Plant Physiology

Plant Physiology
 
  •        Climate Change

  •        Energy Crops

  •        Hyperspectral Imaging of Plants

  •        Non-Destructive Plant Phenotyping

  •        Phenomics

 
 
  •        Plant Phenomics

  •        Plant Phenotyping

  •        Directed Plant Breeding

  •        Fertiliser Developer

  •        Pesticide Development

  •        Plant Fortifiers

Crop plant research

Climate Change

Crop production is strongly related to climate change. One of the most important aims of crop plant research and plant breeding is to understand how plants react to climate change and how they can be bred to perform better under changing conditions. While plant stressors like drought, waterlogging, heat and salinity occur even without climate change, the influence of elevated CO2 levels is a new environmental variable with a potentially major influence on plant development.

As gradually changing CO2 levels are just one of many factors influencing plant development, its realistic effects are not easy to determine. On the other side, obtaining sound estimates of plant reaction to elevated CO2 levels gets increasingly important, both for crop science and for climate modelling.

Experiments with thousands of (different) plants under selected general environmental conditions (light, soil humidity etc.) at different, but realistic CO2 levels can help enormously to understand influences on plant development.

 

Contribution of LemnaTec plant phenotyping systems to climate change research

1.          LemnaTec scanalyzer plant phenotyping systems can measure even small changes in plant development with a high reproducibility, showing the dynamics of such changes.

2.          To eliminate nearly all other environmental factors, the non-destructive plant phenotyping of the LemnaTec scanalyzer imaging systems allow measuring of individual plant reactions to a change of the CO2 level during the experiment.

3.          The randomisation of plants in greenhouses or growth chambers and the transparent structure of the LemnaTec conveyor belt systems provide the best way to average out CO2 gradients, thus keeping growth condition as homogenous as possible.

4.          Comprehensive combinations of VIS, NIR and IR imaging provide the best options to discriminate the reaction patterns of specific plants.

5.          As one scanalyzer3D imaging system can serve a large set of greenhouses or growth chambers with different CO2 concentrations, direct comparison of plants grown under different CO2 conditions becomes possible. If necessary, the imaging systems can be adapted to the CO2 conditions of the actually measured greenhouse or growth room to avoid adaptation reactions. Alternatively, gas sluices can be installed to avoid significant gas exchange into the growth compartments.

6.          Due to the high degree of automation, there is almost no need for CO2 emitting humans to work in the growth areas during CO2 experiments, which enables constant CO2 conditions in the plant environment and experiments with massively increased CO2 conditions.

7.          Automation even facilitates experiments with isotope enriched CO2 as human (emission) interference is minimised.

Drought and changing CO2 levels are just some aspects of the very complex phenomenon of climate change

 

 

Biomass production

Energy Crops

On the way to a bio economy that is increasingly based on renewable energy sources, plants will play a much larger role in the future. Depending on the specific crop, biomass production is the final target of breeding – as demonstrated by switchgrass or maize kernel yield for starch-based bioethanol. Nevertheless, many intermediate questions regarding water usage efficiency, nutrient efficiency or the ability to grow on degraded soils will gain in importance.

Contribution of LemnaTec scanalyzer systems to energy crop optimisation

·         Growth rate quantification: In order to identify genes or gene constellations that lead to high growth rates, it is essential to measure biomass non-destructively during the entire observation period. This is necessary as one-point measurements of a harvested biomass merely reflect the historic result of plant growth, but do not allow for a differentiation between germination times, growth rates and other influencing parameters. LemnaTec scanalyzer3D and scanalyzerHTS imaging systems provide the technology for a non-destructive image-based assessment of biomass development.

·         Compatibility with degraded soils: While most crops are actually designed to produce the best yield under optimal nutrient conditions, much more research is required to screen for specific genes that will support plant growth even in degraded soils. Testing real soils and quantifying both shoot and root development under controlled soil humidity conditions is easily possible with LemnaTec scanalyzer3D imaging systems using VIS and NIR root and shoot imaging.

