Root systems play an essential role in ensuring plant productivity. Experiments conducted in controlled environments and simulation models suggest that root geometry and responses of root architecture to environmental factors should be studied as a priority. However, compared with aboveground plant organs, roots are not easily accessible by non-invasive analyses and field research is still based almost completely on manual, destructive methods. Contributing to reducing the gap between laboratory and field experiments, we present a novel phenotyping system (GROWSCREEN-Rhizo), which is capable of automatically imaging roots and shoots of plants grown in soil-filled rhizotrons (up to a volume of ~18 L) with a throughput of 60 rhizotrons per hour. Analysis of plants grown in this setup is restricted to a certain plant size (up to a shoot height of 80 cm and root-system depth of 90 cm). We performed validation experiments using six different species and for barley and maize, we studied the effect of moderate soil compaction, which is a relevant factor in the field. First, we found that the portion of root systems that is visible through the rhizotrons’ transparent plate is representative of the total root system. The percentage of visible roots decreases with increasing average root diameter of the plant species studied and depends, to some extent, on environmental conditions. Second, we could measure relatively minor changes in root-system architecture induced by a moderate increase in soil compaction. Taken together, these findings demonstrate the good potential of this methodology to characterise root geometry and temporal growth responses with relatively high spatial accuracy and resolution for both monocotyledonous and dicotyledonous species. Our prototype will allow the design of high-throughput screening methodologies simulating environmental scenarios that are relevant in the field and will support breeding efforts towards improved resource use efficiency and stability of crop yields.

Stress caused by environmental factors evokes dynamic changes in plant phenotypes. In this study, we deciphered simultaneously the reaction of plant growth and chlorophyll fluorescence related parameters using a novel approach which combines existing imaging technologies (GROWSCREEN FLUORO). Three different abiotic stress situations were investigated demonstrating the benefit of this approach to distinguish between effects related to (1) growth, (2) chlorophyll-fluorescence, or (3) both of these aspects of the phenotype. In a drought stress experiment with more than 500 plants, poly(ADP-ribose) polymerase (PARP) deficient lines of Arabidopsis thaliana (L.) Heynh showed increased relative growth rates (RGR) compared with C24 wild-type plants. In chilling stress, growth of PARP and C24 lines decreased rapidly, followed by a decrease in Fv/Fm. Here, PARP-plants showed a more pronounced decrease of Fv/Fm than C24, which can be interpreted as a more efficient strategy for survival in mild chilling stress. Finally, the reaction of Nicotiana tabacum L. to altered spectral composition of the intercepted light was monitored as an example of a moderate stress situation that affects chlorophyll-fluorescence related, but not growth-related parameters. The examples investigated in this study show the capacity for improved plant phenotyping based on an automated and simultaneous evaluation of growth and photosynthesis at high throughput.

Abstract. Root phenotyping is a challenging task, mainly because of the hidden nature of this organ. Only recently, imaging technologies have become available that allow us to elucidate the dynamic establishment of root structure and function in the soil. In root tips, optical analysis of the relative elemental growth rates in root expansion zones of hydroponically-grown plants revealed that it is the maximum intensity of cellular growth processes rather than the length of the root growth zone that control the acclimation to dynamic changes in temperature. Acclimation of entire root systems was studied at high throughput in agar-filled Petri dishes. In the present study, optical analysis of root system architecture showed that low temperature induced smaller branching angles between primary and lateral roots, which caused a reduction in the volume that roots access at lower temperature. Simulation of temperature gradients similar to natural soil conditions led to differential responses in basal and apical parts of the root system, and significantly affected the entire root system. These results were supported by first data on the response of root structure and carbon transport to different root zone temperatures. These data were acquired by combined magnetic resonance imaging (MRI) and positron emission tomography (PET). They indicate acclimation of root structure and geometry to temperature and preferential accumulation of carbon near the root tip at low root zone temperatures. Overall, this study demonstrated the value of combining different phenotyping technologies that analyse processes at different spatial and temporal scales. Only such an integrated approach allows us to connect differences between genotypes obtained in artificial high throughput conditions with specific characteristics relevant for field performance. Thus, novel routes may be opened up for improved plant breeding as well as for mechanistic understanding of root structure and function.

Summary• 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.

Root systems determine the water and nutrients for photosynthesis and harvested products, underpinning agricultural productivity. We highlight 11 programs that integrated root traits into germplasm for breeding, relying on phenotyping. Progress was successful but slow. Today's phenotyping technologies will speed up root trait improvement. They combine multiple new alleles in germplasm for target environments, in parallel. Roots and shoots are detected simultaneously and nondestructively, seed to seed measures are automated, and field and laboratory technologies are increasingly linked. Available simulation models can aid all phenotyping decisions. This century will see a shift from single root traits to rhizosphere selections that can be managed dynamically on farms and a shift to phenotype-based improvement to accommodate the dynamic complexity of whole crop systems.Root system traits (see Glossary) have long been a key target by researchers and breeders for crop improvement [1,2]. Root system architecture supplies water and nutrients for photosynthesis and growth, stabilizes the plant, and prevents soil toxic elements and pathogens from entering leaves and reproductive organs. Roots also host soil microorganisms that can contribute to plant growth and resource efficiency and modulate the supply of resources and signals to shoots, influencing partitioning to organs, including flowers, seed, and fruit. Despite the challenges that plant roots present for measurement, root traits have been incorporated into crops using phenotyping. The observation of roots using phenotyping is central to the discovery of root traits beneficial to crops, their incorporation into new cultivars using prebreeding [3,4], and to their management using precision agriculture. Highlights in Root PhenotypingThe 11 programs highlighted in Figure 1 (Key Figure) exemplify root traits incorporated into new genotypes by phenotyping to increase crop productivity. The examples cover the two main plant types and root system developments: monocotyledons (two major cereal crops, wheat and rice) with seed and stem-borne roots with no cambial thickening, and dicotyledons (two major legume crops, bean