Ulrich Schurr

Future Scenarios for Plant Phenotyping

With increasing demand to support and accelerate progress in breeding for novel traits, the plant research community faces the need to accurately measure increasingly large numbers of plants and plant parameters. The goal is to provide quantitative analyses of plant structure and function relevant for traits that help plants better adapt to low-input agriculture and resource-limited environments. We provide an overview of the inherently multidisciplinary research in plant phenotyping, focusing on traits that will assist in selecting genotypes with increased resource use efficiency. We highlight opportunities and challenges for integrating noninvasive or minimally invasive technologies into screening protocols to characterize plant responses to environmental challenges for both controlled and field experimentation. Although technology evolves rapidly, parallel efforts are still required because large-scale phenotyping demands accurate reporting of at least a minimum set of information concerning experimental protocols, data management schemas, and integration with modeling. The journey toward systematic plant phenotyping has only just begun.

Decreased ribulose-1,5-bisphosphate carboxylase-oxygenase in transgenic tobacco transformed with "antisense" rbcS : I. Impact on photosynthesis in ambient growth conditions.

The effect of nitrogen supply during growth on the contribution of ribulose-1,5-bisphosphate carboxylase-oxygenase (Rubisco; EC 4.1.1.39) to the control of photosynthesis was examined in tobacco (Nicotiana tabacum L.). Transgenic plants transformed with antisense rbcS to produce a series of plants with a progressive decrease in the amount of Rubisco were used to allow the calculation of the flux-control coefficient of Rubisco for photosynthesis (CR). Several points emerged from the data: (i) The strength of Rubisco control of photosynthesis, as measured by CR, was altered by changes in the short-term environmental conditions. Generally, CR was increased in conditions of increased irradiance or decreased CO2. (ii) The amount of Rubisco in wild-type plants was reduced as the nitrogen supply during growth was reduced and this was associated with an increase in CR. This implied that there was a specific reduction in the amount of Rubisco compared with other components of the photosynthetic machinery. (iii) Plants grown with low nitrogen and which had genetically reduced levels of Rubisco had a higher chlorophyll content and a lower chlorophyll a/b ratio than wild-type plants. This indicated that the nitrogen made available by genetically reducing the amount of Rubisco had been re-allocated to other cellular components including light-harvesting and electron-transport proteins. It is argued that there is a “luxury” additional investment of nitrogen into Rubisco in tobacco plants grown in high nitrogen, and that Rubisco can also be considered a nitrogen-store, all be it one where the opportunity cost of the nitrogen storage is higher than in a non-functional storage protein (i.e. it allows for a slightly higher water-use efficiency and for photosynthesis to respond to temporarily high irradiance).

Agriculture: Feeding the future

Humanity depends on fewer than a dozen of the approximately 300,000 species of flowering plants for 80% of its caloric intake. And we capitalize on only a fraction of the genetic diversity that resides within each of these species. This is not enough to support our food system in the future. Food availability must double in the next 25 years to keep pace with population and income growth around the world. Already, food-production systems are precarious in the face of intensifying demand, climate change, soil degradation and water and land shortages. Farmers have saved the seeds of hundreds of crop species and hundreds of thousands of ‘primitive’ varieties (local domesticates called landraces), as well as the wild relatives of crop species and modern varieties no longer in use. These are stored in more than 1,700 gene banks worldwide. Maintaining the 11 international gene-bank collections alone costs about US

Combined MRI–PET dissects dynamic changes in plant structures and functions

18 million a year.

Simultaneous phenotyping of leaf growth and chlorophyll fluorescence via GROWSCREEN FLUORO allows detection of stress tolerance in Arabidopsis thaliana and other rosette plants.

Unravelling the factors determining the allocation of carbon to various plant organs is one of the great challenges of modern plant biology. Studying allocation under close to natural conditions requires non-invasive methods, which are now becoming available for measuring plants on a par with those developed for humans. By combining magnetic resonance imaging (MRI) and positron emission tomography (PET), we investigated three contrasting root/shoot systems growing in sand or soil, with respect to their structures, transport routes and the translocation dynamics of recently fixed photoassimilates labelled with the short-lived radioactive carbon isotope (11)C. Storage organs of sugar beet (Beta vulgaris) and radish plants (Raphanus sativus) were assessed using MRI, providing images of the internal structures of the organs with high spatial resolution, and while species-specific transport sectoralities, properties of assimilate allocation and unloading characteristics were measured using PET. Growth and carbon allocation within complex root systems were monitored in maize plants (Zea mays), and the results may be used to identify factors affecting root growth in natural substrates or in competition with roots of other plants. MRI-PET co-registration opens the door for non-invasive analysis of plant structures and transport processes that may change in response to genomic, developmental or environmental challenges. It is our aim to make the methods applicable for quantitative analyses of plant traits in phenotyping as well as in understanding the dynamics of key processes that are essential to plant performance.