·         Homogeneous growth conditions: Growing of one of the most efficient energy crops, sugar cane, involves a very high sensitivity to changes in light and temperature conditions. To allow the screening of different cultivars in controlled environments, it is important to keep the environmental conditions as comparable as possible. The plant randomisation of LemnaTec scanalyzer MovingField systems is the optimum solution, as it allows handling such plants in greenhouses, as well as assessing the quantitative influence of genetic and environmental factors on plant development.

For energy crops, quantification of growth and biomass production is essential, so it is important to select the best genes for specific soil condition and climates

Hyperspectral imaging
LemnaTec hyperspec technologies

Hyperspectral Imaging of Plants

Hyperspectral imaging is a technology widely used for remote imaging, in an effort to extract a maximum of information out of images made under strongly varying imaging conditions, caused by the variability of the sunlight and changing atmospheric conditions. On the other end of the spatial scale, Fourier Transform spectroscopy of biological material is used to assess specific ingredients contained in samples that are often grinded and dried, and thus show no spatial resolution at all.

The application of hyperspectral imaging under highly controlled illumination conditions, as is standard in all LemnaTec scanalyzer3D imaging stations, provides new options for data generation with high spectral resolution in a certain range of the full electromagnetic spectrum of frequencies. In contrast to the LemnaTec usage of multiple frequency imaging (VIS, NIR IR), hyperspectral imaging is rather focused on a smaller range (e.g. 400–1000 nm), but takes images at a spectral resolution between 1 and 10 nm. The user is thus enabled either to acquire full-spectrum datasets for each individual pixel of the image, or to restrict data acquisition to some specifically interesting frequency ranges. These will strongly depend on the substances, the substance groups or the general approach to hyperspectral data acquisition.

Approaches to hyperspectral imaging using LemnaTec hyperspec technologies

Substance-specific approach:

If the absorption and reflectance spectra of substances like chlorophyll, anthocyans or others are identified, hyperspectral images can achieve at least a semi-quantitative value for substance concentration. To obtain reliable data, a larger validation experiment, including measurement of the values with other methods, is necessary in order to develop a concentration model that relates spectral information to concentration.

 

Learned finger printing or pattern approach

When an individual substance would only be used as a surrogate value for a more complex physiological phenotype, it may often make sense not to replicate the chemical measurement by hyperspectral imaging (substance-specific approach), but to try accessing the physiological phenomenon more directly. Based on a larger set of full-spectral information and a combination of specific measurement methods or plant pre-treatments (or plants with known specific backgrounds), a set of spectra is generated with a correlation to specific plant conditions such as biotic or abiotic stressors, senescence, nutrient deficiencies or different stages of ripeness. By employing direct comparison of spectra, advanced statistical analysis or machine-learning processes, different patterns and the spectral regions of interest for the discrimination are identified. These areas will then be monitored under routine conditions to assess details of the plant status.

 

Pure pattern finding approach

To make the best of screening, which means to look out for the unknown, it is useful to assess a certain spectral resolution for the entire spectrum and the whole plant. After the experiment, specific algorithms search for patterns or deviations from control plants or similarities to known, interesting plant types in the experiment. This open approach minimises the need for extensive calibrations and retains the flexibility to detect the truly new and innovative traits.

Hyperspectral imaging for in-depth analysis of spectral information is complemented by the high-throughput options that LemnaTec scanalyzer systems can provide.

Plant Phenotyping
LemnaTec scanalyzer technologies

Non-destructive Plant Phenotyping

Non-destructive plant phenotyping is a key component of any phenotyping with comparatively low plant numbers (compared to field conditions) under highly controlled environmental conditions in greenhouses or growth chambers. These methods have the huge advantage of not destroying or harming test objects, and they therefore allow monitoring plants over their entire growth period. As a result, the plants act as their own control, eliminating all variability normally caused by harvesting of subsets and thus enhancing statistical data quality. Besides, plants are often far too valuable to be destroyed (up to 700 $ per piece), or even, depending on their origin in breeding programmes, simply unique and thus irreplaceable.

