity.

Air pressure in leaf chambers is thought to affect gas exchange measurements through changes in partial pressure of the air components. However, other effects may come into play when homobaric leaves are measured in which internal lateral gas flow may occur. When there was no pressure difference between the leaf chamber and ambient air (DeltaP=0), it was found in previous work that lateral CO(2) diffusion could affect measurements performed with clamp-on leaf chambers. On the other hand, overpressure (DeltaP0) in leaf chambers has been reported to minimize artefacts possibly caused by leaks in chamber sealing. In the present work, net CO(2) exchange rates (NCER) were measured under different DeltaP values (0.0-3.0 kPa) on heterobaric and homobaric leaves. In heterobaric leaves which have internal barriers for lateral gas movement, changes in DeltaP had no significant effect on NCER. For homobaric leaves, effects of DeltaP0 on measured NCER were significant, obviously due to lateral gas flux inside the leaf mesophyll. The magnitude of the effect was largely defined by stomatal conductance; when stomata were widely open, the impact of DeltaP on measured NCER was up to 7 mumol CO(2) m(-2) s(-1) kPa(-1). Since many other factors are also involved, neither DeltaP=0 nor DeltaP0 was found to be the 'one-size fits all' solution to avoid erroneous effects of lateral gas transport on measurements with clamp-on leaf chambers.

Diffusion of CO2 inside leaves is generally regarded to be from the substomatal cavities to the assimilating tissues, i.e. in the vertical direction of the leaf blades. However, lateral gas diffusion within intercellular air spaces may be much more effective than hitherto considered. In a previous work it was demonstrated that, when 'clamp-on' leaf chambers are used, leaf internal 'CO2 leakage' beyond the leaf chamber gaskets may seriously affect gas exchange measurement. This effect has been used in the present paper to quantify gas conductance (g(leaf,l), mmol m(-2) s(-1)) in the lateral directions within leaves and significant differences between homo- and heterobaric leaves were observed. For the homobaric leaves, lateral gas conductance measured over a distance of 6 or 8 mm (the widths of the chamber gaskets) was 2-20% of vertical conductance taken from published data measured over much smaller distances of 108-280 microm (the thickness of the leaves). The specific internal gas diffusion properties of the leaves have been characterized by gas conductivities (g*(leaf), micromol m(-1) s(-1)). Gas conductivities in the lateral directions of heterobaric leaves were found to be small but not zero. In homobaric leaves, they were between 67 and 209 micromol m(-1) s(-1) and thus even larger than those in the vertical direction of the leaf blades (between 15 and 78 micromol m(-1) s(-1)). The potential implications for experimentalists performing gas exchange measurements are discussed.

Recognising that plant leaves are the fundamental productive units of terrestrial vegetation and the complexity of different environments in which they must function, this review considers a few of the ways in which these functions may be measured and potentially scaled to the canopy. Although canopy photosynthetic productivity is clearly the sum of all leaves in the canopy, we focus on the quest for ‘economical insights’ from measurements that might facilitate integration of leaf photosynthetic activities into canopy performance, to better inform modelling based on the ‘insights of economics’. It is focussed on the reversible downregulation of photosynthetic efficiency in response to light environment and stress and summarises various xanthophyll-independent and dependent forms of photoprotection within the inner and outer canopy of woody plants. Two main themes are developed. First, we review experiments showing the retention of leaves that grow old in the shade may involve more than the ‘payback times’ required to recover the costs of their construction and maintenance. In some cases at least, retention of these leaves may reflect selection for distinctive properties that contribute to canopy photosynthesis through utilisation of sun flecks or provide ‘back up’ capacity following damage to the outer canopy. Second, we report experiments offering hope that remote sensing of photosynthetic properties in the outer canopy (using chlorophyll fluorescence and spectral reflectance technologies) may overcome problems of access and provide integrated measurements of these properties in the canopy as a whole. Finding appropriate tools to scale photosynthesis from the leaf to the landscape still presents a challenge but this synthesis identifies some measurements and criteria in the laboratory and the field that improve our understanding of inner and outer canopy processes.

Chlorophyll fluorescence measurements have been widely applied to quantify the photosynthetic efficiency of plants non-destructively. The most commonly used pulse amplitude modulated (PAM) technique provides a saturating light pulse, which is not practical at the canopy scale. We report here on a recently developed technique, laser induced fluorescence transient (LIFT), which is capable of remotely measuring the photosynthetic efficiency of selected leaves at a distance of up to 50 m. The LIFT approach correlated well with gas exchange measurements under laboratory conditions and was tested in a field experiment monitoring the combined effect of low temperatures and high light intensity on a variety of plants during the early winter in California. We observed a reduction in maximum and effective quantum yield in electron transport for Capsicum annuum L., Lycopersicon esculentum L. and Persea americana Mill. as the temperatures fell, while a grass community was not affected by combined low temperature and high light stress. The ability to make continuous, automatic and remote measurements of the photosynthetic efficiency of leaves with the LIFT system provides a new approach for studying and monitoring of stress effects on the canopy scale.

A new, compact, spatially scanning, open-path 2.7 microm tunable diode laser absorption spectrometer with short absorption path lengths below 10 cm was developed to analyze the spatiotemporal dynamics of one-dimensional (1D) spatial water vapor gradients. This spectrometer, which is based on a room-temperature distributed feedback diode laser, is capable of measuring absolute, calibration-free, line-of-sight averaged, but laterally resolved 1D H(2)O concentration profiles with a minimum fractional optical resolution of 2.1x10(-3) optical density (OD) (2.5x10(-4) OD after a background subtraction procedure), which permits a signal-to-noise-ratio of 407 (3400) at 10,000 parts in 10(6) (ppm)H(2)O, or normalized sensitivities of 2.6 ppm x m (0.32 ppm m) at 0.5 Hz duty cycle. The spectrometer's lateral spatial resolution (governed by the 500 microm sampling beam diameter) was validated by analyzing a well-defined laminar jet of nitrogen gas in humidified air. This scanning setup was then used to (a) quantitatively investigate for what we believe to be the first time the H(2)O boundary layer from 0.7 to 11 mm beneath the stomatous side of a single, undetached plant leaf, and (b) to study the temporal boundary layer dynamics and its dependence on stepwise light stimulation of the photosynthetic system. In addition the 2.7 microm diode laser was carefully characterized in terms of spectral purity, beam profile, as well as quasi-static and dynamic wavelength tuning coefficients.

A plant develops the dynamic phenotypes from the interaction of the plant with the environment. Understanding these processes that span plant’s lifetime in a permanently changing environment is essential for the advancement of basic plant science and its translation into application including breeding and crop management. The plant research community was thus confronted with the need to accurately measure diverse traits of an increasingly large number of plants to help plants to adapt to resource-limiting environment and low-input agriculture. In this overview, we outline the development of plant phenotyping as a multidisciplinary field. We sketch the technological advancement that laid the foundation for the development of phenotyping centers and evaluate the upcoming challenges for further advancement of plant phenotyping specifically with respect to standardization of data acquisition and reusability. Finally, we describe the development of the plant phenotyping community as an essential step to integrate the community and effectively use the emerging synergies.