Decreased ribulose-1,5-bisphosphate carboxylase-oxygenase in transgenic tobacco transformed with 'antisense' rbcS : II. Flux-control coefficients for photosynthesis in varying light, CO2, and air humidity.

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.

Temperature responses of roots: impact on growth, root system architecture and implications for phenotyping

Transgenic tobacco (Nicotiana tabacum L.) plants transformed with ‘antisense’ rbcS to produce a series of plants with a progressive decrease in the amount of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) have been used to investigate the contribution of Rubsico to the control of photosynthesis at different irradiance, CO2 concentrations and vapour-pressure deficits. Assimilation rates, transpiration, the internal CO2 concentration and chlorophyll fluorescence were measured in each plant. (i) The flux-control coefficient of Rubisco was estimated from the slope of the plot of Rubisco content versus assimilation rate. The flux-control coefficient had a value of 0.8 or more in high irradiance, (1050 μmol·m−2·s−1), low-vapour pressure deficit (4 mbar) and ambient CO2 (350 μbar). Control was marginal in enhanced CO2 (450 μbar) or low light (310 μmol·m−2·s−1) and was also decreased at high vapour-pressure deficit (17 mbar). No control was exerted in 5% CO2. (ii) The flux-control coefficients of Rubisco were compared with the fractional demand placed on the calculated available Rubisco capacity. Only a marginal control on photosynthetic flux is exerted by Rubisco until over 50% of the available capacity is being used. Control increases as utilisation rises to 80%, and approaches unity (i.e. strict limitation) when more than 80% of the available capacity is being used. (iii) In low light, plants with reduced Rubisco have very high energy-dependent quenching of chlorophyll fluorescence (qE) and a decreased apparent quantum yield. It is argued that Rubisco still exerts marginal control in these conditions because decreased Rubisco leads to increased thylakoid energisation and high-energy dependent dissipation of light energy, and lower light-harvesting efficiency. (iv) The flux-control coefficient of stomata for photosynthesis was calculated from the flux-control coefficient of Rubisco and the internal CO2 concentration, by applying the connectivity theorem. Control by the stomata varies between zero and about 0.25. It is increased by increased irradiance, decreased CO2 or decreased vapour-pressure deficit. (v) Photosynthetic oscillations in saturating irradiance and CO2 are suppressed in decreased-activity transformants before the steady-state rate of photosynthesis is affected. This provides direct evidence that these oscillations reveal the presence of “excess” Rubisco. (vi) Comparison of the flux-control coefficients of Rubisco with mechanistic models of photosynthesis provides direct support for the reliability of these models in conditions where Rubisco has a flux-control coefficient approach unity (i.e. “limits” photosynthesis), but also indicates that these models are less useful in conditions where control is shared between Rubisco and other components of the photosynthetic apparatus.

The Effects of Elevated CO2 Concentration on Soybean Gene Expression. An Analysis of Growing and Mature Leaves

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.

Imaging plants dynamics in heterogenic environments.

Improvements in carbon assimilation and water-use efficiency lead to increases in maximum leaf area index at elevated carbon dioxide concentration ([CO2]); however, the molecular drivers for this increase are unknown. We investigated the molecular basis for changes in leaf development at elevated [CO2] using soybeans (Glycine max) grown under fully open air conditions at the Soybean Free Air CO2 Enrichment (SoyFACE) facility. The transcriptome responses of rapidly growing and fully expanded leaves to elevated [CO2] were investigated using cDNA microarrays. We identified 1,146 transcripts that showed a significant change in expression in growing versus fully expanded leaves. Transcripts for ribosomal proteins, cell cycle, and cell wall loosening, necessary for cytoplasmic growth and cell proliferation, were highly expressed in growing leaves. We further identified 139 transcripts with a significant [CO2] by development interaction. Clustering of these transcripts showed that transcripts involved in cell growth and cell proliferation were more highly expressed in growing leaves that developed at elevated [CO2] compared to growing leaves that developed at ambient [CO2]. The 327 [CO2]-responsive genes largely suggest that elevated [CO2] stimulates the respiratory breakdown of carbohydrates, which provides increased energy and biochemical precursors for leaf expansion and growth at elevated [CO2]. While increased photosynthesis and carbohydrate production at elevated [CO2] are well documented, this research demonstrates that at the transcript and metabolite level, respiratory breakdown of starch is also increased at elevated [CO2].

Analyzing lateral root development: how to move forward.

Noninvasive imaging sensors and computer vision approaches are key technologies to quantify plant structure, physiological status, and performance. Today, imaging sensors exploit a wide range of the electromagnetic spectrum, and they can be deployed to measure a growing number of traits, also in heterogenic environments. Recent advances include the possibility to acquire high-resolution spectra by imaging spectroscopy and classify signatures that might be informative of plant development, nutrition, health, and disease. Three-dimensional (3D) reconstruction of surfaces and volume is of particular interest, enabling functional and mechanistic analyses. While taking pictures is relatively easy, quantitative interpretation often remains challenging and requires integrating knowledge of sensor physics, image analysis, and complex traits characterizing plant phenotypes.