Non-destructive plant phenotyping using LemnaTec scanalyzer technologies

LemnaTec scanalyzer systems provide a wide range of non-destructive methods to characterise plant phenotypes. Imaging methods using specific cameras for visible light (scanalyzerVIS), near infrared light (scanalyzerNIR) or infrared light (scanalyzerIR) for both shoots and – if applicable – roots provide fast data acquisition at high spatial resolutions. Hyperspectral imaging can increase the spectral resolution even further. Specific imaging modes such as fluorescence imaging add specific information to chlorophyll fluorescence, chemical markers or genetically initialised fluorescent markers such as GRP, YFP or RFP.

Water usage and evaporation is monitored by automated LemnaTec weighing and watering stations. Additional sensors, for example for soil humidity and leaf thickness, can complement individual plant measurements at very high time resolutions. All these data can be correlated to environmental parameters that are measured in the greenhouse and used for example to normalise growth data based on standard developmental models.

Non-destructive plant phenotyping, combining the best of image-based analysis with additional techniques, is the key concept of the LemnaTec scanalyzer3D and scanalyzerHTS systems.

Plant Phenomics

The development of genomics over the last few years has resulted in a set of core technologies that enable an almost exponentially increase in the generation of information on the genetic background of plants. Based on high-throughput genotyping and gene sequencing, the availability of genetic data related to specific plants has reached a point where the mapping of entire genomes is merely a question of weeks. Moreover, the use of molecular markers and mapping populations in combination with the array-based identification of gene regulation mechanisms has led to the accumulation of an unprecedented amount of genetic data.

The role of LemnaTec scanalyzer systems in plant phenomics

The advances in plant genomics can now be complemented by high-throughput plant phenomics, using LemnaTec scanalyzerHTS systems for small plants like Arabidopsis and scanalyzer3D systems for bigger plants up to maize and sugar cane sizes. In all cases, high-resolution phenotyping data on plant growth and development is generated in abundance, which can subsequently be linked to genes via QTLs (Quantitative Trait Loci).

Plant Phenotyping

Plant phenotyping is the comprehensive assessment of plant complex traits such as growth, development, tolerance, resistance, architecture, physiology, ecology, yield, and the basic measurement of individual quantitative parameters that form the basis for the more complex traits. Examples for such direct measurement parameters are image-based projected leaf area, chlorophyll fluorescence, stem diameter, plant height/width, compactness, stress pigment concentration, tip burn, internode length, colour, leaf angle, leaf rolling, leaf elongation, seed number, seed size, tiller number, flowering time, germination time etc.

After all, plant phenotyping has been performed by farmers and above all breeders for the last seven or more thousand years, essentially since the days humans started to carefully select grasses to increase yield or enhance other desirable traits. In the past, phenotyping was mostly based on experience and intuition, in a process where measurement and interpretation were not separated. This highly integrated approach compensated for the human deficiencies in performing reproducible, objective measurements and dealt with the individual subjectivity factor of the phenotyping person.

A large set of different aspects led to the development of the ever-increasing new field of highly automated, non-destructive plant phenotyping.

Incentives for automated, non-destructive plant phenotyping with LemnaTec scanalyzer technologies:

1.            The need to generate more quantitative data for genetic analysis (QTL, MAS, SMART breeding) and modelling of plant development.

2.            The requirement to integrate more researchers into the worldwide, interconnected breeding and trait validation process.

3.            The recognition that information far beyond the direct perception of the human senses (gathered by X-ray, Fluorescence, IR, spectroscopy, terahertz etc.) can contribute efficiently to phenotype description.

4.            The development of information and data storage technologies, providing suitable tools for the analysis of complex structures like plants.

5.            The need to accelerate breeding.

6.            The impossibility for individual breeders and senior research experts to acquire all important data themselves, in order to keep in control of subjectivity effects.

7.            The urgency to quantify more complex traits.

8.            The necessity to spot increasingly smaller differences.

9.            The urgent search for breakthroughs in dealing with the eminent global challenges of climate change and a rising need for more agricultural products.

 

LemnaTec scanalyzer systems provide these automated and largely image-based, non-destructive plant phenotyping technologies as an integrated system. Depending on the kind of research, customisable systems are available, based on the scanalyzerPL, scanalyzerHTS or scanalyzer3D concept.

LemnaTec scanalyzer plant phenotyping provides a maximum of data for individual plants concerning development, water use, architecture, shapes and reflectance at a wide range of wavelengths, from visible light to heat imaging.