Plant Phenotyping: Past, Present, and Future.

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.

Pampered inside, pestered outside? Differences and similarities between plants growing in controlled conditions and in the field.

I. 839 II. 839 III. 841 IV. 845 V. 847 VI. 848 VII. 849 VIII. 851 851 852 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.

The art of growing plants for experimental purposes: a practical guide for the plant biologist.

Every year thousands of experiments are conducted using plants grown under more-or-less controlled environmental conditions. The aim of many such experiments is to compare the phenotype of different species or genotypes in a specific environment, or to study plant performance under a range of suboptimal conditions. Our paper aims to bring together the minimum knowledge necessary for a plant biologist to set up such experiments and apply the environmental conditions that are appropriate to answer the questions of interest. We first focus on the basic choices that have to be made with regard to the experimental setup (e.g. where are the plants grown; what rooting medium; what pot size). Second, we present practical considerations concerning the number of plants that have to be analysed considering the variability in plant material and the required precision. Third, we discuss eight of the most important environmental factors for plant growth (light quantity, light quality, CO2, nutrients, air humidity, water, temperature and salinity); what critical issues should be taken into account to ensure proper growth conditions in controlled environments and which specific aspects need attention if plants are challenged with a certain a-biotic stress factor. Finally, we propose a simple checklist that could be used for tracking and reporting experimental conditions.

A method to construct dose-response curves for a wide range of environmental factors and plant traits by means of a meta-analysis of phenotypic data.

In the past, biologists have characterized the responses of a wide range of plant species to their environment. As a result, phenotypic data from hundreds of experiments are publicly available now. Unfortunately, this information is not structured in a way that enables quantitative and comparative analyses. We aim to fill this gap by building a large database which currently contains data on 1000 experiments and 800 species. This paper presents methodology to generalize across different experiments and species, taking the response of specific leaf area (SLA; leaf area:leaf mass ratio) to irradiance as an example. We show how to construct and quantify a normalized mean light-response curve, and subsequently test whether there are systematic differences in the form of the curve between contrasting subgroups of species. This meta-analysis is then extended to a range of other environmental factors important for plant growth as well as other phenotypic traits, using >5300 mean values. The present approach, which we refer to as 'meta-phenomics', represents a valuable tool in understanding the integrated response of plants to their environment and could serve as a benchmark for future phenotyping efforts as well as for modelling global change effects on both wild species and crops.

New particle formation in forests inhibited by isoprene emissions.

It has been suggested that volatile organic compounds (VOCs) are involved in organic aerosol formation, which in turn affects radiative forcing and climate. The most abundant VOCs emitted by terrestrial vegetation are isoprene and its derivatives, such as monoterpenes and sesquiterpenes. New particle formation in boreal regions is related to monoterpene emissions and causes an estimated negative radiative forcing of about -0.2 to -0.9 W m(-2). The annual variation in aerosol growth rates during particle nucleation events correlates with the seasonality of monoterpene emissions of the local vegetation, with a maximum during summer. The frequency of nucleation events peaks, however, in spring and autumn. Here we present evidence from simulation experiments conducted in a plant chamber that isoprene can significantly inhibit new particle formation. The process leading to the observed decrease in particle number concentration is linked to the high reactivity of isoprene with the hydroxyl radical (OH). The suppression is stronger with higher concentrations of isoprene, but with little dependence on the specific VOC mixture emitted by trees. A parameterization of the observed suppression factor as a function of isoprene concentration suggests that the number of new particles produced depends on the OH concentration and VOCs involved in the production of new particles undergo three to four steps of oxidation by OH. Our measurements simulate conditions that are typical for forested regions and may explain the observed seasonality in the frequency of aerosol nucleation events, with a lower number of nucleation events during summer compared to autumn and spring. Biogenic emissions of isoprene are controlled by temperature and light, and if the relative isoprene abundance of biogenic VOC emissions increases in response to climate change or land use change, the new particle formation potential may decrease, thus damping the aerosol negative radiative forcing effect.

Analysis of alkaloids in single plant cells by capillary electrophoresis.

In this chapter, capillary electrophoresis (CE) is demonstrated to be a useful technique for the determination of alkaloids in microsamples of single plant cells. A single cell sampling technique with microcapillaries that includes extraction of sample volumes in the pl range from single cells, division into aliquots, addition of internal standard, and injection into the CE capillary is described. The danger of contamination and evaporation of such low sample volumes has been avoided by handling them under an inert protective layer of silicone oil. For the determination of alkaloids in cell samples, CE with direct ultraviolet detection using a high concentration of citric acid as background electrolyte provides sufficient sensitivity.

Dynamics of seedling growth acclimation towards altered light conditions can be quantified via GROWSCREEN: a setup and procedure designed for rapid optical phenotyping of different plant species.

Using a novel setup, we assessed how fast growth of Nicotiana tabacum seedlings responds to alterations in the light regime and investigated whether starch-free mutants of Arabidopsis thaliana show decreased growth potential at an early developmental stage. Leaf area and relative growth rate were measured based on pictures from a camera automatically placed above an array of 120 seedlings. Detection of total seedling leaf area was performed via global segmentation of colour images for preset thresholds of the parameters hue, saturation and value. Dynamic acclimation of relative growth rate towards altered light conditions occurred within 1 d in N. tabacum exposed to high nutrient availability, but not in plants exposed to low nutrient availability. Increased leaf area was correlated with an increase in shoot fresh and dry weight as well as root growth in N. tabacum. Relative growth rate was shown to be a more appropriate parameter than leaf area for detection of dynamic growth acclimation. Clear differences in leaf growth activity were also observed for A. thaliana. As growth responses are generally most flexible in early developmental stages, the procedure described here is an important step towards standardized protocols for rapid detection of the effects of changes in internal (genetic) and external (environmental) parameters regulating plant growth.

Nutrient translocation in the xylem of poplar--diurnal variations and spatial distribution along the shoot axis.

This investigation shows diurnal variations in the xylem sap composition of poplar (Populus tremula x P. alba). All major macronutrients reached a maximum concentration in the first half of the light period and decreased to the middle of the night. The relative abundance of the nutrients did not change during the day. The sap flow, which responded very fast to the environmental changes (2.2-fold increase within 10-20 min of illumination), reached a maximum value in the second half of the light period. Transpiration (and photosynthesis) was constant throughout the light phase. The calculated translocation rates displayed a maximum in the first half of the light period and therefore did not fit the time course of sap flow. During the night, translocation rates were 63-69% lower than the maximum. The regulation of nutrient translocation is discussed taking the active xylem loading into account. The axial distribution located the nitrate assimilation in younger leaves and storage of nitrate (and other macronutrients) in older leaves. Nitrate and potassium concentrations in the xylem sap did not change along the plant axis. However, the sap flow was greater in younger shoot sections than in older sections. We assume that the greater demand for nitrate in the younger shoot section was satisfied via an increased volume flow rather an increased nitrate concentration.