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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.

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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.

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.